diff --git a/tools/ncbi_egapx/macros.xml b/tools/ncbi_egapx/macros.xml
index ae1333b..d7c1bf3 100644
--- a/tools/ncbi_egapx/macros.xml
+++ b/tools/ncbi_egapx/macros.xml
@@ -4,8 +4,8 @@
             <container type="docker">quay.io/galaxy/egapx:@TOOL_VERSION@</container>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.5.0</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">0.5.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">25.0</token>
     <xml name="edam_ontology">
         <edam_operations>
diff --git a/tools/ncbi_egapx/ncbi_egapx.xml b/tools/ncbi_egapx/ncbi_egapx.xml
index 837d9ba..e069524 100644
--- a/tools/ncbi_egapx/ncbi_egapx.xml
+++ b/tools/ncbi_egapx/ncbi_egapx.xml
@@ -89,8 +89,8 @@
     #end if
     ]]></command>
     <environment_variables>
-         <environment_variable name="NXF_DEBUG">3</environment_variable>
-         <environment_variable name="EGAPX_RNASEQ_QUERY_LIMIT">$getVar('developer.query_limit.rnaseq_query_limit', '20')</environment_variable>
+        <environment_variable name="NXF_DEBUG">3</environment_variable>
+        <environment_variable name="EGAPX_RNASEQ_QUERY_LIMIT">$getVar('developer.query_limit.rnaseq_query_limit', '20')</environment_variable>
     </environment_variables>
     <configfiles>
         <configfile name="short_reads_config"><![CDATA[#slurp
@@ -240,16 +240,16 @@ $row
                         <option value="list">Type in a list of SRA identifiers and/or remote short RNA-seq FASTA URI</option>
                     </param>
                     <when value="history">
-                        <param name="short_reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" optional="true" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration"/>
+                        <param name="short_reads" type="data" format="fastqsanger,fastqsanger.gz" optional="true" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration" multiple="true"/>
                         <repeat name="reads_lists" title="Single-end reads" min="0">
-                            <param name="short_reads_single" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration"/>
+                            <param name="short_reads_single" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration" collection_type="list"/>
                         </repeat>
                         <repeat name="reads_paired_lists" title="Paired-end reads" min="0">
-                            <param name="short_reads_paired" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list:paired" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration"/>
+                            <param name="short_reads_paired" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration" collection_type="list:paired"/>
                         </repeat>
                     </when>
                     <when value="list">
-                        <param name="short_reads" type="text" area="true" label="List all required individual short RNA-seq URI or SRA identifiers, separated by spaces or newlines" help="Either a working URI for a short RNA-seq FASTA, or a bare SRA identifier will work - can be mixed">
+                        <param name="short_reads" type="text" label="List all required individual short RNA-seq URI or SRA identifiers, separated by spaces or newlines" help="Either a working URI for a short RNA-seq FASTA, or a bare SRA identifier will work - can be mixed" area="true">
                             <validator type="empty_field"/>
                         </param>
                     </when>
@@ -260,16 +260,16 @@ $row
                         <option value="list">Type in a list of SRA identifiers and/or remote long RNA-seq FASTA URI</option>
                     </param>
                     <when value="history">
-                        <param name="long_reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" optional="true" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration"/>
+                        <param name="long_reads" type="data" format="fastqsanger,fastqsanger.gz" optional="true" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration" multiple="true"/>
                         <repeat name="reads_lists" title="Single-end reads" min="0">
-                            <param name="long_reads_single" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration"/>
+                            <param name="long_reads_single" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration" collection_type="list"/>
                         </repeat>
                         <repeat name="reads_paired_lists" title="Paired-end reads" min="0">
-                            <param name="long_reads_paired" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list:paired" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration"/>
+                            <param name="long_reads_paired" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration" collection_type="list:paired"/>
                         </repeat>
                     </when>
                     <when value="list">
-                        <param name="long_reads" type="text" area="true" label="List all required individual long RNA-seq URI or SRA identifiers, separated by spaces or newlines" help="Either a working URI for a long RNA-seq FASTA, or a bare SRA identifier will work - can be mixed">
+                        <param name="long_reads" type="text" label="List all required individual long RNA-seq URI or SRA identifiers, separated by spaces or newlines" help="Either a working URI for a long RNA-seq FASTA, or a bare SRA identifier will work - can be mixed" area="true">
                             <validator type="empty_field"/>
                         </param>
                     </when>
@@ -301,8 +301,7 @@ $row
                 </conditional>
                 <param name="trnascan_enabled" type="boolean" checked="false" label="Enable prediction of tRNA features using tRNAscan."/>
                 <param name="cmsearch_enabled" type="boolean" checked="false" label="Enable prediction of rRNAs, snoRNAs and snRNAs by searching the RFAM database using cmsearch distributed in Infernal."/>
-                <param name="extra" type="text" area="true" optional="true" label="Additional yaml to append to the egapx.yaml configuration"
-                    help="Not normally needed but useful for testing additional configuration elements">
+                <param name="extra" type="text" optional="true" label="Additional yaml to append to the egapx.yaml configuration" help="Not normally needed but useful for testing additional configuration elements" area="true">
                     <sanitizer invalid_char="">
                         <valid initial="string.printable"/>
                     </sanitizer>
@@ -324,7 +323,7 @@ $row
                 </when>
                 <when value="false"/>
             </conditional>
-            <param label="Gigabase pairs" name="gigabase_pairs" type="integer" size="3" min="1" max="8" value="1" help="Approximate gigabase pair count for scheduling hints" />
+            <param name="gigabase_pairs" type="integer" min="1" max="8" value="1" label="Gigabase pairs" help="Approximate gigabase pair count for scheduling hints" size="3"/>
         </section>
     </inputs>
     <outputs>
@@ -362,7 +361,7 @@ $row
         </collection>
     </outputs>
     <tests>
-        <test expect_num_outputs="27" expect_test_failure="true">
+        <test expect_num_outputs="27" expect_test_failure="false">
             <conditional name="cond_input_style">
                 <param name="input_style" value="fillform"/>
                 <conditional name="cond_genome_style">
@@ -384,7 +383,7 @@ $row
             </section>
             <expand macro="test_outputs"/>
         </test>
-        <test expect_num_outputs="27" expect_test_failure="true">
+        <test expect_num_outputs="27" expect_test_failure="false">
             <conditional name="cond_input_style">
                 <param name="input_style" value="history"/>
                 <param name="yamlin" value="input.yaml"/>
diff --git a/tools/ncbi_egapx/ncbi_egapx_execute.xml b/tools/ncbi_egapx/ncbi_egapx_execute.xml
index 862038b..5ae0335 100644
--- a/tools/ncbi_egapx/ncbi_egapx_execute.xml
+++ b/tools/ncbi_egapx/ncbi_egapx_execute.xml
@@ -25,8 +25,8 @@
     #end if
     ]]></command>
     <environment_variables>
-         <environment_variable name="NXF_DEBUG">3</environment_variable>
-         <environment_variable name="EGAPX_RNASEQ_QUERY_LIMIT">$getVar('developer.query_limit.rnaseq_query_limit', '20')</environment_variable>
+        <environment_variable name="NXF_DEBUG">3</environment_variable>
+        <environment_variable name="EGAPX_RNASEQ_QUERY_LIMIT">$getVar('developer.query_limit.rnaseq_query_limit', '20')</environment_variable>
     </environment_variables>
     <inputs>
         <param name="input_config" type="data" format="yaml" label="EGAPx configuration YAML file to pass to Nextflow"/>
@@ -43,7 +43,7 @@
                 </when>
                 <when value="false"/>
             </conditional>
-            <param label="Gigabase pairs" name="gigabase_pairs" type="integer" size="3" min="1" max="8" value="1" help="Approximate gigabase pair count for scheduling hints"/>
+            <param name="gigabase_pairs" type="integer" min="1" max="8" value="1" label="Gigabase pairs" help="Approximate gigabase pair count for scheduling hints" size="3"/>
         </section>
     </inputs>
     <outputs>
diff --git a/tools/ncbi_egapx/ncbi_egapx_prepare_input.xml b/tools/ncbi_egapx/ncbi_egapx_prepare_input.xml
index c12ad87..8b61b10 100644
--- a/tools/ncbi_egapx/ncbi_egapx_prepare_input.xml
+++ b/tools/ncbi_egapx/ncbi_egapx_prepare_input.xml
@@ -81,11 +81,11 @@
     #if $developer.query_limit.query_limit_selector == "false"
         --force
     #end if
-    '$yamlconfig' --executor galaxy --output 'egapx_out' --download-only --local-cache '$output.extra_files_path'
+    '$yamlconfig' --executor galaxy --output 'egapx_out' --download-needed --local-cache '$output.extra_files_path'
     ]]></command>
     <environment_variables>
-         <environment_variable name="NXF_DEBUG">3</environment_variable>
-         <environment_variable name="EGAPX_RNASEQ_QUERY_LIMIT">$getVar('developer.query_limit.rnaseq_query_limit', '20')</environment_variable>
+        <environment_variable name="NXF_DEBUG">3</environment_variable>
+        <environment_variable name="EGAPX_RNASEQ_QUERY_LIMIT">$getVar('developer.query_limit.rnaseq_query_limit', '20')</environment_variable>
     </environment_variables>
     <configfiles>
         <configfile name="short_reads_config"><![CDATA[#slurp
@@ -237,16 +237,16 @@ $row
                         <option value="list">Type in a list of SRA identifiers and/or remote short RNA-seq FASTA URIs</option>
                     </param>
                     <when value="history">
-                        <param name="short_reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" optional="true" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration"/>
+                        <param name="short_reads" type="data" format="fastqsanger,fastqsanger.gz" optional="true" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration" multiple="true"/>
                         <repeat name="reads_lists" title="Single-end reads" min="0">
-                            <param name="short_reads_single" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration"/>
+                            <param name="short_reads_single" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration" collection_type="list"/>
                         </repeat>
                         <repeat name="reads_paired_lists" title="Paired-end reads" min="0">
-                            <param name="short_reads_paired" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list:paired" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration"/>
+                            <param name="short_reads_paired" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select multiple short RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration" collection_type="list:paired"/>
                         </repeat>
                     </when>
                     <when value="list">
-                        <param name="short_reads" type="text" area="true" label="List all required individual short RNA-seq URI or SRA identifiers, separated by spaces or newlines" help="Either a working URI for a short RNA-seq FASTA, or a bare SRA identifier will work - can be mixed"/>
+                        <param name="short_reads" type="text" label="List all required individual short RNA-seq URI or SRA identifiers, separated by spaces or newlines" help="Either a working URI for a short RNA-seq FASTA, or a bare SRA identifier will work - can be mixed" area="true"/>
                     </when>
                 </conditional>
                 <conditional name="cond_long_reads_style">
@@ -255,16 +255,16 @@ $row
                         <option value="list">Type in a list of SRA identifiers and/or remote long RNA-seq FASTA URIs</option>
                     </param>
                     <when value="history">
-                        <param name="long_reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" optional="true" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration"/>
+                        <param name="long_reads" type="data" format="fastqsanger,fastqsanger.gz" optional="true" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration" multiple="true"/>
                         <repeat name="reads_lists" title="Single-end reads" min="0">
-                            <param name="long_reads_single" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration"/>
+                            <param name="long_reads_single" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration" collection_type="list"/>
                         </repeat>
                         <repeat name="reads_paired_lists" title="Paired-end reads" min="0">
-                            <param name="long_reads_paired" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list:paired" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration"/>
+                            <param name="long_reads_paired" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select multiple long RNA-seq fastqsanger inputs from the current history" help="All selected RNA-seq fastqsanger inputs will be added to the YAML for EGAPx configuration" collection_type="list:paired"/>
                         </repeat>
                     </when>
                     <when value="list">
-                        <param name="long_reads" type="text" area="true" label="List all required individual long RNA-seq URIs or SRA identifiers, separated by spaces or newlines" help="Either a working URI for a long RNA-seq FASTA, or a bare SRA identifier will work - can be mixed">
+                        <param name="long_reads" type="text" label="List all required individual long RNA-seq URIs or SRA identifiers, separated by spaces or newlines" help="Either a working URI for a long RNA-seq FASTA, or a bare SRA identifier will work - can be mixed" area="true">
                             <validator type="empty_field"/>
                         </param>
                     </when>
@@ -296,8 +296,7 @@ $row
                 </conditional>
                 <param name="trnascan_enabled" type="boolean" checked="false" label="Enable prediction of tRNA features using tRNAscan"/>
                 <param name="cmsearch_enabled" type="boolean" checked="false" label="Enable prediction of rRNAs, snoRNAs and snRNAs by searching the RFAM database using cmsearch distributed in Infernal"/>
-                <param name="extra" type="text" area="true" optional="true" label="Additional YAML to append to the EGAPx configuration"
-                    help="Not normally needed but useful for testing additional configuration elements">
+                <param name="extra" type="text" optional="true" label="Additional YAML to append to the EGAPx configuration" help="Not normally needed but useful for testing additional configuration elements" area="true">
                     <sanitizer invalid_char="">
                         <valid initial="string.printable"/>
                     </sanitizer>
@@ -306,7 +305,7 @@ $row
             <when value="history">
                 <param name="yamlin" type="data" format="yaml" label="EGAPx configuration YAML file to pass to Nextflow"/>
             </when>
-        </conditional> 
+        </conditional>
         <section name="developer" title="Developer options" expanded="false">
             <conditional name="query_limit">
                 <param name="query_limit_selector" type="select" label="Enforce SRA query limit">
@@ -321,13 +320,10 @@ $row
         </section>
     </inputs>
     <outputs>
-        <data name="egapx_yaml" format="yaml" label="EGAPx configuration">
-            <filter>cond_input_style["input_style"] == "fillform"</filter>
-        </data>
         <data name="output" format="directory" label="EGAPx local cache"/>
     </outputs>
     <tests>
-        <test expect_num_outputs="1" expect_test_failure="true">
+        <test expect_num_outputs="1" expect_test_failure="false">
             <conditional name="cond_input_style">
                 <param name="input_style" value="history"/>
                 <param name="yamlin" value="input.yaml"/>