Skip to content

some cleanup #123

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
richard-burhans wants to merge 1 commit into from
+33 −38
Closed

some cleanup #123

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions tools/ncbi_egapx/macros.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
29 changes: 14 additions & 15 deletions tools/ncbi_egapx/ncbi_egapx.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand Down Expand Up @@ -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">
Expand All @@ -384,7 +383,7 @@ $row
</section>
<expand macro="test_outputs"/>
</test>
<test expect_num_outputs="27" expect_test_failure="true">
<test expect_num_outputs="27" expect_test_failure="false">
<conditional name="cond_input_style">
<param name="input_style" value="history"/>
<param name="yamlin" value="input.yaml"/>
Expand Down
6 changes: 3 additions & 3 deletions tools/ncbi_egapx/ncbi_egapx_execute.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@
#end if
]]></command>
<environment_variables>
<environment_variable name="NXF_DEBUG">3</environment_variable>
<environment_variable name="EGAPX_RNASEQ_QUERY_LIMIT">$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"/>
Expand All @@ -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>
Expand Down
32 changes: 14 additions & 18 deletions tools/ncbi_egapx/ncbi_egapx_prepare_input.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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">
Expand All @@ -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>
Expand Down Expand Up @@ -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>
Expand All @@ -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">
Expand All @@ -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"/>
Expand Down
Loading