Mercurial > repos > devteam > cuffquant
changeset 3:25cf1ab351df draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author | devteam |
---|---|
date | Tue, 07 Feb 2017 18:39:37 -0500 |
parents | 6c7e4034e354 |
children | d2daca60e139 |
files | cuff_macros.xml cuffquant_wrapper.xml tool_dependencies.xml |
diffstat | 3 files changed, 19 insertions(+), 17 deletions(-) [+] |
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--- a/cuff_macros.xml Mon Nov 09 12:06:19 2015 -0500 +++ b/cuff_macros.xml Tue Feb 07 18:39:37 2017 -0500 @@ -1,11 +1,13 @@ <macros> <token name="@VERSION@">2.2.1</token> + <xml name="requirements"> <requirements> <requirement type="package" version="2.2.1">cufflinks</requirement> <yield /> </requirements> </xml> + <xml name="stdio"> <stdio> <exit_code range="1:" /> @@ -26,21 +28,21 @@ </param> <when value="BAM"> <repeat name="conditions" title="Condition" min="2"> - <param name="name" title="Condition name" type="text" label="Name"/> + <param name="name" label="Condition name" type="text"/> <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> </repeat> </when> <when value="CXB"> <repeat name="conditions" title="Condition" min="2"> - <param name="name" title="Condition name" type="text" label="Name"/> + <param name="name" label="Condition name" type="text"/> <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> </repeat> </when> <when value="CONDITION_LIST"> - <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" /> + <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> </when> <when value="CONDITION_REPLICATE_LIST"> - <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> + <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> </when> </conditional> </xml> @@ -48,16 +50,16 @@ #if $in_type.set_in_type in ['BAM', 'CXB'] #for $condition in $in_type.conditions: #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) - $samples + '$samples' #end for #elif $in_type.set_in_type == 'CONDITION_LIST' #for $sample in $in_type.conditions: - $sample + '$sample' #end for #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' #for $condition_list in $in_type.conditions: #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) - $samples + '$samples' #end for #end if </token> @@ -79,11 +81,11 @@ <token name="@CUFFLINKS_GTF_INPUTS@"> ## Inputs. #for $input_file in $inputs: - "${input_file}" + '${input_file}' #end for #for $additional_input in $additional_inputs: #for $input_file in $additional_input.additional_inputs: - "${input_file}" + '${input_file}' #end for #end for </token>
--- a/cuffquant_wrapper.xml Mon Nov 09 12:06:19 2015 -0500 +++ b/cuffquant_wrapper.xml Tue Feb 07 18:39:37 2017 -0500 @@ -1,11 +1,11 @@ <tool id="cuffquant" name="Cuffquant" version="@VERSION@.0"> <!-- Wrapper supports Cuffdiff versions 2.2.1 --> <description>Precompute gene expression levels</description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <import>cuff_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <version_command>cuffquant 2>&1 | head -n 1</version_command> <command> cuffquant @@ -27,10 +27,10 @@ -b #if $bias_correction.seq_source.index_source == "history": ## Custom genome from history. - $bias_correction.seq_source.ref_file + '$bias_correction.seq_source.ref_file' #else: ## Built-in genome. - "${ bias_correction.seq_source.index.fields.path }" + '${bias_correction.seq_source.index.fields.path}' #end if #end if @@ -42,15 +42,15 @@ --library-type=$advanced_settings.library_type #end if #if $advanced_settings.mask_file: - --mask-file=$advanced_settings.mask_file + --mask-file '$advanced_settings.mask_file' #end if --max-mle-iterations=$advanced_settings.max_mle_iterations --max-bundle-frags=$advanced_settings.max_bundle_frags #end if ## Inputs. - $gtf_input + '$gtf_input' #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] ) - $samplestring + '$samplestring' </command> <inputs> <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts"
--- a/tool_dependencies.xml Mon Nov 09 12:06:19 2015 -0500 +++ b/tool_dependencies.xml Tue Feb 07 18:39:37 2017 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="cufflinks" version="2.2.1"> - <repository changeset_revision="8f755957b6a1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="87f239da61af" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>