| Previous changeset 2:b2ee2bef1926 (2017-02-07) Next changeset 4:679d93c99757 (2020-06-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 |
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modified:
cuff_macros.xml cuffquant_wrapper.xml |
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removed:
tool_dependencies.xml |
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| diff -r b2ee2bef1926 -r 6dc45faebc1d cuff_macros.xml --- a/cuff_macros.xml Tue Feb 07 18:40:42 2017 -0500 +++ b/cuff_macros.xml Sun Feb 19 12:09:41 2017 -0500 |
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| @@ -8,14 +8,6 @@ </requirements> </xml> - <xml name="stdio"> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error" /> - <regex match="Exception" /> - </stdio> - </xml> <xml name="condition_inputs"> <!-- DEFAULT : use BAM/SAM files --> <conditional name="in_type"> |
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| diff -r b2ee2bef1926 -r 6dc45faebc1d cuffquant_wrapper.xml --- a/cuffquant_wrapper.xml Tue Feb 07 18:40:42 2017 -0500 +++ b/cuffquant_wrapper.xml Sun Feb 19 12:09:41 2017 -0500 |
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| @@ -1,13 +1,12 @@ -<tool id="cuffquant" name="Cuffquant" version="@VERSION@.0"> +<tool id="cuffquant" name="Cuffquant" version="@VERSION@.1"> <!-- Wrapper supports Cuffdiff versions 2.2.1 --> <description>Precompute gene expression levels</description> <macros> <import>cuff_macros.xml</import> </macros> <expand macro="requirements" /> - <expand macro="stdio" /> <version_command>cuffquant 2>&1 | head -n 1</version_command> - <command> + <command detect_errors="aggressive"><![CDATA[ cuffquant --no-update-check --num-threads=\${GALAXY_SLOTS:-4} @@ -51,7 +50,7 @@ '$gtf_input' #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] ) '$samplestring' - </command> + ]]></command> <inputs> <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/> |
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| diff -r b2ee2bef1926 -r 6dc45faebc1d tool_dependencies.xml --- a/tool_dependencies.xml Tue Feb 07 18:40:42 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="cufflinks" version="2.2.1"> - <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |