Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix
diff abundance_estimates_to_matrix.xml @ 5:8b5039bdf1f6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
author | iuc |
---|---|
date | Fri, 31 Mar 2017 11:37:24 -0400 |
parents | fba77b1f69b4 |
children | 74217fbfba4d |
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--- a/abundance_estimates_to_matrix.xml Thu Mar 23 10:18:33 2017 -0400 +++ b/abundance_estimates_to_matrix.xml Fri Mar 31 11:37:24 2017 -0400 @@ -1,17 +1,17 @@ -<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1"> +<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.0"> <description>for a de novo assembly of RNA-Seq data by Trinity</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="3.14.0">bioconductor-edger</requirement> - <requirement type="package" version="0.7.2">salmon</requirement> + <requirement type="package" version="3.16.5">bioconductor-edger</requirement> + <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 --> + <requirement type="package" version="0.8.1">salmon</requirement> </expand> - <expand macro="stdio"/> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ #import re #for $entry in $samples: - ln -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && + ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && #end for abundance_estimates_to_matrix.pl