Mercurial > repos > iuc > trinity_align_and_estimate_abundance
diff align_and_estimate_abundance.xml @ 5:be3607a306af draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
| author | iuc |
|---|---|
| date | Fri, 31 Mar 2017 11:37:01 -0400 |
| parents | 515119330a55 |
| children | 04bd98a9c751 |
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--- a/align_and_estimate_abundance.xml Thu Mar 23 10:17:49 2017 -0400 +++ b/align_and_estimate_abundance.xml Fri Mar 31 11:37:01 2017 -0400 @@ -1,18 +1,16 @@ -<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.2"> +<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.0"> <description>on a de novo assembly of RNA-Seq data</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="1.1.2">bowtie</requirement> - <requirement type="package" version="2.2.6">bowtie2</requirement> - <requirement type="package" version="1.2.28">rsem</requirement> - <requirement type="package" version="1.5.1">eXpress</requirement> - <requirement type="package" version="0.6.0">salmon</requirement> + <requirement type="package" version="1.3.0">rsem</requirement> + <requirement type="package" version="1.5.1">express</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[ - ln -s '$transcripts' input.fa && + <command detect_errors="aggressive"><![CDATA[ + ln -f -s '$transcripts' input.fa && #if $inputs.paired_or_single == "paired": #if $inputs.left_input.is_of_type('fasta'):