Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix
comparison 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 |
comparison
equal
deleted
inserted
replaced
4:1fc32fd3fb3f | 5:8b5039bdf1f6 |
---|---|
1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1"> | 1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.0"> |
2 <description>for a de novo assembly of RNA-Seq data by Trinity</description> | 2 <description>for a de novo assembly of RNA-Seq data by Trinity</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
7 <requirement type="package" version="3.14.0">bioconductor-edger</requirement> | 7 <requirement type="package" version="3.16.5">bioconductor-edger</requirement> |
8 <requirement type="package" version="0.7.2">salmon</requirement> | 8 <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 --> |
9 <requirement type="package" version="0.8.1">salmon</requirement> | |
9 </expand> | 10 </expand> |
10 <expand macro="stdio"/> | 11 <command detect_errors="aggressive"><![CDATA[ |
11 <command><![CDATA[ | |
12 #import re | 12 #import re |
13 #for $entry in $samples: | 13 #for $entry in $samples: |
14 ln -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && | 14 ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && |
15 #end for | 15 #end for |
16 | 16 |
17 abundance_estimates_to_matrix.pl | 17 abundance_estimates_to_matrix.pl |
18 | 18 |
19 --est_method ${est_method} | 19 --est_method ${est_method} |