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comparison abundance_estimates_to_matrix.xml @ 8:258c64019e50 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 811337eaab815f54f0fd93a3dd23a1153993ea2a
author iuc
date Tue, 28 Jun 2016 12:22:40 -0400
parents 1b7800489efb
children
comparison
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7:1b7800489efb 8:258c64019e50
1 <tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1"> 1 <tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1.1">
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 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1.1">trinity</requirement> 4 <requirement type="package" version="2.1.1">trinity</requirement>
5 <requirement type="package" version="3.14.0">bioconductor-edger</requirement> 5 <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code range="1:"/> 8 <exit_code range="1:"/>
9 </stdio> 9 </stdio>
10 <command><![CDATA[ 10 <command><![CDATA[
11 #for $entry in $samples: 11 #for $entry in $samples:
12 ln -s "${entry.file}" "${entry.sample_name}.tsv" && 12 ln -s "${entry.file}" "${entry.sample_name}" &&
13 #end for 13 #end for
14 14
15 abundance_estimates_to_matrix.pl 15 abundance_estimates_to_matrix.pl
16 16
17 --est_method ${est_method} 17 --est_method ${est_method}
18 --cross_sample_norm ${additional_params.cross_sample_norm} 18 --cross_sample_norm ${additional_params.cross_sample_norm}
19 19
20 #for $entry in $samples: 20 #for $entry in $samples:
21 "${entry.sample_name}.tsv" 21 "${entry.sample_name}"
22 #end for 22 #end for
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <repeat name="samples" title="Abundance estimates for samples"> 25 <repeat name="samples" title="Abundance estimates for samples">
26 <param name="file" label="Add file" type="data" format="tabular"/> 26 <param name="file" label="Add file" type="data" format="tabular"/>