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comparison abundance_estimation_to_matrix.xml @ 6:e673d9dd4928 draft

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Changing input format type.
author trinity_ctat
date Fri, 29 Sep 2017 11:38:03 -0400
parents 27fe7db7444b
children deed5e162203
comparison
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5:27fe7db7444b 6:e673d9dd4928
3 <description>Join RSEM estimates from multiple samples into a single matrix</description> 3 <description>Join RSEM estimates from multiple samples into a single matrix</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.7">python</requirement> 5 <requirement type="package" version="2.7">python</requirement>
6 <requirement type="package">trinity</requirement> 6 <requirement type="package">trinity</requirement>
7 </requirements> 7 </requirements>
8 <command interpreter="python"> 8 <command>
9 9 <![CDATA[
10 abundance_estimation_to_matrix_wrapper.py 10 python abundance_estimation_to_matrix_wrapper.py
11 #for $q in $RSEM_samples 11 #for $q in $RSEM_samples
12 ${q.file} "${q.column_label}" 12 ${q.file} "${q.column_label}"
13 #end for 13 #end for
14 ]]>
14 15
15 </command> 16 </command>
16 <inputs> 17 <inputs>
17 18
18 <repeat name="RSEM_samples" title="RSEM abundance estimates for samples"> 19 <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
19 <param name="file" label="Add file" type="data" format="text"/> 20 <param name="file" label="Add file" type="data" format="txt"/>
20 <param name="column_label" label="column label" type="text" /> 21 <param name="column_label" label="column label" type="text" />
21 </repeat> 22 </repeat>
22 23
23 </inputs> 24 </inputs>
24 <outputs> 25 <outputs>
25 <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/> 26 <data format="txt" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/>
26 <data format="text" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="matrix.TMM.EXPR.matrix"/> 27 <data format="txt" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="matrix.TMM.EXPR.matrix"/>
27 </outputs> 28 </outputs>
28 <tests> 29 <tests>
29 <test> 30 <test>
30 <repeat name="RSEM_samples"> 31 <repeat name="RSEM_samples">
31 <param name="file" value="Sp_ds.RSEM.genes.results" /> 32 <param name="file" value="Sp_ds.RSEM.genes.results" />