|
0
|
1 <tool id='abundance_estimates_to_matrix' name='abundance estimates to matrix' version='1.0'>
|
|
|
2 <description> Generates combined Matrix for abundance estimates </description>
|
|
|
3 <!--requirement></requirement-->
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
|
|
|
6 <requirement type="R-module">edgeR</requirement>
|
|
|
7 <requirement type="set_environment">TRINITY_HOME</requirement>
|
|
|
8
|
|
|
9 </requirements>
|
|
|
10 <command interpreter='perl'>\$TRINITY_HOME/util/abundance_estimates_to_matrix.pl
|
|
|
11 --est_method $est_method
|
|
|
12 #for $i in $isoform_sample:
|
|
|
13 $i.isoform_sample_matrix
|
|
|
14 #end for
|
|
|
15 > $output_log 2>&1;
|
|
|
16 </command>
|
|
|
17
|
|
|
18 <inputs>
|
|
|
19 <!-- Required -->
|
|
|
20
|
|
|
21 <param name='est_method' type='select' display="radio" label='Select est_method'>
|
|
|
22 <option value="RSEM" selected='true'>RSEM</option>
|
|
|
23 <option value="eXpress">eXpress</option>
|
|
|
24 </param>
|
|
|
25
|
|
|
26
|
|
|
27 <repeat name="isoform_sample" title="Isoform Sample" min="2">
|
|
|
28 <param name="isoform_sample_matrix" type="data" label="Isoform Sample Matrix"/>
|
|
|
29 </repeat>
|
|
|
30
|
|
|
31 <!-- Optional -->
|
|
|
32
|
|
|
33 </inputs>
|
|
|
34 <outputs>
|
|
|
35 <data name='matrix_count' format='tabular' label="${tool.name} on ${on_string}: matrix_count" from_work_dir="matrix.counts.matrix"/>
|
|
|
36 <data name='matrix_fpkm' format='tabular' label="${tool.name} on ${on_string} : matrix_fpkm" from_work_dir="matrix.TMM.fpkm.matrix"/>
|
|
|
37 <data name='output_log' format='txt' label="${tool.name} on ${on_string} : matrix_log"/>
|
|
|
38 </outputs>
|
|
|
39 </tool>
|
