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comparison ctat_abundance_estimation_to_matrix.xml @ 0:5eca0c75b178 draft default tip

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author trinity_ctat
date Tue, 17 Jul 2018 11:47:32 -0400
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1 <tool id="ctat_abundance_estimation_to_matrix" name="ctat_abundance_estimation_to_matrix" version="1.0.0" profile="17.05">
2
3 <description>Join RSEM estimates from multiple samples into a single matrix</description>
4 <requirements>
5 <requirement type="package" version="2.7">python</requirement>
6 <requirement type="package">subprocess32</requirement>
7 <requirement type="package">bzip2</requirement>
8 <requirement type="package" version="1.3.0">rsem</requirement>
9 <requirement type="package" version="3">bioconductor-edger</requirement>
10 <requirement type="package" version="2">bioconductor-qvalue</requirement>
11 <requirement type="package" version="2.6.6">trinity</requirement>
12 </requirements>
13 <command detect_errors="exit_code">
14 <![CDATA[
15 python $__tool_directory__/ctat_abundance_estimation_to_matrix.py
16 #for $q in $RSEM_samples
17 ${q.file} "${q.column_label}"
18 #end for
19 ]]>
20
21 </command>
22 <inputs>
23
24 <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
25 <param name="file" label="Add file" type="data" format="txt"/>
26 <param name="column_label" label="column label" type="text" />
27 </repeat>
28
29 </inputs>
30 <outputs>
31 <data format="tabular" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.isoform.counts.matrix"/>
32 <data format="tabular" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="RSEM.isoform.TMM.EXPR.matrix"/>
33 </outputs>
34 <tests>
35 <test>
36 <repeat name="RSEM_samples">
37 <param name="file" value="Sp_ds.RSEM.genes.results" />
38 <param name="column_label" value="Sp_ds" />
39 </repeat>
40 <repeat name="RSEM_samples">
41 <param name="file" value="Sp_hs.RSEM.genes.results" />
42 <param name="column_label" value="Sp_hs" />
43 </repeat>
44
45 <output name="counts_matrix" >
46 <assert_contents>
47 <has_line_matching expression=".+" />
48 <has_line line="&#009;Sp_ds&#009;Sp_hs" />
49 <has_n_columns n="3" />
50 <has_line_matching expression="TRINITY_DN.+" />
51 </assert_contents>
52 </output>
53 <output name="tmm_expr_matrix" >
54 <assert_contents>
55 <has_line_matching expression=".+" />
56 <has_line line="&#009;Sp_ds&#009;Sp_hs" />
57 <has_n_columns n="3" />
58 <has_line_matching expression="TRINITY_DN.+" />
59 </assert_contents>
60 </output>
61 </test>
62 <!-- The following test has not been tested to see if it works.
63 <test>
64 <repeat name="RSEM_samples">
65 <param name="file" value="Sp_ds.RSEM.isoforms.results" />
66 <param name="column_label" value="Sp_ds" />
67 </repeat>
68 <repeat name="RSEM_samples">
69 <param name="file" value="Sp_hs.RSEM.isoforms.results" />
70 <param name="column_label" value="Sp_hs" />
71 </repeat>
72
73 <output name="counts_matrix" >
74 <assert_contents>
75 <has_line_matching expression=".+" />
76 </assert_contents>
77 </output>
78 <output name="tmm_expr_matrix" >
79 <assert_contents>
80 <has_line_matching expression=".+" />
81 </assert_contents>
82 </output>
83 </test>
84 -->
85 </tests>
86 <help>
87 .. class:: infomark
88
89 This step will join the RSEM-computed gene or isoform fragment counts into a matrix file, which will be used to run edgeR and identify differentially expressed transcripts in next few steps. Execution of this will generate a counts matrix file with a name 'abundance_estimation_to_matrix: counts_matrix'.
90
91 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.
92
93 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
94 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
95 </help>
96
97 <citations>
98 <citation type="doi">10.1038/nbt.1883</citation>
99 </citations>
100
101 </tool>