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Adding Abundance Estimation to Matrix.
author trinity_ctat
date Fri, 29 Sep 2017 09:44:42 -0400
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children a68238baa3e4
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-1:000000000000 0:e4876b8c81ec
1 <tool id="abundance_estimation_to_matrix" name="abundance_estimation_to_matrix" version="1.0.0">
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">trinity</requirement>
7 </requirements>
8 <command interpreter="python">
9
10 abundance_estimation_to_matrix_wrapper.py
11 #for $q in $RSEM_samples
12 ${q.file} "${q.column_label}"
13 #end for
14
15 </command>
16 <inputs>
17
18 <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
19 <param name="file" label="Add file" type="data" format="text"/>
20 <param name="column_label" label="column label" type="text" />
21 </repeat>
22
23 </inputs>
24 <outputs>
25 <data format="txt" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/>
26 <data format="txt" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="matrix.TMM.EXPR.matrix"/>
27 </outputs>
28 <tests>
29 <test>
30 <repeat name="RSEM_samples">
31 <param name="file" value="Sp_ds.RSEM.genes.results" />
32 <param name="column_label" value="Sp_ds" />
33 </repeat>
34 <repeat name="RSEM_samples">
35 <param name="file" value="Sp_hs.RSEM.genes.results" />
36 <param name="column_label" value="Sp_hs" />
37 </repeat>
38
39 <output name="counts_matrix" >
40 <assert_contents>
41 <has_line_matching expression=".+" />
42 <has_line line="&#009;Sp_ds&#009;Sp_hs" />
43 <has_n_columns n="3" />
44 <has_line_matching expression="TRINITY_DN.+" />
45 </assert_contents>
46 </output>
47 <output name="tmm_expr_matrix" >
48 <assert_contents>
49 <has_line_matching expression=".+" />
50 <has_line line="&#009;Sp_ds&#009;Sp_hs" />
51 <has_n_columns n="3" />
52 <has_line_matching expression="TRINITY_DN.+" />
53 </assert_contents>
54 </output>
55 </test>
56 <!-- The following test has not been tested to see if it works.
57 <test>
58 <repeat name="RSEM_samples">
59 <param name="file" value="Sp_ds.RSEM.isoforms.results" />
60 <param name="column_label" value="Sp_ds" />
61 </repeat>
62 <repeat name="RSEM_samples">
63 <param name="file" value="Sp_hs.RSEM.isoforms.results" />
64 <param name="column_label" value="Sp_hs" />
65 </repeat>
66
67 <output name="counts_matrix" >
68 <assert_contents>
69 <has_line_matching expression=".+" />
70 </assert_contents>
71 </output>
72 <output name="tmm_expr_matrix" >
73 <assert_contents>
74 <has_line_matching expression=".+" />
75 </assert_contents>
76 </output>
77 </test>
78 -->
79 </tests>
80 <help>
81 .. class:: infomark
82
83 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'.
84
85 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.
86
87 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
88 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
89 </help>
90 </tool>