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comparison ctat_abundance_estimation_to_matrix.xml @ 0:5eca0c75b178 draft default tip
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author | trinity_ctat |
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date | Tue, 17 Jul 2018 11:47:32 -0400 |
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-1:000000000000 | 0:5eca0c75b178 |
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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="	Sp_ds	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="	Sp_ds	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> |