Mercurial > repos > iuc > trinity_run_de_analysis

comparison run_de_analysis.xml @ 9:48537273a30b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author iuc
date Thu, 14 Jun 2018 03:13:26 -0400
parents 2be382e6918a
children 55cf05b65ad5
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8:047c22569787 9:48537273a30b
1 <tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.0"> 1 <tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@">
2 <description>using a Trinity assembly</description> 2 <description>using a Trinity assembly</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="3.16.5">bioconductor-edger</requirement> 7 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
8 <requirement type="package" version="3.30.13">bioconductor-limma</requirement> 8 <requirement type="package" version="3.34.9">bioconductor-limma</requirement>
9 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> 9 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
10 </expand> 10 </expand>
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 12
13 ln -f -s "${matrix}" "input.matrix" 13 ln -f -s '${matrix}' "input.matrix"
14 14
15 && 15 &&
16 16
17 run_DE_analysis.pl 17 run_DE_analysis.pl
18 18
19 --matrix "input.matrix" 19 --matrix "input.matrix"
20 20
21 --samples_file "${samples}" 21 --samples_file '${samples}'
22 22
23 --method ${method_choice.method} 23 --method ${method_choice.method}
24 24
25 #if $method_choice.method == "edgeR": 25 #if $method_choice.method == "edgeR":
26 --dispersion ${method_choice.edger_dispersion} 26 --dispersion ${method_choice.edger_dispersion}
101 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix"/> 101 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix"/>
102 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix"/> 102 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix"/>
103 </output_collection> 103 </output_collection>
104 <output_collection name="PDF_results"> 104 <output_collection name="PDF_results">
105 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/> 105 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/>
106 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> 106 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="200" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
107 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> 107 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
108 </output_collection> 108 </output_collection>
109 </test> 109 </test>
110 <test> 110 <test>
111 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> 111 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>