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comparison run_DE_analysis.xml @ 2:1317615eff73 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3c4a2b13b0f3a280de4f98f4f5e0dc29e10fc7a0
author iuc
date Tue, 29 Mar 2016 06:46:09 -0400
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1:fd94a21c2131 2:1317615eff73
1 <tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1">
2 <description>using a Trinity assembly</description>
3 <requirements>
4 <requirement type="package" version="2.1.1">trinity</requirement>
5 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
6 <requirement type="package" version="1.10.0">deseq2</requirement>
7 <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
8 <requirement type="package" version="3.12.0">edger</requirement>
9 <requirement type="package" version="3.12.0">bioconductor-edger</requirement>
10 <requirement type="package" version="3.25.3">limma</requirement>
11 <requirement type="package" version="3.27.4">bioconductor-limma</requirement>
12 </requirements>
13 <stdio>
14 <exit_code range="1:"/>
15 </stdio>
16 <command><![CDATA[
17
18 ln -s "${matrix}" "input.matrix"
19
20 &&
21
22 run_DE_analysis.pl
23
24 --matrix "input.matrix"
25
26 --samples_file "${samples}"
27
28 --method ${method_choice.method}
29
30 #if $method_choice.method == "edgeR":
31 --dispersion ${method_choice.edger_dispersion}
32 #end if
33
34 #if $method_choice.method == "ROTS":
35 --ROTS_B ${method_choice.rots_b}
36 --ROTS_K ${method_choice.rots_k}
37 #end if
38
39 --min_rowSum_counts ${additional_params.min_rowSum_counts}
40
41 #if $additional_params.reference_sample:
42 --reference_sample ${additional_params.reference_sample}
43 #end if
44
45 #if $additional_params.contrasts:
46 --contrasts ${additional_params.contrasts}
47 #end if
48
49 --output results
50
51 ]]></command>
52 <inputs>
53 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
54 <param format="tabular" name="samples" type="data" label="Sample description" help="file describing samples and replicates"/>
55
56 <conditional name="method_choice">
57 <param type="select" name="method" label="Differential analysis method">
58 <option value="edgeR">edgeR</option>
59 <option value="DESeq2">DESeq2</option>
60 <option value="voom">voom</option>
61 <option value="ROTS">ROTS</option>
62 </param>
63 <when value="edgeR">
64 <param name="edger_dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" />
65 </when>
66 <when value="ROTS">
67 <param name="rots_b" type="integer" value="500" label="number of bootstraps and permutation resampling" />
68 <param name="rots_k" type="integer" value="5000" label="largest top genes size" />
69 </when>
70 <when value="voom">
71 </when>
72 <when value="DESeq2">
73 </when>
74 </conditional>
75
76 <section name="additional_params" title="Additional Options" expanded="False">
77 <param name="min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/>
78 <param name="reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/>
79 <param format="tabular" name="contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/>
80 </section>
81 </inputs>
82 <outputs>
83 <collection name="DE_results" type="list" label="Differential expression results on ${on_string}">
84 <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results" ext="tabular" directory="results" visible="true" />
85 </collection>
86 <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}">
87 <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf" ext="pdf" directory="results" visible="true" />
88 </collection>
89 </outputs>
90 <tests>
91 <test>
92 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
93 <param name="samples" value="count/samples.txt"/>
94 <param name="method" value="DESeq2"/>
95 <output_collection name="DE_results">
96 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/>
97 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/>
98 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/>
99 </output_collection>
100 <output_collection name="PDF_results">
101 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/>
102 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
103 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
104 </output_collection>
105 </test>
106 </tests>
107 <help>
108 <![CDATA[
109 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
110 This tool performs differential expression analyses on a transcriptome assembled with Trinity.
111
112 **Inputs**
113
114 This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
115
116 You must describe your samples and replicates with a tabular file looking like this:
117
118 =========== ================
119 ConditionA CondA_replicate1
120 ----------- ----------------
121 ConditionA CondA_replicate2
122 ----------- ----------------
123 ConditionB CondB_replicate1
124 ----------- ----------------
125 ConditionB CondB_replicate2
126 ----------- ----------------
127 ConditionC CondC_replicate1
128 ----------- ----------------
129 ConditionC CondC_replicate2
130 ----------- ----------------
131 ConditionC CondC_replicate3
132 =========== ================
133
134 It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'.
135 The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
136
137
138 .. _Trinity: http://trinityrnaseq.github.io
139 ]]>
140 </help>
141
142 <citations>
143 <citation type="doi">doi:10.1038/nbt.1883</citation>
144 </citations>
145 </tool>
146