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comparison run_de_analysis.xml @ 0:0b06ab8d5f88 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
author iuc
date Mon, 01 Aug 2016 11:52:05 -0400
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-1:000000000000 0:0b06ab8d5f88
1 <tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.0">
2 <description>using a Trinity assembly</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
8 <requirement type="package" version="1.10.0">deseq2</requirement>
9 <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
10 <requirement type="package" version="3.28.10">bioconductor-limma</requirement>
11 <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
12 </expand>
13 <expand macro="stdio"/>
14 <command><![CDATA[
15
16 ln -s "${matrix}" "input.matrix"
17
18 &&
19
20 run_DE_analysis.pl
21
22 --matrix "input.matrix"
23
24 --samples_file "${samples}"
25
26 --method ${method_choice.method}
27
28 #if $method_choice.method == "edgeR":
29 --dispersion ${method_choice.edger_dispersion}
30 #end if
31
32 #if $method_choice.method == "ROTS":
33 --ROTS_B ${method_choice.rots_b}
34 --ROTS_K ${method_choice.rots_k}
35 #end if
36
37 --min_rowSum_counts ${additional_params.min_rowSum_counts}
38
39 #if $additional_params.reference_sample:
40 --reference_sample ${additional_params.reference_sample}
41 #end if
42
43 #if $additional_params.contrasts:
44 --contrasts ${additional_params.contrasts}
45 #end if
46
47 --output results
48
49 ]]></command>
50 <inputs>
51 <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
52 <param format="tabular" name="samples" argument="--samples_file" type="data" label="Sample description" help="file describing samples and replicates"/>
53
54 <conditional name="method_choice">
55 <param type="select" name="method" argument="--method" label="Differential analysis method">
56 <option value="edgeR">edgeR</option>
57 <option value="DESeq2">DESeq2</option>
58 <option value="voom">voom</option>
59 <option value="ROTS">ROTS</option>
60 </param>
61 <when value="edgeR">
62 <param name="edger_dispersion" argument="--dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" />
63 </when>
64 <when value="ROTS">
65 <param name="rots_b" argument="--ROTS_B" type="integer" value="500" label="number of bootstraps and permutation resampling" />
66 <param name="rots_k" argument="--ROTS_K" type="integer" value="5000" label="largest top genes size" />
67 </when>
68 <when value="voom">
69 </when>
70 <when value="DESeq2">
71 </when>
72 </conditional>
73
74 <section name="additional_params" title="Additional Options" expanded="False">
75 <param name="min_rowSum_counts" argument="--min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/>
76 <param name="reference_sample" argument="--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"/>
77 <param format="tabular" name="contrasts" argument="--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"/>
78 </section>
79 </inputs>
80 <outputs>
81 <collection name="DE_results" type="list" label="Differential expression results on ${on_string}">
82 <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results$" ext="tabular" directory="results" />
83 </collection>
84 <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}">
85 <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf$" ext="pdf" directory="results" />
86 </collection>
87 </outputs>
88 <tests>
89 <test>
90 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
91 <param name="samples" value="count/samples.txt"/>
92 <param name="method" value="DESeq2"/>
93 <output_collection name="DE_results">
94 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/>
95 <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.DE_results"/>
96 <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.DE_results"/>
97 </output_collection>
98 <output_collection name="PDF_results">
99 <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"/>
100 <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"/>
101 <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"/>
102 </output_collection>
103 </test>
104 <test>
105 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
106 <param name="samples" value="count/samples.txt"/>
107 <param name="method" value="edgeR"/>
108 <output_collection name="DE_results">
109 <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results"/>
110 <element name="input.matrix.wt_37_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results"/>
111 <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results"/>
112 </output_collection>
113 <output_collection name="PDF_results">
114 <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf"/>
115 <element name="input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/>
116 <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/>
117 </output_collection>
118 </test>
119 <test>
120 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
121 <param name="samples" value="count/samples.txt"/>
122 <param name="method" value="voom"/>
123 <output_collection name="DE_results">
124 <element name="input.matrix.wt_37_vs_wt_GSNO.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results"/>
125 <element name="input.matrix.wt_37_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results"/>
126 <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results"/>
127 </output_collection>
128 <output_collection name="PDF_results">
129 <element name="input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf"/>
130 <element name="input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf"/>
131 <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf"/>
132 </output_collection>
133 </test>
134 </tests>
135 <help>
136 <![CDATA[
137 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
138 This tool performs differential expression analyses on a transcriptome assembled with Trinity.
139
140 **Inputs**
141
142 This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
143
144 You must describe your samples and replicates with a tabular file looking like this:
145
146 =========== ================
147 ConditionA CondA_replicate1
148 ----------- ----------------
149 ConditionA CondA_replicate2
150 ----------- ----------------
151 ConditionB CondB_replicate1
152 ----------- ----------------
153 ConditionB CondB_replicate2
154 ----------- ----------------
155 ConditionC CondC_replicate1
156 ----------- ----------------
157 ConditionC CondC_replicate2
158 ----------- ----------------
159 ConditionC CondC_replicate3
160 =========== ================
161
162 It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'.
163 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'.
164
165
166 .. _Trinity: http://trinityrnaseq.github.io
167 ]]>
168 </help>
169
170 <expand macro="citation" />
171 </tool>