Mercurial > repos > iuc > trinity_run_de_analysis
comparison run_de_analysis.xml @ 0:1563554bb3f0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
author | iuc |
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date | Mon, 01 Aug 2016 14:43:38 -0400 |
parents | |
children | 18213f29e0b9 |
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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 ${on_string}"> | |
82 <discover_datasets pattern="(?P<name>.+)\.DE_results$" ext="tabular" directory="results" /> | |
83 </collection> | |
84 <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}"> | |
85 <discover_datasets pattern="(?P<name>.+)\.pdf$" 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> |