Mercurial > repos > iuc > trinity

comparison run_DE_analysis.xml @ 4:692491de7df5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617
author iuc
date Thu, 12 May 2016 07:02:10 -0400
parents c7555bc21812
children e4a9e0798360
comparison
equal deleted inserted replaced
3:c7555bc21812 4:692491de7df5
1 <tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1"> 1 <tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1.1">
2 <description>using a Trinity assembly</description> 2 <description>using a Trinity assembly</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1.1">trinity</requirement> 4 <requirement type="package" version="2.1.1">trinity</requirement>
5 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> 5 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
6 <requirement type="package" version="1.10.0">deseq2</requirement> 6 <requirement type="package" version="1.10.0">deseq2</requirement>
7 <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement> 7 <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
8 <requirement type="package" version="3.12.0">edger</requirement> 8 <requirement type="package" version="3.12.0">edger</requirement>
9 <requirement type="package" version="3.12.0">bioconductor-edger</requirement> 9 <requirement type="package" version="3.12.0">bioconductor-edger</requirement>
10 <requirement type="package" version="3.27.4">limma</requirement> 10 <requirement type="package" version="3.28.2">limma</requirement>
11 <requirement type="package" version="3.27.4">bioconductor-limma</requirement> 11 <requirement type="package" version="3.27.4">bioconductor-limma</requirement>
12 </requirements> 12 </requirements>
13 <stdio> 13 <stdio>
14 <exit_code range="1:"/> 14 <exit_code range="1:"/>
15 </stdio> 15 </stdio>
16 <command><![CDATA[ 16 <command><![CDATA[
17 17
18 ln -s "${matrix}" "input.matrix" 18 ln -s "${matrix}" "input.matrix"
19 19
20 && 20 &&
21 21
22 run_DE_analysis.pl 22 run_DE_analysis.pl
23 23
24 --matrix "input.matrix" 24 --matrix "input.matrix"
25 25
26 --samples_file "${samples}" 26 --samples_file "${samples}"
27 27
28 --method ${method_choice.method} 28 --method ${method_choice.method}
29 29
30 #if $method_choice.method == "edgeR": 30 #if $method_choice.method == "edgeR":
31 --dispersion ${method_choice.edger_dispersion} 31 --dispersion ${method_choice.edger_dispersion}
32 #end if 32 #end if
33 33
34 #if $method_choice.method == "ROTS": 34 #if $method_choice.method == "ROTS":
35 --ROTS_B ${method_choice.rots_b} 35 --ROTS_B ${method_choice.rots_b}
36 --ROTS_K ${method_choice.rots_k} 36 --ROTS_K ${method_choice.rots_k}
37 #end if 37 #end if
38 38
39 --min_rowSum_counts ${additional_params.min_rowSum_counts} 39 --min_rowSum_counts ${additional_params.min_rowSum_counts}
40 40
41 #if $additional_params.reference_sample: 41 #if $additional_params.reference_sample:
42 --reference_sample ${additional_params.reference_sample} 42 --reference_sample ${additional_params.reference_sample}
43 #end if 43 #end if
44 44
45 #if $additional_params.contrasts: 45 #if $additional_params.contrasts:
46 --contrasts ${additional_params.contrasts} 46 --contrasts ${additional_params.contrasts}
47 #end if 47 #end if
48 48
49 --output results 49 --output results
50 50
51 ]]></command> 51 ]]></command>
52 <inputs> 52 <inputs>
53 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/> 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"/> 54 <param format="tabular" name="samples" type="data" label="Sample description" help="file describing samples and replicates"/>
55 55
56 <conditional name="method_choice"> 56 <conditional name="method_choice">
57 <param type="select" name="method" label="Differential analysis method"> 57 <param type="select" name="method" label="Differential analysis method">
58 <option value="edgeR">edgeR</option> 58 <option value="edgeR">edgeR</option>
59 <option value="DESeq2">DESeq2</option> 59 <option value="DESeq2">DESeq2</option>
60 <option value="voom">voom</option> 60 <option value="voom">voom</option>
70 <when value="voom"> 70 <when value="voom">
71 </when> 71 </when>
72 <when value="DESeq2"> 72 <when value="DESeq2">
73 </when> 73 </when>
74 </conditional> 74 </conditional>
75 75
76 <section name="additional_params" title="Additional Options" expanded="False"> 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"/> 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"/> 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"/> 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> 80 </section>
136 136
137 137
138 .. _Trinity: http://trinityrnaseq.github.io 138 .. _Trinity: http://trinityrnaseq.github.io
139 ]]> 139 ]]>
140 </help> 140 </help>
141 141
142 <citations> 142 <citations>
143 <citation type="doi">doi:10.1038/nbt.1883</citation> 143 <citation type="doi">doi:10.1038/nbt.1883</citation>
144 </citations> 144 </citations>
145 </tool> 145 </tool>
146 146