Mercurial > repos > mvdbeek > r_goseq_1_22_0

comparison goseq.xml @ 0:a6427f7893b0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author mvdbeek
date Fri, 26 Feb 2016 06:57:47 -0500
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1 <tool id="goseq" name="goseq gene ontology analyser" version="0.1.2">
2 <description />
3 <requirements>
4 <requirement type="package" version="3.2.1">R</requirement>
5 <requirement type="package" version="1.22.0">goseq</requirement>
6 </requirements>
7 <command interpreter="Rscript">
8 goseq.r --dge_file "$dge_file"
9 --p_adj_column "$p_adj_column"
10 --cutoff "$p_adj_cutoff"
11 #if $source.use_length_file == "yes":
12 --length_file "$length_file"
13 #end if
14 --genome "$genome"
15 --gene_id "$gene_id"
16 --wallenius_tab "$wallenius_tab"
17 --sampling_tab "$sampling_tab"
18 --nobias_tab "$nobias_tab"
19 --length_bias_plot "$length_bias_plot"
20 --sample_vs_wallenius_plot "$sample_vs_wallenius_plot"
21 --repcnt "$repcnt"
22 </command>
23 <inputs>
24 <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" />
25 <param help="Select the column that contains the multiple-testing corrected p-value" label="p adjust column" name="p_adj_column" type="data_column" data_ref="dge_file"/>
26 <param help="Typically 0.05 after multiple testing correction" max="1" label="Minimum p adjust value to consider genes as differentially expressed" name="p_adj_cutoff" type="float" value="0.05" />
27 <conditional name="source">
28 <param help="This is needed if the gene length is not available in goseq. e.g. hg38 and mm10." label="Use gene length file?" name="use_length_file" type="select">
29 <option value="no">no</option>
30 <option value="yes">yes</option>
31 </param>
32 <when value="yes">
33 <param label="Gene length file" name="length_file" type="data" format="tabular" required="false" />
34 </when>
35 </conditional>
36 <param help="Needed to retrieve gene length for length correction" label="Select the genome source" name="genome" size="3" type="select">
37 <options from_table="go_genomes"></options>
38 </param>
39 <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select">
40 <options from_table="go_gene_ids"></options>
41 </param>
42 <param help="Do this many random samplings. Set to 0 to not do sampling. Larger values take a long time" label="Number of random sampling" name="repcnt" size="3" type="integer" min="0" max="10000" value="0" />
43 </inputs>
44 <outputs>
45 <data format="pdf" label="length bias plot" name="length_bias_plot" />
46 <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot">
47 <filter>repcnt == "0"</filter>
48 </data>
49 <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" />
50 <data format="tabular" label="Ranked category list - sampling" name="sampling_tab">
51 <filter>repcnt == "0"</filter>
52 </data>
53 <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" />
54 </outputs>
55 <tests>
56 <test>
57 <param name="dge_file" value="dge_list.tab" />
58 <param name="use_length_file" value="no" />
59 <param name="p_adj_column" value="2" />
60 <param name="genome" value="hg19" />
61 <param name="gene_id" value="ensGene" />
62 <output name="wallenius_tab" file="wall.tab" />
63 </test>
64 </tests>
65 <help>
66
67 **What it does**
68
69 Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.
70
71 Options map closely to the excellent manual_
72
73 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf
74
75
76 </help>
77 <citations>
78 <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
79 </citations>
80 </tool>