Mercurial > repos > mvdbeek > r_goseq_1_22_0

comparison goseq.xml @ 2:0283381bdafd 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 08:49:05 -0500
parents ba71bc50299b
children 81283f3d65c7
comparison
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1:ba71bc50299b 2:0283381bdafd
1 <tool id="goseq" name="goseq gene ontology analyser" version="0.1.2"> 1 <tool id="goseq" name="goseq gene ontology analyser" version="0.1.4">
2 <description /> 2 <description />
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.2.1">R</requirement> 4 <requirement type="package" version="3.2.1">R</requirement>
5 <requirement type="package" version="1.22.0">goseq</requirement> 5 <requirement type="package" version="1.22.0">goseq</requirement>
6 </requirements> 6 </requirements>
20 --sample_vs_wallenius_plot "$sample_vs_wallenius_plot" 20 --sample_vs_wallenius_plot "$sample_vs_wallenius_plot"
21 --repcnt "$repcnt" 21 --repcnt "$repcnt"
22 </command> 22 </command>
23 <inputs> 23 <inputs>
24 <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" /> 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"/> 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" numeric="true" 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" /> 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"> 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"> 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> 29 <option value="no">no</option>
30 <option value="yes">yes</option> 30 <option value="yes">yes</option>
31 </param> 31 </param>
32 <when value="yes"> 32 <when value="yes">
33 <param label="Gene length file" name="length_file" type="data" format="tabular" required="false" /> 33 <param label="Gene length file" name="length_file" type="data" format="tabular" required="false" />
34 </when> 34 </when>
35 <when value="no">
36 </when>
35 </conditional> 37 </conditional>
36 <param help="Needed to retrieve gene length for length correction" label="Select the genome source" name="genome" size="3" type="select"> 38 <param help="Needed to retrieve gene length for length correction" label="Select the genome source" name="genome" size="3" type="select">
37 <options from_data_table="go_genomes"></options> 39 <options from_data_table="go_genomes"></options>
38 </param> 40 </param>
39 <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select"> 41 <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select">
40 <options from_data_table="go_gene_ids"></options> 42 <options from_data_table="go_gene_ids"></options>
41 </param> 43 </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" /> 44 <param help="Draw this many random control gene sets. Set to 0 to not do sampling. Larger values take a long time" label="sampling depth" name="repcnt" size="3" type="integer" min="0" max="10000" value="0" />
43 </inputs> 45 </inputs>
44 <outputs> 46 <outputs>
45 <data format="pdf" label="length bias plot" name="length_bias_plot" /> 47 <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"> 48 <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot">
47 <filter>repcnt == "0"</filter> 49 <filter>repcnt != 0</filter>
48 </data> 50 </data>
49 <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" /> 51 <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" />
50 <data format="tabular" label="Ranked category list - sampling" name="sampling_tab"> 52 <data format="tabular" label="Ranked category list - sampling" name="sampling_tab">
51 <filter>repcnt == "0"</filter> 53 <filter>repcnt != 0</filter>
52 </data> 54 </data>
53 <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" /> 55 <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" />
54 </outputs> 56 </outputs>
55 <tests> 57 <tests>
56 <test> 58 <test>
57 <param name="dge_file" value="dge_list.tab" /> 59 <param name="dge_file" value="dge_list.tab" ftype="tabular"/>
58 <param name="use_length_file" value="no" /> 60 <param name="use_length_file" value="no" />
59 <param name="p_adj_column" value="2" /> 61 <param name="p_adj_column" value="2" />
60 <param name="genome" value="hg19" /> 62 <param name="genome" value="hg19" />
61 <param name="gene_id" value="ensGene" /> 63 <param name="gene_id" value="ensGene" />
62 <output name="wallenius_tab" file="wall.tab" /> 64 <output name="wallenius_tab" file="wall.tab" compare="contains"/>/>
63 </test> 65 </test>
64 </tests> 66 </tests>
65 <help> 67 <help>
66 68
67 **What it does** 69 **What it does**