Mercurial > repos > artbio > gsc_mannwhitney_de

comparison mannwhitney_de.xml @ 2:60964af87364 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 9d570db083bd51751f4784dc367ee18aa0024ecd
author artbio
date Mon, 01 Jul 2019 09:05:28 -0400
parents aef09ac6d0a5
children 3d86c89f15bf
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1:aef09ac6d0a5 2:60964af87364
1 <tool id="mannwhitney_de" name="Perform a differential analysis" version="0.9.1"> 1 <tool id="mannwhitney_de" name="Perform a differential analysis" version="0.9.2">
2 <description>using a Mann-Whitney test</description> 2 <description>using a Mann-Whitney test</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
32 <param name="colnames" type="select" label="Firt row contains column names"> 32 <param name="colnames" type="select" label="Firt row contains column names">
33 <option value="TRUE" selected="true">Yes</option> 33 <option value="TRUE" selected="true">Yes</option>
34 <option value="FALSE">No</option> 34 <option value="FALSE">No</option>
35 </param> 35 </param>
36 <param name="comparison_factor_file" type="data" format="tabular" label="Comparison factor table" 36 <param name="comparison_factor_file" type="data" format="tabular" label="Comparison factor table"
37 help="A tsv table file with two columns : cell identifiers and a column that split cells into two categories." /> 37 help="A tsv table file with two columns : cell identifiers and a column that split cells into two categories.
38 Other columns are ignored" />
38 <param name="factor1" type="text" label="Condition-1. The first level (value) that the comparison factor can take." help="typical values could be 'LOW', 'wt', 't1', etc."/> 39 <param name="factor1" type="text" label="Condition-1. The first level (value) that the comparison factor can take." help="typical values could be 'LOW', 'wt', 't1', etc."/>
39 <param name="factor2" type="text" label="Condition-2. The second level (value) that the comparison factor can take." help="typical values could be 'HIGH', 'mutant', 't2', etc."/> 40 <param name="factor2" type="text" label="Condition-2. The second level (value) that the comparison factor can take." help="typical values could be 'HIGH', 'mutant', 't2', etc."/>
40 <param name="fdr" type="float" value="0.01" label="FDR threshold" 41 <param name="fdr" type="float" value="0.01" label="FDR threshold"
41 help="Reject H0 of no differential expression if adjusted p-values (Benjamini-Hochberg correction) is higher than the FDR cut-off."/> 42 help="Reject H0 of no differential expression if adjusted p-values (Benjamini-Hochberg correction) is higher than the FDR cut-off."/>
42 <param name="log" type="boolean" checked="false" label="Expression data are log-transformed" truevalue="--log" falsevalue=""/> 43 <param name="log" type="boolean" checked="false" label="Expression data are log-transformed" truevalue="--log" falsevalue=""/>
49 <test> 50 <test>
50 <param name="input" value="filtered-0.05.tab" ftype="txt"/> 51 <param name="input" value="filtered-0.05.tab" ftype="txt"/>
51 <param name="sep" value="tab" /> 52 <param name="sep" value="tab" />
52 <param name="colnames" value="TRUE"/> 53 <param name="colnames" value="TRUE"/>
53 <param name="comparison_factor_file" value="signature_2columns.tsv" ftype="tabular"/> 54 <param name="comparison_factor_file" value="signature_2columns.tsv" ftype="tabular"/>
55 <param name="factor1" value="LOW"/>
56 <param name="factor2" value="HIGH"/>
57 <param name="fdr" value="0.01"/>
58 <param name="log" value="true"/>
59 <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/>
60 </test>
61 <test>
62 <param name="input" value="filtered-0.05.tab" ftype="txt"/>
63 <param name="sep" value="tab" />
64 <param name="colnames" value="TRUE"/>
65 <param name="comparison_factor_file" value="signature_3columns.tsv" ftype="tabular"/>
54 <param name="factor1" value="LOW"/> 66 <param name="factor1" value="LOW"/>
55 <param name="factor2" value="HIGH"/> 67 <param name="factor2" value="HIGH"/>
56 <param name="fdr" value="0.01"/> 68 <param name="fdr" value="0.01"/>
57 <param name="log" value="true"/> 69 <param name="log" value="true"/>
58 <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/> 70 <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/>