Mercurial > repos > artbio > gsc_mannwhitney_de

changeset 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
files mannwhitney_de.xml test-data/signature_3columns.tsv
diffstat 2 files changed, 115 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/mannwhitney_de.xml	Mon Jun 24 19:17:26 2019 -0400
+++ b/mannwhitney_de.xml	Mon Jul 01 09:05:28 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="mannwhitney_de" name="Perform a differential analysis" version="0.9.1">
+<tool id="mannwhitney_de" name="Perform a differential analysis" version="0.9.2">
     <description>using a Mann-Whitney test</description>
     <requirements>
         <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
@@ -34,7 +34,8 @@
             <option value="FALSE">No</option>
         </param>
         <param name="comparison_factor_file" type="data" format="tabular" label="Comparison factor table"
-               help="A tsv table file with two columns : cell identifiers and a column that split cells into two categories." />
+               help="A tsv table file with two columns : cell identifiers and a column that split cells into two categories.
+                     Other columns are ignored" />
         <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."/>
         <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."/>
         <param name="fdr" type="float" value="0.01" label="FDR threshold"
@@ -58,6 +59,17 @@
             <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/>
         </test>
         <test>
+            <param name="input" value="filtered-0.05.tab" ftype="txt"/>
+            <param name="sep" value="tab" />
+            <param name="colnames" value="TRUE"/>
+            <param name="comparison_factor_file" value="signature_3columns.tsv" ftype="tabular"/>
+            <param name="factor1" value="LOW"/>
+            <param name="factor2" value="HIGH"/>
+            <param name="fdr" value="0.01"/>
+            <param name="log" value="true"/>
+            <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/>
+        </test>
+        <test>
             <param name="input" value="filterCells_100.tsv" ftype="txt"/>
             <param name="sep" value="tab" />
             <param name="colnames" value="TRUE"/>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/signature_3columns.tsv	Mon Jul 01 09:05:28 2019 -0400
@@ -0,0 +1,101 @@
+cells	factor	add_column
+1001000173.B4	LOW	1001000173.B4
+1001000173.A2	LOW	1001000173.A2
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+1001000173.H1	HIGH	1001000173.H1
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+1001000173.C2	LOW	1001000173.C2
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+1001000173.F2	LOW	1001000173.F2
+1001000173.H9	LOW	1001000173.H9
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+1001000173.B3	LOW	1001000173.B3
+1001000173.D7	HIGH	1001000173.D7
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+1001000173.E1	LOW	1001000173.E1
+1001000173.G12	HIGH	1001000173.G12
+1001000173.C10	HIGH	1001000173.C10
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