Mercurial > repos > mvdbeek > r_goseq_1_22_0

changeset 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
files goseq.xml test-data/wall.tab
diffstat 1 files changed, 9 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/goseq.xml	Fri Feb 26 07:41:42 2016 -0500
+++ b/goseq.xml	Fri Feb 26 08:49:05 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="goseq" name="goseq gene ontology analyser" version="0.1.2">
+<tool id="goseq" name="goseq gene ontology analyser" version="0.1.4">
     <description />
     <requirements>
         <requirement type="package" version="3.2.1">R</requirement>
@@ -22,7 +22,7 @@
     </command>
     <inputs>
         <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" />
-        <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"/>
+        <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"/>
         <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" />
         <conditional name="source">
             <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">
@@ -32,6 +32,8 @@
             <when value="yes">
                 <param label="Gene length file" name="length_file" type="data" format="tabular" required="false" />
             </when>
+            <when value="no">
+            </when>
         </conditional>
         <param help="Needed to retrieve gene length for length correction" label="Select the genome source" name="genome" size="3" type="select">
             <options from_data_table="go_genomes"></options>
@@ -39,27 +41,27 @@
         <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select">
             <options from_data_table="go_gene_ids"></options>
         </param>
-        <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" />
+        <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" />
     </inputs>
     <outputs>
         <data format="pdf" label="length bias plot" name="length_bias_plot" />
         <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot">
-            <filter>repcnt == "0"</filter>
+            <filter>repcnt != 0</filter>
         </data>
         <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" />
         <data format="tabular" label="Ranked category list - sampling" name="sampling_tab">
-            <filter>repcnt == "0"</filter>
+            <filter>repcnt != 0</filter>
         </data>
         <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" />
     </outputs>
     <tests>
         <test>
-            <param name="dge_file" value="dge_list.tab" />
+            <param name="dge_file" value="dge_list.tab" ftype="tabular"/>
             <param name="use_length_file" value="no" />
             <param name="p_adj_column" value="2" />
             <param name="genome" value="hg19" />
             <param name="gene_id" value="ensGene" />
-            <output name="wallenius_tab" file="wall.tab" />
+            <output name="wallenius_tab" file="wall.tab" compare="contains"/>/>
         </test>
     </tests>
     <help>