diff dexseq.xml @ 10:df929f257179 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140

--- a/dexseq.xml	Tue May 03 20:23:18 2022 +0000
+++ b/dexseq.xml	Tue Apr 04 08:25:51 2023 +0000
@@ -1,15 +1,10 @@
-<tool id="dexseq" name="DEXSeq" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="dexseq" name="DEXSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Determines differential exon usage from count tables</description>
-    <xrefs>
-        <xref type="bio.tools">dexseq</xref>
-    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.20.2">r-getopt</requirement>
-        <requirement type="package" version="0.2.20">r-rjson</requirement>
-    </expand>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <code file="dexseq_helper.py" />
     <stdio>
         <regex match="Execution halted"
@@ -102,7 +97,11 @@
         <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
     </inputs>
     <outputs>
-        <data name="dexseq_out" format="tabular" label="${tool.name} on ${on_string}: result" />
+        <data name="dexseq_out" format="tabular" label="${tool.name} on ${on_string}: result">
+            <actions>
+                <action name="column_names" type="metadata" default="GeneID,ExonID,Exon base mean,Dispersion,Stat,p-value,p-adj,X1_group1,X2_group2,log2(FC),Chr. name,Start,End,Width,Strand,Raw counts"/>
+            </actions>
+        </data>
         <data name="htmlreport" format="html" label="${tool.name} on ${on_string}: report">
             <filter>report is True</filter>
         </data>