Mercurial > repos > iuc > dexseq

changeset 8:2872c633f07e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit d6fb005b0dbf26037aab1748d9b5df12876c674d"
author iuc
date Sun, 19 Dec 2021 23:02:46 +0000
parents 62adf13b86ea
children b47c006d90c5
files dexseq.xml dexseq_count.xml macros.xml plotdexseq.xml
diffstat 4 files changed, 19 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/dexseq.xml	Fri Mar 19 09:45:03 2021 +0000
+++ b/dexseq.xml	Sun Dec 19 23:02:46 2021 +0000
@@ -1,5 +1,8 @@
-<tool id="dexseq" name="DEXSeq" version="@VERSION@+galaxy1">
+<tool id="dexseq" name="DEXSeq" version="@TOOL_VERSION@+galaxy2" 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>
@@ -99,11 +102,11 @@
         <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="DEXSeq result file on ${on_string}" />
-        <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}">
+        <data name="dexseq_out" format="tabular" label="${tool.name} on ${on_string}: result" />
+        <data name="htmlreport" format="html" label="${tool.name} on ${on_string}: report">
             <filter>report is True</filter>
         </data>
-        <data name="rds_out" format="rdata" from_work_dir="DEXSeqResults.rds" label="DEXSeq rds file on ${on_string}">
+        <data name="rds_out" format="rds" from_work_dir="DEXSeqResults.rds" label="${tool.name} on ${on_string}: rds file">
             <filter>rds is True</filter>
         </data>
     </outputs>
@@ -171,7 +174,7 @@
             <param name="rds" value="True"/>
             <param name="fdr_cutoff" value="0.05"/>
             <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/>
-            <output name="rds_out" ftype="rdata" file="dexseq.rds" compare="sim_size"/>
+            <output name="rds_out" ftype="rds" file="dexseq.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
--- a/dexseq_count.xml	Fri Mar 19 09:45:03 2021 +0000
+++ b/dexseq_count.xml	Sun Dec 19 23:02:46 2021 +0000
@@ -1,5 +1,8 @@
-<tool id="dexseq_count" name="DEXSeq-Count" version="@VERSION@.0">
+<tool id="dexseq_count" name="DEXSeq-Count" version="@TOOL_VERSION@.1" profile="@PROFILE@">
     <description>Prepare and count exon abundancies from RNA-seq data</description>
+    <xrefs>
+        <xref type="bio.tools">dexseq</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/macros.xml	Fri Mar 19 09:45:03 2021 +0000
+++ b/macros.xml	Sun Dec 19 23:02:46 2021 +0000
@@ -1,9 +1,10 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">1.28.1</token>
+    <token name="@TOOL_VERSION@">1.28.1</token>
+    <token name="@PROFILE@">21.01</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">bioconductor-dexseq</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">bioconductor-dexseq</requirement>
             <yield />
         </requirements>
     </xml>
--- a/plotdexseq.xml	Fri Mar 19 09:45:03 2021 +0000
+++ b/plotdexseq.xml	Sun Dec 19 23:02:46 2021 +0000
@@ -1,5 +1,8 @@
-<tool id="plotdexseq" name="plotDEXSeq" version="@VERSION@.0">
+<tool id="plotdexseq" name="plotDEXSeq" version="@VERSION@.1" profile="@PROFILE@">
     <description>Visualization of the per gene DEXSeq results</description>
+    <xrefs>
+        <xref type="bio.tools">dexseq</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>