Mercurial > repos > devteam > picard

diff picard_CollectRnaSeqMetrics.xml @ 19:5053a18d9bc8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
author iuc
date Mon, 16 Apr 2018 21:27:29 -0400
parents fc288950c3b7
children 2a17c789e0a5
line wrap: on
line diff
--- a/picard_CollectRnaSeqMetrics.xml	Sat Jan 20 08:28:24 2018 -0500
+++ b/picard_CollectRnaSeqMetrics.xml	Mon Apr 16 21:27:29 2018 -0400
@@ -1,12 +1,13 @@
-<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.1">
+<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
     <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description>
     <macros>
         <import>picard_macros.xml</import>
+    <token name="@WRAPPER_VERSION@">0</token>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.3.1">r</requirement>
-        <requirement type="package" version="324">ucsc-gff3togenepred</requirement>
-        <requirement type="package" version="324">ucsc-gtftogenepred</requirement>
+        <requirement type="package" version="3.4.1">r-base</requirement>
+        <requirement type="package" version="357">ucsc-gff3togenepred</requirement>
+        <requirement type="package" version="357">ucsc-gtftogenepred</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
       ## Set up input files
@@ -15,11 +16,7 @@
 
       #set $reference_fasta_filename = "localref.fa"
 
-      #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
-      #else:
-        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
-      #end if
+      @handle_reference_source@
 
       ## refFlat data
       ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
@@ -62,7 +59,7 @@
       OUTPUT="${outFile}"
       REFERENCE_SEQUENCE="${reference_fasta_filename}"
       ASSUME_SORTED="${assume_sorted}"
-     
+
       VALIDATION_STRINGENCY=${validation_stringency}
 
    ]]></command>
@@ -139,7 +136,7 @@
       <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
       <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
       <param name="assume_sorted" value="true" />
-      
+
       <param name="gene_reference_source_selector" value="refflat" />
       <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" />
       <param name="metric_accumulation_level" value="ALL_READS" />
@@ -154,7 +151,7 @@
       <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
       <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
       <param name="assume_sorted" value="true" />
-      
+
       <param name="gene_reference_source_selector" value="gtf" />
       <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf" />
       <param name="metric_accumulation_level" value="ALL_READS" />
@@ -169,7 +166,7 @@
       <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
       <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
       <param name="assume_sorted" value="true" />
-      
+
       <param name="gene_reference_source_selector" value="gtf" />
       <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3" />
       <param name="metric_accumulation_level" value="ALL_READS" />
@@ -257,4 +254,5 @@
 @more_info@
 
   </help>
+  <expand macro="citations" />
 </tool>