Mercurial > repos > mvdbeek > bam_readtagger

diff findcluster.xml @ 34:240c901dedc0 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
author mvdbeek
date Mon, 20 Nov 2017 10:50:42 -0500
parents c7f140920cc1
children 02afdbc69591
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--- a/findcluster.xml	Thu Nov 09 06:49:15 2017 -0500
+++ b/findcluster.xml	Mon Nov 20 10:50:42 2017 -0500
@@ -1,13 +1,15 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.4.0">
+<tool id="findcluster" name="Find clusters of reads" version="0.4.1">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.0">readtagger</requirement>
+        <requirement type="package" version="0.4.1">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
+        #import re
+        #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier))
         ln -f -s $input input.bam &&
         ln -f -s $input.metadata.bam_index input.bam.bai &&
         findcluster
@@ -29,7 +31,7 @@
         --output_bam '$output_bam'
         --output_gff '$output_gff'
         --output_fasta '$output_fasta'
-        --sample_name '$input.element_identifier'
+        --sample_name '$sample_name'
         --threads "\${GALAXY_SLOTS:-2}"
     ]]></command>
     <inputs>