Mercurial > repos > mvdbeek > bam_readtagger

comparison 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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33:c7f140920cc1 34:240c901dedc0
1 <tool id="findcluster" name="Find clusters of reads" version="0.4.0"> 1 <tool id="findcluster" name="Find clusters of reads" version="0.4.1">
2 <description>in bam files</description> 2 <description>in bam files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="0.4.0">readtagger</requirement> 7 <requirement type="package" version="0.4.1">readtagger</requirement>
8 </requirements> 8 </requirements>
9 <version_command>findcluster --version</version_command> 9 <version_command>findcluster --version</version_command>
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 #import re
12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier))
11 ln -f -s $input input.bam && 13 ln -f -s $input input.bam &&
12 ln -f -s $input.metadata.bam_index input.bam.bai && 14 ln -f -s $input.metadata.bam_index input.bam.bai &&
13 findcluster 15 findcluster
14 --input_path input.bam 16 --input_path input.bam
15 #if $transposon_source.ref_file: 17 #if $transposon_source.ref_file:
27 #end if 29 #end if
28 #end if 30 #end if
29 --output_bam '$output_bam' 31 --output_bam '$output_bam'
30 --output_gff '$output_gff' 32 --output_gff '$output_gff'
31 --output_fasta '$output_fasta' 33 --output_fasta '$output_fasta'
32 --sample_name '$input.element_identifier' 34 --sample_name '$sample_name'
33 --threads "\${GALAXY_SLOTS:-2}" 35 --threads "\${GALAXY_SLOTS:-2}"
34 ]]></command> 36 ]]></command>
35 <inputs> 37 <inputs>
36 <param name="input" argument="--input_path" type="data" format="bam"/> 38 <param name="input" argument="--input_path" type="data" format="bam"/>
37 39