Mercurial > repos > mvdbeek > bam_readtagger

comparison findcluster.xml @ 36:e19ff7992765 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8a8cc2ebb37a86df6a63be57acf86c9c299ac5bf-dirty
author mvdbeek
date Thu, 09 Nov 2017 06:48:57 -0500
parents 5aa7745dd6e3
children 73e3060d104f
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35:5aa7745dd6e3 36:e19ff7992765
1 <tool id="findcluster" name="Find clusters of reads" version="0.3.25"> 1 <tool id="findcluster" name="Find clusters of reads" version="0.4.0">
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="0.3.25">readtagger</requirement> 7 <requirement type="package" version="0.4.0">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 ln -f -s $input input.bam && 11 ln -f -s $input input.bam &&
12 ln -f -s $input.metadata.bam_index input.bam.bai && 12 ln -f -s $input.metadata.bam_index input.bam.bai &&
14 --input_path input.bam 14 --input_path input.bam
15 #if $transposon_source.ref_file: 15 #if $transposon_source.ref_file:
16 #if str($transposon_source.reference_source_selector) == "history": 16 #if str($transposon_source.reference_source_selector) == "history":
17 --transposon_reference_fasta '$transposon_source.ref_file' 17 --transposon_reference_fasta '$transposon_source.ref_file'
18 #else : 18 #else :
19 --transposon_bwa_index '$transposon_source.ref_file.fields.path' 19 --transposon_bwa_index '$reference_source.ref_file.fields.path'
20 #end if 20 #end if
21 #end if 21 #end if
22 #if $genome_source.ref_file: 22 #if $genome_source.ref_file:
23 #if str($genome_source.reference_source_selector) == "history": 23 #if str($genome_source.reference_source_selector) == "history":
24 --genome_reference_fasta '$genome_source.ref_file' 24 --genome_reference_fasta '$genome_source.ref_file'
25 #else : 25 #else :
26 --genome_bwa_index '$genome_source.ref_file.fields.path' 26 --genome_bwa_index '$reference_source.ref_file.fields.path'
27 #end if 27 #end if
28 #end if 28 #end if
29 --output_bam '$output_bam' 29 --output_bam '$output_bam'
30 --output_gff '$output_gff' 30 --output_gff '$output_gff'
31 --output_fasta '$output_fasta' 31 --output_fasta '$output_fasta'