Mercurial > repos > mvdbeek > bam_readtagger

comparison findcluster.xml @ 38:700df574a69c draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e4cd04d8a19b57d6b23da64c3fda8978b51e33ef
author mvdbeek
date Thu, 14 Dec 2017 03:51:39 -0500
parents 73e3060d104f
children 7cad80dc3b58
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37:73e3060d104f 38:700df574a69c
1 <tool id="findcluster" name="Find clusters of reads" version="0.4.1"> 1 <tool id="findcluster" name="Find clusters of reads" version="0.4.4">
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="0.4.1">readtagger</requirement> 7 <requirement type="package" version="0.4.4">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 11 #import re
12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier)) 12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier))
16 --input_path input.bam 16 --input_path input.bam
17 #if $transposon_source.ref_file: 17 #if $transposon_source.ref_file:
18 #if str($transposon_source.reference_source_selector) == "history": 18 #if str($transposon_source.reference_source_selector) == "history":
19 --transposon_reference_fasta '$transposon_source.ref_file' 19 --transposon_reference_fasta '$transposon_source.ref_file'
20 #else : 20 #else :
21 --transposon_bwa_index '$reference_source.ref_file.fields.path' 21 --transposon_bwa_index '$transposon_source.ref_file.fields.path'
22 #end if 22 #end if
23 #end if 23 #end if
24 #if $genome_source.ref_file: 24 #if $genome_source.ref_file:
25 #if str($genome_source.reference_source_selector) == "history": 25 #if str($genome_source.reference_source_selector) == "history":
26 --genome_reference_fasta '$genome_source.ref_file' 26 --genome_reference_fasta '$genome_source.ref_file'
27 #else : 27 #else :
28 --genome_bwa_index '$reference_source.ref_file.fields.path' 28 --genome_bwa_index '$genome_source.ref_file.fields.path'
29 #end if 29 #end if
30 #end if 30 #end if
31 --output_bam '$output_bam' 31 --output_bam '$output_bam'
32 --output_gff '$output_gff' 32 --output_gff '$output_gff'
33 --output_fasta '$output_fasta' 33 --output_fasta '$output_fasta'