Mercurial > repos > mvdbeek > bam_readtagger
comparison findcluster.xml @ 34:240c901dedc0 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
author | mvdbeek |
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date | Mon, 20 Nov 2017 10:50:42 -0500 |
parents | c7f140920cc1 |
children | 02afdbc69591 |
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33:c7f140920cc1 | 34:240c901dedc0 |
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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 |