Mercurial > repos > mvdbeek > bam_readtagger

comparison findcluster.xml @ 19:97c1b92dbd28 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e3effe4ab3ded37fb610f53deb4d0082daf7fdac-dirty
author mvdbeek
date Wed, 05 Apr 2017 17:34:55 -0400
parents 8fef53971086
children 03415763c62c
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18:8fef53971086 19:97c1b92dbd28
1 <tool id="findcluster" name="Find clusters of reads" version="0.3.12"> 1 <tool id="findcluster" name="Find clusters of reads" version="0.3.13">
2 <description>in bam files</description> 2 <description>in bam files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.3.12">readtagger</requirement> 4 <requirement type="package" version="0.3.13">readtagger</requirement>
5 </requirements> 5 </requirements>
6 <version_command>findcluster --version</version_command> 6 <version_command>findcluster --version</version_command>
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 ln -f -s $input input.bam && 8 ln -f -s $input input.bam &&
9 ln -f -s $input.metadata.bam_index input.bam.bai && 9 ln -f -s $input.metadata.bam_index input.bam.bai &&
12 #if $reference_fasta: 12 #if $reference_fasta:
13 --reference_fasta '$reference_fasta' 13 --reference_fasta '$reference_fasta'
14 #end if 14 #end if
15 --output_bam '$output_bam' 15 --output_bam '$output_bam'
16 --output_gff '$output_gff' 16 --output_gff '$output_gff'
17 --output_fasta '$output_fasta'
17 --sample_name '$input.element_identifier' 18 --sample_name '$input.element_identifier'
18 --threads "\${GALAXY_SLOTS:-2}" 19 --threads "\${GALAXY_SLOTS:-2}"
19 ]]></command> 20 ]]></command>
20 <inputs> 21 <inputs>
21 <param name="input" argument="--input_path" type="data" format="bam"/> 22 <param name="input" argument="--input_path" type="data" format="bam"/>
22 <param argument="--reference_fasta" label="Reference Fasta" help="Reconstructed contigs at clusters will be blasted against this sequence." type="data" format="fasta" optional="True"/> 23 <param argument="--reference_fasta" label="Reference Fasta" help="Reconstructed contigs at clusters will be blasted against this sequence." type="data" format="fasta" optional="True"/>
23 </inputs> 24 </inputs>
24 <outputs> 25 <outputs>
25 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> 26 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
27 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/>
26 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/> 28 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
27 </outputs> 29 </outputs>
28 <tests> 30 <tests>
29 <test> 31 <test>
30 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> 32 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>