Mercurial > repos > mvdbeek > damidseq_core

comparison damidseq_core.xml @ 5:6c00620084a5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1
author mvdbeek
date Wed, 18 Apr 2018 15:02:42 -0400
parents b07936a3962d
children 9b13b8bda9d8
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4:b07936a3962d 5:6c00620084a5
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4">damidseq_pipeline</requirement> 4 <requirement type="package" version="1.4">damidseq_pipeline</requirement>
5 </requirements> 5 </requirements>
6 <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command> 6 <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 ln -f -s '$dam_fusion' A002.fastq && 8 #set dam_file = 'A001.fastq.gz' if str($dam.ext).endswith('.gz') else 'A001.fastq'
9 ln -f -s '$dam_only' A001.fastq && 9 #set dam_fusion_file = 'A002.fastq.gz' if str($dam_fusion.ext).endswith('.gz') else 'A002.fastq'
10 ln -f -s '$dam' $dam_file &&
11 ln -f -s '$dam_fusion' $dam_fusion_file &&
10 ln -f -s '$index' index.txt && 12 ln -f -s '$index' index.txt &&
11 HOME="\$PWD" damidseq_pipeline 13 HOME="\$PWD" damidseq_pipeline
12 --bins=$bins 14 --bins=$bins
13 --bowtie=1 15 --bowtie=1
14 --bowtie2_genome_dir='$reference_index.fields.path' 16 --bowtie2_genome_dir='$reference_index.fields.path'
34 <configfile name="index">A1 Dam 36 <configfile name="index">A1 Dam
35 A2 Fusion</configfile> 37 A2 Fusion</configfile>
36 </configfiles> 38 </configfiles>
37 <inputs> 39 <inputs>
38 <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/> 40 <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
39 <param name="dam_only" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/> 41 <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
40 <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> 42 <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
41 <options from_data_table="bowtie2_indexes"> 43 <options from_data_table="bowtie2_indexes">
42 <filter type="sort_by" column="2"/> 44 <filter type="sort_by" column="2"/>
43 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 45 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
44 </options> 46 </options>
104 </actions> 106 </actions>
105 </data> 107 </data>
106 </outputs> 108 </outputs>
107 <tests> 109 <tests>
108 <test> 110 <test>
111 <param name="dam" value="A001.fastq.gz"/>
112 <param name="dam_fusion" value="A002.fastq.gz"/>
113 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
114 <param name="reference_index" value="dm6"/>
115 <param name="norm_method" value="rpm"/>
116 <output name="output_ratio" file="output_ratio.bed"/>
117 <output name="control_output" file="control.bam"/>
118 <output name="fusion_output" file="fusion.bam"/>
119 </test>
120 <test>
121 <param name="dam" value="A001.fastq"/>
109 <param name="dam_fusion" value="A002.fastq"/> 122 <param name="dam_fusion" value="A002.fastq"/>
110 <param name="dam_only" value="A001.fastq"/>
111 <param name="gatc_frag_file" value="dm6.GATC.gff"/> 123 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
112 <param name="reference_index" value="dm6"/> 124 <param name="reference_index" value="dm6"/>
113 <param name="norm_method" value="rpm"/> 125 <param name="norm_method" value="rpm"/>
114 <output name="output_ratio" file="output_ratio.bed"/> 126 <output name="output_ratio" file="output_ratio.bed"/>
115 <output name="control_output" file="control.bam"/> 127 <output name="control_output" file="control.bam"/>