Mercurial > repos > mvdbeek > damidseq_core

comparison patch @ 4:b07936a3962d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
author mvdbeek
date Sun, 26 Mar 2017 15:53:05 -0400
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3:e47f77820200 4:b07936a3962d
1 diff -r e47f77820200 damidseq_core.xml
2 --- a/damidseq_core.xml Sun Mar 26 10:31:55 2017 -0400
3 +++ b/damidseq_core.xml Sun Mar 26 21:49:38 2017 +0200
4 @@ -5,8 +5,8 @@
5 </requirements>
6 <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
7 <command detect_errors="aggressive"><![CDATA[
8 - ln -f -s '$dam' A001.fastq &&
9 ln -f -s '$dam_fusion' A002.fastq &&
10 + ln -f -s '$dam_only' A001.fastq &&
11 ln -f -s '$index' index.txt &&
12 HOME="\$PWD" damidseq_pipeline
13 --bins=$bins
14 @@ -36,7 +36,7 @@
15 </configfiles>
16 <inputs>
17 <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
18 - <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
19 + <param name="dam_only" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
20 <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
21 <options from_data_table="bowtie2_indexes">
22 <filter type="sort_by" column="2"/>
23 @@ -106,8 +106,8 @@
24 </outputs>
25 <tests>
26 <test>
27 - <param name="dam" value="A001.fastq"/>
28 <param name="dam_fusion" value="A002.fastq"/>
29 + <param name="dam_only" value="A001.fastq"/>
30 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
31 <param name="reference_index" value="dm6"/>
32 <param name="norm_method" value="rpm"/>