Mercurial > repos > mvdbeek > damidseq_core
diff patch @ 4:b07936a3962d draft
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 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/patch Sun Mar 26 15:53:05 2017 -0400 @@ -0,0 +1,32 @@ +diff -r e47f77820200 damidseq_core.xml +--- a/damidseq_core.xml Sun Mar 26 10:31:55 2017 -0400 ++++ b/damidseq_core.xml Sun Mar 26 21:49:38 2017 +0200 +@@ -5,8 +5,8 @@ + </requirements> + <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command> + <command detect_errors="aggressive"><![CDATA[ +- ln -f -s '$dam' A001.fastq && + ln -f -s '$dam_fusion' A002.fastq && ++ ln -f -s '$dam_only' A001.fastq && + ln -f -s '$index' index.txt && + HOME="\$PWD" damidseq_pipeline + --bins=$bins +@@ -36,7 +36,7 @@ + </configfiles> + <inputs> + <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/> +- <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/> ++ <param name="dam_only" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/> + <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_data_table="bowtie2_indexes"> + <filter type="sort_by" column="2"/> +@@ -106,8 +106,8 @@ + </outputs> + <tests> + <test> +- <param name="dam" value="A001.fastq"/> + <param name="dam_fusion" value="A002.fastq"/> ++ <param name="dam_only" value="A001.fastq"/> + <param name="gatc_frag_file" value="dm6.GATC.gff"/> + <param name="reference_index" value="dm6"/> + <param name="norm_method" value="rpm"/>