Mercurial > repos > mvdbeek > damidseq_core
diff damidseq_core.xml @ 5:6c00620084a5 draft
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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--- a/damidseq_core.xml Sun Mar 26 15:53:05 2017 -0400 +++ b/damidseq_core.xml Wed Apr 18 15:02:42 2018 -0400 @@ -5,8 +5,10 @@ </requirements> <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command> <command detect_errors="aggressive"><![CDATA[ - ln -f -s '$dam_fusion' A002.fastq && - ln -f -s '$dam_only' A001.fastq && + #set dam_file = 'A001.fastq.gz' if str($dam.ext).endswith('.gz') else 'A001.fastq' + #set dam_fusion_file = 'A002.fastq.gz' if str($dam_fusion.ext).endswith('.gz') else 'A002.fastq' + ln -f -s '$dam' $dam_file && + ln -f -s '$dam_fusion' $dam_fusion_file && ln -f -s '$index' index.txt && HOME="\$PWD" damidseq_pipeline --bins=$bins @@ -36,7 +38,7 @@ </configfiles> <inputs> <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/> - <param name="dam_only" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/> + <param argument="--dam" 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 +108,18 @@ </outputs> <tests> <test> + <param name="dam" value="A001.fastq.gz"/> + <param name="dam_fusion" value="A002.fastq.gz"/> + <param name="gatc_frag_file" value="dm6.GATC.gff"/> + <param name="reference_index" value="dm6"/> + <param name="norm_method" value="rpm"/> + <output name="output_ratio" file="output_ratio.bed"/> + <output name="control_output" file="control.bam"/> + <output name="fusion_output" file="fusion.bam"/> + </test> + <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"/>