Mercurial > repos > plus91-technologies > softsearch
diff softsearch_wrapper.xml @ 12:c86e4787940e draft
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author | plus91-technologies |
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date | Sat, 07 Jun 2014 03:54:35 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/softsearch_wrapper.xml Sat Jun 07 03:54:35 2014 -0400 @@ -0,0 +1,56 @@ +<?xml version="1.0"?> +<tool id="Softsearch" name="softsearch" version="0.6"> + <requirements> + <requirement type="package" version="0.6">softsearch</requirement> + </requirements> + <description>for structure variation</description> + <command>#if $source.index_source=="history" + samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1 + #else + samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1 + #end if + </command> + <inputs> + <param name="bam_file" type="data" format="bam" label="BAM Files" /> + <conditional name="source"> + <param name="index_source" type="select" label="Choose the source for the reference list"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="history"> + <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/> + </when> + <when value="cached"> + <param name="ref_fasta" type="select" > + <options from_data_table="fasta_indexes"> + <validator type="no_options" message="No Fasta file is available" /> + </options> + </param> + </when> + </conditional> + <param name="inc" type="hidden" value="n=$RANDOM" /> + <param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> + <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" /> + <param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> + <param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> + <param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" /> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <help> + </help> +</tool> + + + + + + + + + + + + +