Mercurial > repos > plus91-technologies > softsearch
comparison softsearch_wrapper.xml @ 6:c82ca5cd3c3a draft
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| author | plus91-technologies |
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| date | Fri, 06 Jun 2014 08:58:44 -0400 |
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| 5:4a6a4e873319 | 6:c82ca5cd3c3a |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="Softsearch" name="softsearch" version="0.6"> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.6">softsearch</requirement> | |
| 5 </requirements> | |
| 6 <description>for structure variation</description> | |
| 7 <command>#if $source.index_source=="history" | |
| 8 samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | perl ~/galaxy-dist/tool_dependency_dir/softsearch/0.6/plus91-technologies/softsearch_dependency/f86686ac4ccc/src/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 | |
| 9 #else | |
| 10 samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | perl ~/galaxy-dist/tool_dependency_dir/softsearch/0.6/plus91-technologies/softsearch_dependency/f86686ac4ccc/src/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 $out_file1 | |
| 11 #end if | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param name="bam_file" type="data" format="bam" label="BAM Files" /> | |
| 15 <conditional name="source"> | |
| 16 <param name="index_source" type="select" label="Choose the source for the reference list"> | |
| 17 <option value="cached">Locally cached</option> | |
| 18 <option value="history">History</option> | |
| 19 </param> | |
| 20 <when value="history"> | |
| 21 <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/> | |
| 22 </when> | |
| 23 <when value="cached"> | |
| 24 <param name="ref_fasta" type="select" > | |
| 25 <options from_data_table="fasta_indexes"> | |
| 26 <validator type="no_options" message="No Fasta file is available" /> | |
| 27 </options> | |
| 28 </param> | |
| 29 </when> | |
| 30 </conditional> | |
| 31 <param name="inc" type="hidden" value="n=$RANDOM" /> | |
| 32 <param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> | |
| 33 <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" /> | |
| 34 <param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> | |
| 35 <param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> | |
| 36 <param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" /> | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data format="vcf" name="out_file1" /> | |
| 40 </outputs> | |
| 41 <help> | |
| 42 </help> | |
| 43 </tool> | |
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