Mercurial > repos > plus91-technologies-pvt-ltd > softsearch
comparison softsearch.xml @ 23:a97f2518fe6b draft default tip
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| author | plus91-technologies-pvt-ltd |
|---|---|
| date | Fri, 06 Jun 2014 08:35:52 -0400 |
| parents | 06581c4fe59f |
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| 22:06581c4fe59f | 23:a97f2518fe6b |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="SoftSearch" name="SoftSearch"> | |
| 3 <description>for structure variation</description> | |
| 4 <command>#if $source.index_source=="history" | |
| 5 samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | /home/plus91/2.4/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 | |
| 6 #else | |
| 7 samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | /home/plus91/2.4/src//2.4/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 $out_file1 | |
| 8 #end if | |
| 9 </command> | |
| 10 <inputs> | |
| 11 <param name="bam_file" type="data" format="bam" label="BAM Files" /> | |
| 12 <conditional name="source"> | |
| 13 <param name="index_source" type="select" label="Choose the source for the reference list"> | |
| 14 <option value="cached">Locally cached</option> | |
| 15 <option value="history">History</option> | |
| 16 </param> | |
| 17 <when value="history"> | |
| 18 <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/> | |
| 19 </when> | |
| 20 <when value="cached"> | |
| 21 <param name="ref_fasta" type="select" > | |
| 22 <options from_data_table="fasta_indexes"> | |
| 23 <validator type="no_options" message="No Fasta file is available" /> | |
| 24 </options> | |
| 25 </param> | |
| 26 </when> | |
| 27 </conditional> | |
| 28 <param name="inc" type="hidden" value="n=$RANDOM" /> | |
| 29 <param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> | |
| 30 <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" /> | |
| 31 <param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> | |
| 32 <param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> | |
| 33 <param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" /> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data format="vcf" name="out_file1" /> | |
| 37 </outputs> | |
| 38 <help> | |
| 39 </help> | |
| 40 </tool> | |
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