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1 <?xml version="1.0"?>
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2 <tool id="SoftSearch" name="SoftSearch" version="2.4">
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3 <requirements>
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4 <requirement type="package" version="2.4">softsearch</requirement>
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5 </requirements>
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6 <description>for structure variation</description>
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7 <command>#if $source.index_source=="history"
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8 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
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9 #else
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10 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 $out_file1
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11 #end if
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12 </command>
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13 <inputs>
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14 <param name="bam_file" type="data" format="bam" label="BAM Files" />
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15 <conditional name="source">
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16 <param name="index_source" type="select" label="Choose the source for the reference list">
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17 <option value="cached">Locally cached</option>
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18 <option value="history">History</option>
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19 </param>
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20 <when value="history">
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21 <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/>
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22 </when>
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23 <when value="cached">
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24 <param name="ref_fasta" type="select" >
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25 <options from_data_table="fasta_indexes">
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26 <validator type="no_options" message="No Fasta file is available" />
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27 </options>
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28 </param>
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29 </when>
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30 </conditional>
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31 <param name="inc" type="hidden" value="n=$RANDOM" />
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32 <param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" />
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33 <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" />
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34 <param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" />
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35 <param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" />
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36 <param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" />
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37 </inputs>
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38 <outputs>
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39 <data format="vcf" name="out_file1" />
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40 </outputs>
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41 <help>
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42 </help>
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43 </tool>
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