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annotate samblaster.xml @ 2:5d1a1388a036 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
author mvdbeek
date Sun, 18 Dec 2016 07:54:53 -0500
parents 4f68e55100c3
children
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5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
parents: 1
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1 <tool id="samblaster" name="samblaster" version="0.1.24.2">
0
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
mvdbeek
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2 <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
mvdbeek
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3 <requirements>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
mvdbeek
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4 <requirement type="package" version="0.1.24">samblaster</requirement>
2
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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5 <requirement type="package" version="0.6.5">sambamba</requirement>
0
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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6 </requirements>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
mvdbeek
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7 <command detect_errors="exit_code"><![CDATA[
2
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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8 #if $input.is_of_type('sam'):
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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9 #set stream="<(sambamba view -S -f bam -t ${GALAXY_SLOTS:-4} -h '%s')" % $input
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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10 #else:
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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11 #set stream="'%s'" % $input
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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12 #end if
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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13 sambamba view -t \${GALAXY_SLOTS:-4} -h <(sambamba sort -t \${GALAXY_SLOTS:-4} -n $stream -o /dev/stdout) |
0
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14 samblaster
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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15 $output
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
mvdbeek
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16 $discordantFile
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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17 $splitterFile
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
mvdbeek
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18 $unmappedFile
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19 $acceptDupMarks
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20 $excludeDups
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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21 $removeDups
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22 $addMateTags
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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23 $compatibility_mode
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
mvdbeek
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24 --maxSplitCount '$maxSplitCount'
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
mvdbeek
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25 --maxUnmappedBases '$maxUnmappedBases'
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
mvdbeek
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26 --minIndelSize '$minIndelSize'
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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27 --minNonOverlap '$minNonOverlap'
2
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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28 --minClipSize '$minClipSize'
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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29 #if $output != "-o /dev/null":
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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30 && sambamba sort -o output.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam output.sam)
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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31 #end if
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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32 #if $discordantFile:
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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33 && sambamba sort -o discordant.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam discordant.sam)
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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34 #end if
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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35 #if $splitterFile:
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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36 && sambamba sort -o splitter.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam splitter.sam)
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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37 #end if
0
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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38 ]]></command>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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39 <inputs>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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40 <param name="input" argument="--input" type="data" format="bam,sam"/>
2
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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41 <param name="output" argument="--ouput" label="Output bam file for all input alignments" type="boolean" truevalue="-o output.sam" falsevalue="-o /dev/null"/>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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42 <param name="discordantFile" argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d discordant.sam" falsevalue=""/>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
mvdbeek
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43 <param name="splitterFile" argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s splitter.sam" falsevalue=""/>
0
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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44 <param name="unmappedFile" argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/>
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45 <param name="acceptDupMarks" argument="--acceptDupMarks" label="Accept duplicate marks already in input file instead of looking for duplicates in the input?" type="boolean" truevalue="-a" falsevalue=""/>
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mvdbeek
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46 <param name="excludeDups" argument="--excludeDups" label="Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file?" type="boolean" truevalue="-a" falsevalue=""/>
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47 <param name="removeDups" argument="--removeDups" label="Remove duplicates reads from all output files?" help="(Implies --excludeDups)" type="boolean" truevalue="-e" falsevalue=""/>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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48 <param name="addMateTags" argument="--addMateTags" label="Add MC and MQ tags?" type="boolean" truevalue="--addMateTags" falsevalue=""/>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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49 <param name="compatibility_mode" argument="-M" label="Run in compatibility mode?" help="Both 0x100 and 0x800 are considered chimeric. Similar to BWA MEM -M option." type="boolean" truevalue="-M" falsevalue="" />
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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50 <param name="maxSplitCount" argument="--maxSplitCount" label="Maximum number of split alignments for a read to be included in splitter file." type="integer" value="2"/>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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51 <param name="maxUnmappedBases" argument="--maxUnmappedBases" label="Maximum number of un-aligned bases between two alignments to be included in splitter file." type="integer" value="50" min="1"/>
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52 <param name="minIndelSize" argument="--minIndelSize" label="Minimum structural variant feature size for split alignments to be included in splitter file." type="integer" value="50" min="1"/>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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53 <param name="minNonOverlap" argument="--minNonOverlap" label="Minimum non-overlaping base pairs between two alignments for a read to be included in splitter file." type="integer" value="20" min="1"/>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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54 <param name="minClipSize" argument="--minClipSize" label="Minumum number of bases a mapped read must be clipped to be included in unmapped file." type="integer" value="20" min="1"/>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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55 </inputs>
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56 <outputs>
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57 <data name="output_bam" format="bam" label="samblaster alignments on ${on_string}" from_work_dir="output.bam">
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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58 <filter>output</filter>
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59 </data>
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60 <data name="discordant_bam" format="bam" label="samblaster discordant alignments on ${on_string}" from_work_dir="discordant.bam">
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61 <filter>discordantFile</filter>
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62 </data>
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63 <data name="splitter_bam" format="bam" label="samblaster split alignments on ${on_string}" from_work_dir="splitter.bam">
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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64 <filter>splitterFile</filter>
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65 </data>
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66 <data name="unmapped_fastq" format="fastqsanger" label="samblaster unmapped fastq on ${on_string}" from_work_dir="unmapped.fastq">
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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67 <filter>unmappedFile</filter>
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68 </data>
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69 </outputs>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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70 <tests>
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71 <test>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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72 <param name="input" value="sr.input.bam"/>
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73 <param name="output" value="true"/>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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74 <param name="discordandFile" value="false"/>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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75 <param name="splitterFile" value="true"/>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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76 <param name="unmappedFile" value="true"/>
2
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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77 <output name="output_bam" file="output.bam" lines_diff="10"/>
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78 <output name="splitter_bam" file="splitters.bam" lines_diff="10"/>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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79 <output name="unmapped_fastq" file="unmapped.fastq"/>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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80 </test>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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81 <test>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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82 <param name="input" value="sr.input.sam" ftype="sam"/>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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83 <param name="output" value="true"/>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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84 <param name="discordandFile" value="false"/>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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85 <param name="splitterFile" value="true"/>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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86 <param name="unmappedFile" value="true"/>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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87 <output name="output_bam" file="output.bam" lines_diff="10"/>
5d1a1388a036 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
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88 <output name="splitter_bam" file="splitters.bam" lines_diff="10"/>
0
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89 <output name="unmapped_fastq" file="unmapped.fastq"/>
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90 </test>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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91 </tests>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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92 <help><![CDATA[
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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93
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94 ]]></help>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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95 <citations>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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96 <citation type="doi">10.1093/bioinformatics/btu314</citation>
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97 </citations>
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98 </tool>