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annotate samblaster.xml @ 0:5743b5c0209b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
author mvdbeek
date Fri, 16 Dec 2016 04:45:26 -0500
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5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
mvdbeek
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1 <tool id="samblaster" name="samblaster" version="0.1.24">
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2 <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.24">samblaster</requirement>
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5 <requirement type="package" version="1.3.1">samtools</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 samtools sort -O sam -n '$input' |
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9 samblaster
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10 $output
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11 $discordantFile
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12 $splitterFile
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13 $unmappedFile
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14 $acceptDupMarks
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15 $excludeDups
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16 $removeDups
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17 $addMateTags
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18 $compatibility_mode
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19 --maxSplitCount '$maxSplitCount'
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20 --maxUnmappedBases '$maxUnmappedBases'
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21 --minIndelSize '$minIndelSize'
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22 --minNonOverlap '$minNonOverlap'
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23 --minClipSize '$minClipSize' && sleep 1
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24 ]]></command>
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25 <inputs>
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26 <param name="input" argument="--input" type="data" format="bam,sam"/>
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27 <param name="output" argument="--ouput" label="Output bam file for all input alignments" type="boolean" truevalue="-o >(samtools sort -O bam -o output.bam)" falsevalue="-o /dev/null"/>
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28 <param name="discordantFile" argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d >(samtools sort -O bam -o discordant.bam)" falsevalue=""/>
5743b5c0209b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
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29 <param name="splitterFile" argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s >(samtools sort -O bam -o splitter.bam)" falsevalue=""/>
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30 <param name="unmappedFile" argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/>
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31 <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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32 <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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33 <param name="removeDups" argument="--removeDups" label="Remove duplicates reads from all output files?" help="(Implies --excludeDups)" type="boolean" truevalue="-e" falsevalue=""/>
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34 <param name="addMateTags" argument="--addMateTags" label="Add MC and MQ tags?" type="boolean" truevalue="--addMateTags" falsevalue=""/>
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35 <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="" />
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36 <param name="maxSplitCount" argument="--maxSplitCount" label="Maximum number of split alignments for a read to be included in splitter file." type="integer" value="2"/>
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37 <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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38 <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"/>
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39 <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"/>
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40 <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"/>
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41 </inputs>
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42 <outputs>
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43 <data name="output_bam" format="bam" label="samblaster alignments on ${on_string}" from_work_dir="output.bam">
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44 <filter>output</filter>
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45 </data>
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46 <data name="discordant_bam" format="bam" label="samblaster discordant alignments on ${on_string}" from_work_dir="discordant.bam">
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47 <filter>discordantFile</filter>
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48 </data>
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49 <data name="splitter_bam" format="bam" label="samblaster split alignments on ${on_string}" from_work_dir="splitter.bam">
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50 <filter>splitterFile</filter>
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51 </data>
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52 <data name="unmapped_fastq" format="fastqsanger" label="samblaster unmapped fastq on ${on_string}" from_work_dir="unmapped.fastq">
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53 <filter>unmappedFile</filter>
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54 </data>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="input" value="sr.input.bam"/>
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59 <param name="output" value="true"/>
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60 <param name="discordandFile" value="false"/>
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61 <param name="splitterFile" value="true"/>
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62 <param name="unmappedFile" value="true"/>
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63 <output name="output_bam" file="output.bam"/>
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64 <output name="splitter_bam" file="splitters.bam"/>
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65 <output name="unmapped_fastq" file="unmapped.fastq"/>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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69
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70 ]]></help>
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71 <citations>
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72 <citation type="doi">10.1093/bioinformatics/btu314</citation>
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73 </citations>
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74 </tool>