Mercurial > repos > iuc > lumpy_prep
annotate lumpy_preprocessing.xml @ 0:21f2361c32c9 draft
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
author | iuc |
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date | Thu, 12 Nov 2020 16:48:34 +0000 |
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children | 80adce82354c |
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0
21f2361c32c9
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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1 <tool id="lumpy_prep" name="LUMPY preprocessing" version="@WRAPPER_VERSION@"> |
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2 <description>extracts discordant read pairs and split-read alignments from a BAM dataset</description> |
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3 <macros> |
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4 <import>macros.xml</import> |
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5 </macros> |
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6 <requirements> |
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7 <requirement type="package" version="@TOOL_VERSION@">lumpy-sv</requirement> |
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8 </requirements> |
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9 <command detect_errors="exit_code"><![CDATA[ |
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10 samtools collate -O --output-fmt sam '$bam_in' | samblaster $dup_handling --addMateTags | samtools view -bS - > blasted.bam && |
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11 |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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12 samtools view -b -F 1294 blasted.bam > discordants.unsorted.bam && |
21f2361c32c9
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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13 samtools view -h blasted.bam | extractSplitReads_BwaMem -i stdin | samtools view -Sb - > splitters.unsorted.bam && |
21f2361c32c9
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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14 |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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15 samtools sort discordants.unsorted.bam > discordants.bam && |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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16 samtools sort splitters.unsorted.bam > splitters.bam |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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17 ]]></command> |
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18 <inputs> |
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19 <param name="bam_in" type="data" format="bam" label="BAM input dataset" /> |
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20 <param name="dup_handling" type="select" |
21f2361c32c9
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21 label="Duplicate detection and removal" |
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22 help="Duplicate reads can be detected and removed with the help of samblaster. If you have already marked duplicates in the input dataset with another tool, you can choose to skip duplicate detection and remove only pre-marked duplicates. Not handling duplicates is only recommended if you have already deduplicated your input with other tools."> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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23 <option value="--removeDups">Detect and remove duplicates (samblaster -r)</option> |
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24 <option value="--acceptDupMarks --removeDups">Remove duplicates marked in input data (samblaster -a -r)</option> |
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25 <option value="">Don't handle duplicates</option> |
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26 </param> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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27 </inputs> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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28 <outputs> |
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29 <data name="blasted_bam" format="qname_sorted.bam" from_work_dir="blasted.bam" label="${tool.name}: Collated and groomed on ${on_string}" /> |
21f2361c32c9
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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30 <data name="discordants_bam" format="bam" from_work_dir="discordants.bam" label="${tool.name}: Discordant read pairs on ${on_string}" /> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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31 <data name="splitters_bam" format="bam" from_work_dir="splitters.bam" label="${tool.name}: Split-read alignments on ${on_string}" /> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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32 </outputs> |
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33 <tests> |
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34 <test> |
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35 <param name="bam_in" ftype="bam" value="sample.bam" /> |
21f2361c32c9
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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36 <param name="dup_handling" value="" /> |
21f2361c32c9
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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37 <output name="blasted_bam" ftype="qname_sorted.bam" file="blasted.bam" /> |
21f2361c32c9
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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38 <output name="discordants_bam" ftype="bam" file="discordants.bam" /> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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39 <output name="splitters_bam" ftype="bam" file="splitters.bam" /> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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40 </test> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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41 </tests> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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42 <help><![CDATA[ |
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43 **What it does** |
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44 |
21f2361c32c9
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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45 This tool implements the mapped reads preprocessing `suggested for LUMPY <https://github.com/arq5x/lumpy-sv#pre-processing>`__. It uses samblaster_, samtools and LUMPY's extractSplitReads_BwaMem script to collate and groom an input BAM dataset (preferably produced with bwa-mem) and to extract discordant read pairs and split-read alignments from it. The three output datasets can serve as the three inputs to LUMPY. |
21f2361c32c9
"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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46 |
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47 .. _samblaster: https://github.com/GregoryFaust/samblaster |
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48 ]]></help> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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49 <expand macro="citations"> |
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50 <citation type="doi">10.1093/bioinformatics/btu314</citation> |
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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
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51 <citation type="bibtex"> |
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52 @misc{SamTools_github, |
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53 title={SAMTools GitHub page}, |
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54 url = {https://github.com/samtools/samtools},} |
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55 </citation> |
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56 </expand> |
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57 </tool> |
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58 |