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annotate bismark_deduplicate_wrapper.xml @ 13:f211753166bd draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
author bgruening
date Tue, 30 Jul 2019 06:30:36 -0400
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f211753166bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
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1 <tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.22.1" profile="18.01">
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2 <description>Deduplicates reads mapped by Bismark</description>
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3 <requirements>
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f211753166bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
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4 <requirement type="package" version="0.22.1">bismark</requirement>
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5 <requirement type="package" version="1.8">samtools</requirement>
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f211753166bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
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6 <requirement type="package" version="2.3.5">bowtie2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 python '$__tool_directory__/bismark_deduplicate_wrapper.py'
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11 --single_or_paired $sPaired
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13 --input '$mapping_output'
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14 --output_report '$output_report'
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15 --output_bam '$output_bam'
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16 #if $separate_logfile:
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17 --log_report '$log_report'
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18 #end if
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="sPaired" type="select" label="Is this library mate-paired?">
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23 <option value="single">Single-end</option>
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24 <option value="paired">Paired-end</option>
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25 </param>
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26 <param name="mapping_output" type="data" format="qname_input_sorted.bam,bam"
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27 label="Submit the resulting bam/sam file from Bismark bisulfite mapper"/>
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28 <param name="separate_logfile" type="boolean" truevalue="true" falsevalue="false" checked="False"
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29 label="Create a separate logfile, otherwise logs are added to the dataset info."/>
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30 </inputs>
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32 <outputs>
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33 <data name="output_bam" format="qname_sorted.bam"
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34 label="${tool.name} on ${on_string}: deduplicated mapped reads"/>
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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35 <data name="output_report" format="txt" label="${tool.name} on ${on_string}: deduplication report"/>
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36 <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
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37 <filter>( separate_logfile is True )</filter>
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38 </data>
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39 </outputs>
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41 <tests>
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42 <test>
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43 <param name="sPaired" value="single"/>
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44 <param name="mapping_output" value="mapped_reads.bam" ftype="qname_sorted.bam"/>
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45 <output name="output_bam" file="dedup_reads.bam" ftype="qname_sorted.bam"/>
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46 <output name="output_report" file="dedup_report.txt" ftype="txt"/>
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47 </test>
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48 </tests>
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50 <help>
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51 <![CDATA[
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52 **What it does**
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54 | This tool is supposed to remove alignments to the same position in the genome from the Bismark mapping output (both single and paired-end SAM files), which can arise by e.g. excessive PCR amplification. If sequences align to the same genomic position but on different strands they will be scored individually.
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55 |
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56 | Note that deduplication is not recommended for RRBS-type experiments!
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57 |
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58 | For single-end alignments only use the start-coordinate of a read will be used for deduplication.
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59 | For paired-end alignments the start-coordinate of the first read and the end coordinate of the second read will be used for deduplication.
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61 ]]>
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62 </help>
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63 <citations>
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64 <citation type="doi">10.1093/bioinformatics/btr167</citation>
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65 </citations>
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66 </tool>