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comparison bismark_deduplicate_wrapper.xml @ 8:9bfe38410155 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
author bgruening
date Wed, 22 Aug 2018 08:09:42 -0400
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7:fcadce4d9a06 8:9bfe38410155
1 <tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.20.0" profile="18.01">
2 <description>Deduplicates reads mapped by Bismark</description>
3 <requirements>
4 <requirement type="package" version="0.20.0">bismark</requirement>
5 <requirement type="package" version="1.8">samtools</requirement>
6 <requirement type="package" version="2.3.4.2">bowtie2</requirement>
7 </requirements>
8 <command><![CDATA[
9 python '$__tool_directory__/bismark_deduplicate_wrapper.py'
10
11 --single_or_paired $sPaired
12
13 --input '$mapping_output'
14 --output_report '$output_report'
15 --output_bam '$output_bam'
16 #if $separate_logfile:
17 --log_report '$log_report'
18 #end if
19 ]]>
20 </command>
21 <inputs>
22 <param name="sPaired" type="select" label="Is this library mate-paired?">
23 <option value="single">Single-end</option>
24 <option value="paired">Paired-end</option>
25 </param>
26 <param name="mapping_output" type="data" format="qname_input_sorted.bam,bam"
27 label="Submit the resulting bam/sam file from Bismark bisulfite mapper"/>
28 <param name="separate_logfile" type="boolean" truevalue="true" falsevalue="false" checked="False"
29 label="Create a separate logfile, otherwise logs are added to the dataset info."/>
30 </inputs>
31
32 <outputs>
33 <data name="output_bam" format="qname_sorted.bam"
34 label="${tool.name} on ${on_string}: deduplicated mapped reads"/>
35 <data name="output_report" format="txt" label="${tool.name} on ${on_string}: deduplication report"/>
36 <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
37 <filter>( separate_logfile is True )</filter>
38 </data>
39 </outputs>
40
41 <tests>
42 <test>
43 <param name="sPaired" value="single"/>
44 <param name="mapping_output" value="mapped_reads.bam" ftype="qname_sorted.bam"/>
45 <output name="output_bam" file="dedup_reads.bam" ftype="qname_sorted.bam"/>
46 <output name="output_report" file="dedup_report.txt" ftype="txt"/>
47 </test>
48 </tests>
49
50 <help>
51 <![CDATA[
52 **What it does**
53
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.
55 |
56 | Note that deduplication is not recommended for RRBS-type experiments!
57 |
58 | For single-end alignments only use the start-coordinate of a read will be used for deduplication.
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.
60
61 ]]>
62 </help>
63 <citations>
64 <citation type="doi">10.1093/bioinformatics/btr167</citation>
65 </citations>
66 </tool>