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comparison bismark_deduplicate/bismark_deduplicate_wrapper.xml @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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6:0f8646f22b8d 7:fcadce4d9a06
1 <tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.16.3">
2
3 <description>Deduplicates reads mapped by Bismark</description>
4 <!--<version_command>bismark version</version_command>-->
5
6 <requirements>
7 <requirement type="package" version="0.1.19">samtools</requirement>
8 <requirement type="package" version="2.1.0">bowtie2</requirement>
9 </requirements>
10
11 <stdio>
12 <exit_code range="1:" />
13 <exit_code range=":-1" />
14 <regex match="Error:" />
15 <regex match="Exception:" />
16 </stdio>
17
18 <command interpreter="python">
19 <![CDATA[
20 bismark_deduplicate_wrapper.py
21
22 --tool_dir "$__tool_directory__"
23
24 #if str ( $sPaired ) == "single":
25 -s
26 #else
27 -p
28 #end if
29
30 --input "$mapping_output"
31
32 --output_report "$output_report"
33 --output_bam "$output_bam"
34
35 ##--log_report "$log_report"
36 ]]>
37 </command>
38
39 <inputs>
40 <param name="sPaired" type="select" label="Is this library mate-paired?" format="bam">
41 <option value="single">Single-end</option>
42 <option value="paired">Paired-end</option>
43 </param>
44 <param name="mapping_output" type="data" format="bam, sam" label="Submit the resulting bam/sam file from Bismark bisulfite mapper" />
45 </inputs>
46
47 <outputs>
48 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: deduplicated mapped reads" />
49 <data name="output_report" format="txt" label="${tool.name} on ${on_string}: deduplication report"/>
50 <!--<data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)"/>-->
51 </outputs>
52
53 <help>
54 <![CDATA[
55 **What it does**
56
57 | 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.
58 |
59 | Note that deduplication is not recommended for RRBS-type experiments!
60 |
61 | For single-end alignments only use the start-coordinate of a read will be used for deduplication.
62 | For paired-end alignments the start-coordinate of the first read and the end coordinate of the second read will be used for deduplication.
63
64 ]]>
65 </help>
66 <citations>
67 <citation type="doi">10.1093/bioinformatics/btr167</citation>
68 </citations>
69 </tool>