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comparison bismark2report_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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children f211753166bd
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7:fcadce4d9a06 8:9bfe38410155
1 <tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.20.0" profile="17.01">
2 <description>Generates a graphical HTML report page from report outputs of 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 '$__tool_directory__/bismark2report_wrapper.py'
10
11 --alignment_report '$alignment'
12
13 #if $additional_reports['dedup']:
14 --dedup_report '$additional_reports["dedup"]'
15 #end if
16 #if $additional_reports['splitting']:
17 --splitting_report '$additional_reports["splitting"]'
18 #end if
19 #if $additional_reports['mbias']:
20 --mbias_report '$additional_reports["mbias"]'
21 #end if
22 #if $additional_reports['nucleotide']:
23 --nucleotide_report '$additional_reports["nucleotide"]'
24 #end if
25
26 --output_html_report '$output_html_report'
27
28 #if $separate_logfile:
29 --log_report '$log_report'
30 #end if
31 ]]>
32 </command>
33
34 <inputs>
35 <param name="alignment" type="data" format="txt" label="Submit a Bismark mapping report" optional="False"/>
36 <section name="additional_reports" title="Additional reports to include in the HTML page (optional)"
37 expanded="True">
38 <param name="dedup" type="data" format="txt" label="Submit the corresponding Bismark deduplication report"
39 optional="True" help="Optional output of the module *Bismark Deduplicate*"/>
40 <param name="splitting" type="data" format="txt" label="Submit the corresponding Bismark splitting report"
41 optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/>
42 <param name="mbias" type="data" format="txt" label="Submit the corresponding Bismark M-bias report"
43 optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/>
44 <param name="nucleotide" type="data" format="txt" label="Submit the corresponding Bismark nucleotide report"
45 optional="True" help="Optional output of the module *Bismark Mapping*"/>
46 </section>
47 <param name="separate_logfile" type="boolean" truevalue="true" falsevalue="false" checked="False"
48 label="Create a separate logfile, otherwise logs are added to the dataset info."/>
49 </inputs>
50
51 <outputs>
52 <data name="output_html_report" format="html"
53 label="${tool.name} on ${on_string}: Download pretty html report"/>
54 <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
55 <filter>( separate_logfile is True )</filter>
56 </data>
57 </outputs>
58
59 <tests>
60 <test>
61 <param name="alignment" value="mapping_report.txt" ftype="txt"/>
62 <param name="dedup" value="dedup_report.txt" ftype="txt"/>
63 <param name="splitting" value="output_splitting_report.txt" ftype="txt"/>
64 <param name="mbias" value="output_mbias_report.txt" ftype="txt"/>
65 <output name="output_html_report" file="output_html_report.html" ftype="html" lines_diff="8"/>
66 </test>
67 </tests>
68
69 <help>
70 <![CDATA[
71 **What it does**
72
73 | This tool uses a Bismark alignment report to generate a graphical HTML report page.
74 | Optionally, further reports of the Bismark suite such as deduplication, methylation extractor splitting or M-bias reports can be specified as well.
75
76 ]]>
77 </help>
78 <citations>
79 <citation type="doi">10.1093/bioinformatics/btr167</citation>
80 </citations>
81 </tool>