Mercurial > repos > bgruening > bismark
comparison bismark_pretty_report/bismark2report_wrapper.xml @ 7:fcadce4d9a06 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author | bgruening |
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date | Sat, 06 May 2017 13:18:09 -0400 |
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6:0f8646f22b8d | 7:fcadce4d9a06 |
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1 <tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.16.3"> | |
2 | |
3 <description>Generates a graphical HTML report page from report outputs of 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 bismark2report_wrapper.py | |
21 | |
22 --tool_dir "$__tool_directory__" | |
23 | |
24 --alignment_report "$alignment" | |
25 | |
26 #if $additional_reports['dedup']: | |
27 --dedup_report "$additional_reports['dedup']" | |
28 #end if | |
29 #if $additional_reports['splitting']: | |
30 --splitting_report "$additional_reports['splitting']" | |
31 #end if | |
32 #if $additional_reports['mbias']: | |
33 --mbias_report "$additional_reports['mbias']" | |
34 #end if | |
35 #if $additional_reports['nucleotide']: | |
36 --nucleotide_report "$additional_reports['nucleotide']" | |
37 #end if | |
38 | |
39 ##--output_html_report $output_html_report | |
40 --output_html_report_link "$output_html_report_link" | |
41 --output_dir "$output_html_report_link.files_path" | |
42 | |
43 ##--log_report $log_report | |
44 ]]> | |
45 </command> | |
46 | |
47 <inputs> | |
48 <param name="alignment" type="data" format="txt" label="Submit a Bismark mapping report" optional="False"/> | |
49 <section name="additional_reports" title="Additional reports to include in the HTML page (optional)" expanded="True"> | |
50 <param name="dedup" type="data" format="txt" label="Submit the corresponding Bismark deduplication report" optional="True" help="Optional output of the module *Bismark Deduplicate*"/> | |
51 <param name="splitting" type="data" format="txt" label="Submit the corresponding Bismark splitting report" optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/> | |
52 <param name="mbias" type="data" format="txt" label="Submit the corresponding Bismark M-bias report" optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/> | |
53 <param name="nucleotide" type="data" format="txt" label="Submit the corresponding Bismark nucleotide report" optional="True" help="Optional output of the module *Bismark Mapping*"/> | |
54 </section> | |
55 </inputs> | |
56 | |
57 <outputs> | |
58 <!--<data name="output_html_report" format="html" label="${tool.name} on ${on_string}: Download pretty html report"/>--> | |
59 <data name="output_html_report_link" format="html" label="${tool.name} on ${on_string}: Visualize pretty html report"/> | |
60 <!--<data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)"/>--> | |
61 </outputs> | |
62 | |
63 <help> | |
64 <![CDATA[ | |
65 **What it does** | |
66 | |
67 | This tool uses a Bismark alignment report to generate a graphical HTML report page. | |
68 | Optionally, further reports of the Bismark suite such as deduplication, methylation extractor splitting or M-bias reports can be specified as well. | |
69 | |
70 ]]> | |
71 </help> | |
72 <citations> | |
73 <citation type="doi">10.1093/bioinformatics/btr167</citation> | |
74 </citations> | |
75 </tool> |