Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
comparison data_manager/customProDB_annotation.xml @ 0:45755942ae7b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
author | galaxyp |
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date | Tue, 14 Mar 2017 14:11:55 -0400 |
parents | |
children | 9b4ee836e35b |
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1 <tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1"> | |
2 <description>builder</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range=":-1" /> | |
8 <exit_code range="1:" /> | |
9 </stdio> | |
10 <command><![CDATA[ | |
11 Rscript --vanilla '$__tool_directory__/customProDB_annotation.R' | |
12 --outputFile '${out_file}' | |
13 --dbkey '${dbkey}' | |
14 --dbsnp '${dbsnp}' | |
15 $cosmic | |
16 --dbkey_description '${ dbkey.get_display_text() }' | |
17 2>1 | |
18 ]]> | |
19 </command> | |
20 <inputs> | |
21 <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" /> | |
22 <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" /> | |
23 <param type="boolean" name="cosmic" truevalue="--cosmic true" falsevalue="" label="Annotate somatic SNPs from COSMIC (human only)" /> | |
24 </inputs> | |
25 <outputs> | |
26 <data name="out_file" format="data_manager_json"/> | |
27 </outputs> | |
28 <help> | |
29 | |
30 .. class:: infomark | |
31 | |
32 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
33 | |
34 </help> | |
35 <citations> | |
36 <citation type="doi">10.1093/bioinformatics/btt543</citation> | |
37 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, | |
38 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> | |
39 </citations> | |
40 </tool> |