Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/customProDB_annotation.xml Tue Mar 14 14:11:55 2017 -0400 @@ -0,0 +1,40 @@ +<tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1"> + <description>builder</description> + <requirements> + <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement> + </requirements> + <stdio> + <exit_code range=":-1" /> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + Rscript --vanilla '$__tool_directory__/customProDB_annotation.R' + --outputFile '${out_file}' + --dbkey '${dbkey}' + --dbsnp '${dbsnp}' + $cosmic + --dbkey_description '${ dbkey.get_display_text() }' + 2>1 +]]> + </command> + <inputs> + <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" /> + <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" /> + <param type="boolean" name="cosmic" truevalue="--cosmic true" falsevalue="" label="Annotate somatic SNPs from COSMIC (human only)" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <help> + +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btt543</citation> + <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, + year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> + </citations> +</tool>