Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
changeset 10:a0a5aa56d29c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
| author | galaxyp |
|---|---|
| date | Tue, 14 Mar 2017 14:11:41 -0400 |
| parents | 9fec6c7f46eb |
| children | 63c48a6eddb6 |
| files | data_manager/customProDB_annotation.xml |
| diffstat | 1 files changed, 33 insertions(+), 31 deletions(-) [+] |
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--- a/data_manager/customProDB_annotation.xml Fri Jan 13 12:18:39 2017 -0500 +++ b/data_manager/customProDB_annotation.xml Tue Mar 14 14:11:41 2017 -0400 @@ -1,38 +1,40 @@ <tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1"> - <description>builder</description> - <command interpreter="Rscript --vanilla">customProDB_annotation.R - --outputFile "${out_file}" - --dbkey "${dbkey}" - --dbsnp "${dbsnp}" - #if $cosmic - --cosmic true - #end if - --dbkey_description ${ dbkey.get_display_text() } - 2>&1 - </command> - <stdio> - <exit_code range=":-1" /> - <exit_code range="1:" /> - </stdio> - <inputs> - <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" /> - <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" /> - <param type="boolean" name="cosmic" value="" label="Annotate somatic SNPs from COSMIC (human only)" /> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json"/> - </outputs> - - <help> + <description>builder</description> + <requirements> + <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement> + </requirements> + <stdio> + <exit_code range=":-1" /> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + Rscript --vanilla '$__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> + </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>