Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

annotate data_manager/customProDB_annotation.xml @ 10:a0a5aa56d29c draft

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