Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

comparison data_manager/customProDB_annotation.xml @ 5:a0ca66b32792 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author galaxyp
date Tue, 24 May 2016 11:47:26 -0400
parents b42974daa659
children 9fec6c7f46eb
comparison
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4:b42974daa659 5:a0ca66b32792
1 <tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1"> 1 <tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1">
2 <description>builder</description> 2 <description>builder</description>
3 <command interpreter="Rscript --vanilla">customProDB_annotation.R 3 <command interpreter="Rscript --vanilla">customProDB_annotation.R
4 --outputFile "${out_file}" 4 --outputFile "${out_file}"
5 --dbkey "${dbkey}" 5 --dbkey "${dbkey}"
6 --dbsnp "${dbsnp}"
7 #if $cosmic
8 --cosmic true
9 #end if
6 --dbkey_description ${ dbkey.get_display_text() } 10 --dbkey_description ${ dbkey.get_display_text() }
7 2&gt;&amp;1 11 2&gt;&amp;1
8 </command> 12 </command>
9 <stdio> 13 <stdio>
10 <exit_code range=":-1" /> 14 <exit_code range=":-1" />
11 <exit_code range="1:" /> 15 <exit_code range="1:" />
12 </stdio> 16 </stdio>
13 <inputs> 17 <inputs>
14 <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" /> 18 <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" />
19 <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" />
20 <param type="boolean" name="cosmic" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
15 </inputs> 21 </inputs>
16 <outputs> 22 <outputs>
17 <data name="out_file" format="data_manager_json"/> 23 <data name="out_file" format="data_manager_json"/>
18 </outputs> 24 </outputs>
19 25