Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
comparison data_manager/customProDB_annotation.xml @ 5:a0ca66b32792 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author | galaxyp |
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date | Tue, 24 May 2016 11:47:26 -0400 |
parents | b42974daa659 |
children | 9fec6c7f46eb |
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4:b42974daa659 | 5:a0ca66b32792 |
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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>&1 | 11 2>&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 |