Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

diff 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
line wrap: on
line diff
--- a/data_manager/customProDB_annotation.xml	Thu Jan 28 18:46:50 2016 -0500
+++ b/data_manager/customProDB_annotation.xml	Tue May 24 11:47:26 2016 -0400
@@ -3,6 +3,10 @@
     <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&gt;&amp;1
     </command>
@@ -12,6 +16,8 @@
     </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"/>