# HG changeset patch
# User galaxyp
# Date 1489515101 14400
# Node ID a0a5aa56d29c064f42e77413d02df135ccac6771
# Parent  9fec6c7f46eba69be132995fbd833a650fa6f827
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66

diff -r 9fec6c7f46eb -r a0a5aa56d29c data_manager/customProDB_annotation.xml
--- 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 ${ dbkey.get_display_text() }
-      2&gt;&amp;1
-    </command>
-    <stdio>
-        <exit_code range=":-1" />
-        <exit_code range="1:" />
-    </stdio>
-    <inputs>
-        <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" />
-        <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" />
-        <param type="boolean" name="cosmic" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
-    </inputs>
-    <outputs>
-        <data name="out_file" format="data_manager_json"/>
-    </outputs>
-
-    <help>
+  <description>builder</description>
+  <requirements>
+    <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range=":-1" />
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+    Rscript --vanilla '$__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>