Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

diff data_manager/customProDB_annotation.xml @ 9:9fec6c7f46eb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
author galaxyp
date Fri, 13 Jan 2017 12:18:39 -0500
parents a0ca66b32792
children a0a5aa56d29c
line wrap: on
line diff
--- a/data_manager/customProDB_annotation.xml	Wed Jun 08 16:00:30 2016 -0400
+++ b/data_manager/customProDB_annotation.xml	Fri Jan 13 12:18:39 2017 -0500
@@ -1,33 +1,38 @@
-<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 ${ dbkey.get_display_text() }
-      2&gt;&amp;1
-    </command>
-    <stdio>
-        <exit_code range=":-1" />
-        <exit_code range="1:" />
-    </stdio>
-    <inputs>
-        <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" />
-        <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" />
-        <param type="boolean" name="cosmic" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
-    </inputs>
-    <outputs>
-        <data name="out_file" format="data_manager_json"/>
-    </outputs>
-
-    <help>
-
-.. class:: infomark
-
-**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
-
-    </help>
-</tool>
+<tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1">
+    <description>builder</description>
+    <command interpreter="Rscript --vanilla">customProDB_annotation.R
+      --outputFile "${out_file}"
+      --dbkey "${dbkey}"
+      --dbsnp "${dbsnp}"
+      #if $cosmic
+            --cosmic true
+      #end if
+      --dbkey_description ${ dbkey.get_display_text() }
+      2&gt;&amp;1
+    </command>
+    <stdio>
+        <exit_code range=":-1" />
+        <exit_code range="1:" />
+    </stdio>
+    <inputs>
+        <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" />
+        <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" />
+        <param type="boolean" name="cosmic" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+
+    <help>
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
+
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt543</citation>
+        <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
+                                      year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
+    </citations>
+</tool>