--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniprotxml_downloader.xml	Tue Mar 08 12:03:49 2016 -0500
@@ -0,0 +1,90 @@
+<tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.0">
+    <description>proteome</description>
+    <requirements>
+        <requirement type="binary">wget</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"  level="fatal" description="Error downloading proteome." />
+    </stdio>
+    <command interpreter="python">
+<![CDATA[
+uniprotxml_downloader.py -v 
+#if $taxid.choice == 'common':
+--taxon $taxid.organism
+#if $taxid.reviewed:
+--reviewed=$taxid.reviewed
+#end if
+#else:
+#for id in $taxid.taxons.split(','):
+-t $id
+#end for
+#end if
+--output="${proteome}"
+]]>
+    </command>
+    <inputs>
+        <conditional name="taxid">
+            <param name="choice" type="select" label="Select">
+                <option value="common">A Common Organism</option>
+                <option value="taxids">By Organism IDs</option>
+            </param>
+            <when value="common">
+                <param name="organism" type="select" label="Common Organisms"
+                       help="select species for protein database">
+                    <options from_file="uniprot_taxons.loc">
+                        <column name="name" index="0" />
+                        <column name="value" index="1" />
+                    </options>
+                </param>
+                <param name="reviewed" type="select" label="filter by reviewed status" optional="true">
+                    <help><![CDATA[
+                    UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database that may contain 
+                    redundant sequences, but there is a higher chance peptides will be identified. 
+                    UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database with 
+                    less of a chance peptides will be identified but less sequence redundancy
+                    ]]>
+                    </help>
+                    <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option>
+                    <option value="no">UniProtKB/TrEMBL (unreviewed only)</option>
+                </param>
+            </when>
+            <when value="taxids">
+                <param name="taxons" type="text" label="NCBI taxon IDs" 
+                       help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/">
+                    <validator type="regex" message="OrganismID[,OrganismID]">^\d+(,\d+)*$</validator>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="uniprotxml" name="proteome" label="UniProtXML" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="taxons" value="1566990"/>
+            <output name="uniprotxml">
+                <assert_contents>
+                    <has_text text="&lt;/uniprot&gt;" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**UniProtXML Downloader**
+
+Downloads a UniProtXML file from UniProtKB
+
+The Morpheus proteomics search algorithm can use this format as a search database.
+
+Available proteomes: http://www.uniprot.org/proteomes/
+
+UniProtKB help: http://www.uniprot.org/help/uniprotkb
+
+]]>
+    </help>
+    <citations>
+      <citation type="doi">10.1093/nar/gku989</citation>
+    </citations>
+</tool>
+