diff dbbuilder.xml @ 0:487f80fb99ae draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dbbuilder.xml	Wed Dec 19 00:05:32 2012 -0500
@@ -0,0 +1,46 @@
+<tool id="dbbuilder" version="0.1.0" name="Protein Database Downloader">
+  <description>
+  </description>
+  <requirements>
+    <requirement type="binary">wget</requirement>    
+  </requirements>  
+  <stdio>
+    <exit_code range="1:"  level="fatal"   description="Error computing FDR" />
+  </stdio>
+  <command>
+    #if $source.from == "uniprot"
+    #set $url = "http://www.uniprot.org/uniprot/?query=taxonomy%3a%22" + str($source.taxon) + "%22+keyword%3a1185&amp;force=yes&amp;format=fasta" + str($source.include_isoform)
+    #elif $source.from == "cRAP"
+    #set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta"
+    #end if
+    wget -nv '$url' -O '${output_database}'
+  </command>
+  <inputs>
+    <conditional name="source">
+      <param name="from" type="select" label="Download from">
+        <option value="uniprot">UniProtKB</option>
+        <option value="cRAP">cRAP (contaminants)</option>
+      </param>
+      <when value="uniprot">
+        <param name="taxon" type="select" format="text" >
+          <label>Taxonomy</label>
+          <options from_file="uniprot_taxons.loc">
+            <column name="name" index="0" />
+            <column name="value" index="1" />
+          </options>
+        </param>
+        <param name="include_isoform" type="boolean" truevalue="&amp;include=yes" falsevalue="" label="Include isoform data" />
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="output_database" label="Protein Database" />
+  </outputs>
+  <help>
+**Output**
+
+A FASTA file containing the specified protein sequences.
+
+  </help>
+</tool>
+