# HG changeset patch
# User galaxyp
# Date 1481927585 18000
# Node ID e1abc9a35c64b143e761c2c10b70b9b72f2e60eb
# Parent  fc8c4bd28681555164e27a5d5e9b217ec468d77a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347

diff -r fc8c4bd28681 -r e1abc9a35c64 test-data/Helicobacter_strains.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Helicobacter_strains.tsv	Fri Dec 16 17:33:05 2016 -0500
@@ -0,0 +1,2 @@
+PeCan4
+Shi470
diff -r fc8c4bd28681 -r e1abc9a35c64 uniprotxml_downloader.py
--- a/uniprotxml_downloader.py	Wed Dec 07 16:44:14 2016 -0500
+++ b/uniprotxml_downloader.py	Fri Dec 16 17:33:05 2016 -0500
@@ -15,19 +15,32 @@
 import re
 import optparse
 import urllib
+import urllib2
 
 
 def __main__():
     # Parse Command Line
     parser = optparse.OptionParser()
+    parser.add_option('-i', '--input', dest='input', default=None, help='Tabular file containing a column of NCBI Taxon IDs')
+    parser.add_option('-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains Taxon IDs' )
     parser.add_option('-t', '--taxon', dest='taxon', action='append', default=[], help='NCBI taxon ID to download')
-    parser.add_option('-r', '--reviewed', dest='reviewed', help='file path for th downloaed uniprot xml')
+    parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries')
+    parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml',help='output format')
     parser.add_option('-o', '--output', dest='output', help='file path for th downloaed uniprot xml')
     parser.add_option('-v', '--verbose', dest='verbose', action='store_true', default=False, help='Print UniProt Info')
     parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr')
     (options, args) = parser.parse_args()
-
-    taxids = options.taxon if options.taxon else ['9606']
+    taxids = set(options.taxon)
+    if options.input:
+        with open(options.input,'r') as inputFile:
+            for linenum,line in enumerate(inputFile):
+                if line.startswith('#'):
+                    continue
+                fields = line.rstrip('\r\n').split('\t')
+                if len(fields) > abs(options.column):
+                    taxid = fields[options.column].strip()
+                    if taxid:
+                      taxids.add(taxid)
     taxon_queries = ['taxonomy:"%s"' % taxid for taxid in taxids]
     taxon_query = ' OR '.join(taxon_queries)
     if options.output:
@@ -35,26 +48,31 @@
     else:
         dest_path = "uniprot_%s.xml" % '_'.join(taxids)
     reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
-    url = 'http://www.uniprot.org/uniprot/?query=%s%s&force=yes&format=xml' % (taxon_query, reviewed)
-    if options.debug:
-        print >> sys.stderr, url
     try:
-        (fname, msg) = urllib.urlretrieve(url, dest_path)
+        def reporthook(n1,n2,n3):
+            pass   
+        url = 'http://www.uniprot.org/uniprot/'
+        query = "%s%s" % (taxon_query, reviewed)
+        params = {'query' : query, 'force' : 'yes' , 'format' : options.format}
+        if options.debug:
+            print >> sys.stderr, "%s ? %s" % (url,params)
+        data = urllib.urlencode(params)
+        (fname, msg) = urllib.urlretrieve(url, dest_path,reporthook,data)
         headers = {j[0]: j[1].strip() for j in [i.split(':', 1) for i in str(msg).strip().splitlines()]}
         if 'Content-Length' in headers and headers['Content-Length'] == 0:
             print >> sys.stderr, url
             print >> sys.stderr, msg
             exit(1)
-        elif True:
-            pass
-        else:
+        if options.format == 'xml':
             with open(dest_path, 'r') as contents:
                 while True:
                     line = contents.readline()
                     if options.debug:
                         print >> sys.stderr, line
-                    if line is None or not line.startswith('<?'):
+                    if line is None:
                         break
+                    if line.startswith('<?'):
+                        continue
                     # pattern match <root or <ns:root for any ns string
                     pattern = '^<(\w*:)?uniprot'
                     if re.match(pattern, line):
@@ -62,7 +80,6 @@
                     else:
                         print >> sys.stderr, "failed: Not a uniprot xml file"
                         exit(1)
-
         if options.verbose:
             print >> sys.stdout, "NCBI Taxon ID:%s" % taxids
             if 'X-UniProt-Release' in headers:
diff -r fc8c4bd28681 -r e1abc9a35c64 uniprotxml_downloader.xml
--- a/uniprotxml_downloader.xml	Wed Dec 07 16:44:14 2016 -0500
+++ b/uniprotxml_downloader.xml	Fri Dec 16 17:33:05 2016 -0500
@@ -1,33 +1,37 @@
-<tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.1">
-    <description>proteome</description>
+<tool id="uniprotxml_downloader" name="UniProt" version="2.0.0">
+    <description>download proteome as XML or fasta</description>
     <requirements>
-        <requirement type="package" version="2.7.12">python</requirement>
+        <requirement type="package" version="2.7">python</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"  level="fatal" description="Error downloading proteome." />
     </stdio>
     <command>
 <![CDATA[
-    python '$__tool_directory__/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}"
+python $__tool_directory__/uniprotxml_downloader.py -v 
+#if $taxid.input_choice == 'common':
+--taxon $taxid.organism
+#if $taxid.reviewed:
+--reviewed=$taxid.reviewed
+#end if
+#elif $taxid.input_choice == 'taxids':
+#for $id in $taxid.taxons.split(','):
+-t "$id"
+#end for
+#elif $taxid.input_choice == 'history':
+--input="${taxid.taxon_file}"
+--column=#echo int(str($taxid.column)) - 1#
+#end if
+--format=$format
+--output="${proteome}"
 ]]>
     </command>
     <inputs>
         <conditional name="taxid">
-            <param name="choice" type="select" label="Select">
+            <param name="input_choice" type="select" label="Select">
                 <option value="common">A Common Organism</option>
                 <option value="taxids">By Organism IDs</option>
+                <option value="history">A history dataset with an Organism Taxonomy Name column</option>
             </param>
             <when value="common">
                 <param name="organism" type="select" label="Common Organisms"
@@ -50,37 +54,89 @@
                 </param>
             </when>
             <when value="taxids">
-                <param name="taxons" type="text" label="NCBI taxon IDs" 
+                <param name="taxons" type="text" label="NCBI Taxon IDs or names" 
                        help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/">
-                    <validator type="regex" message="OrganismID[,OrganismID]">^\d+(,\d+)*$</validator>
+                    <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator>
                 </param>
             </when>
+            <when value="history">
+                <param name="taxon_file" type="data" format="tabular" label="Dataset with Taxon Name column"/>
+                <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon name"/>
+            </when>
         </conditional>
+        <param name="format" type="select" label="uniprot output format">
+            <option value="xml">xml</option>
+            <option value="fasta">fasta</option>
+        </param>
     </inputs>
     <outputs>
-        <data format="uniprotxml" name="proteome" label="UniProtXML" />
+        <data format="uniprotxml" name="proteome" label="UniProt.${format}">
+            <change_format>
+                <when input="format" value="fasta" format="fasta" />
+            </change_format>
+        </data>
     </outputs>
     <tests>
         <test>
-            <param name="choice" value="taxids"/>
+            <param name="input_choice" value="taxids"/>
             <param name="taxons" value="1566990"/>
-            <output name="uniprotxml">
+            <param name="format" value="xml"/>
+            <output name="proteome">
                 <assert_contents>
                     <has_text text="&lt;/uniprot&gt;" />
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="input_choice" value="taxids"/>
+            <param name="taxons" value="Shi470,PeCan4"/>
+            <param name="format" value="fasta"/>
+            <output name="proteome">
+                <assert_contents>
+                    <has_text text="Shi470" />
+                    <has_text text="PeCan4" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_choice" value="history"/>
+            <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/>
+            <param name="column" value="1"/>
+            <param name="format" value="fasta"/>
+            <output name="proteome">
+                <assert_contents>
+                    <has_text text="Shi470" />
+                    <has_text text="PeCan4" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
-**UniProtXML Downloader**
+**UniProt Downloader**
 
-Downloads a UniProtXML file from UniProtKB
+Downloads either a UniProtXML file or a fasta file from UniProtKB
 
-The Morpheus proteomics search algorithm can use this format as a search database.
+The Morpheus proteomics search algorithm can use the UniProtXML format as a search database.
 
 Available proteomes: http://www.uniprot.org/proteomes/
 
+Available taxon names: http://www.uniprot.org/taxonomy/
+
+Example taxon: http://www.uniprot.org/taxonomy/512562
+
+Taxon IDs or names can be entered as text or read from a column in a tabular dataset from your history.
+
+Example IDs and names releated to the Bacteria Helicobacter pylori (strain Shi470) ::
+
+
+ - 512562
+ - Shi470
+ - Helicobacter pylori
+ - Helicobacter
+ - Helicobacteraceae
+
+
 UniProtKB help: http://www.uniprot.org/help/uniprotkb
 
 ]]>