Mercurial > repos > galaxyp > ms_wiff_loader

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ms_wiff_loader.py	Tue Mar 10 18:26:36 2015 -0400
@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import shutil
+import subprocess
+import re
+import logging
+import urllib2
+from urlparse import urlparse
+
+
+assert sys.version_info[:2] >= (2, 6)
+
+log = logging.getLogger(__name__)
+
+CHUNK_SIZE = 2**20 #1mb
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()
+
+def download_from_url( url, output_dir, basename=None, ext=None ):
+    o = urlparse(url)
+    src_parts = os.path.basename(o.path).split('.',1)
+    file_name = "%s.%s" % ( basename if basename else src_parts[0], ext if ext else src_parts[1] )
+    file_path = os.path.join(output_dir,file_name)
+    reader = urllib2.urlopen( url )
+    writer = open(file_path,'wb')
+    while True:
+        data = reader.read( CHUNK_SIZE )
+        if data:
+            writer.write( data )
+        else:
+            break
+    writer.close()
+    reader.close()
+    return file_path
+
+def __main__():
+    parser = optparse.OptionParser()
+    parser.add_option( '-a', '--archive', dest='archive', default=None, help='URL to archive containing: <name>.wiff file <name>.wiff.scan <name>.wiff.mtd files' )
+    parser.add_option( '-w', '--wiff', dest='wiff', default=None, help='URL to <name>.wiff file' )
+    parser.add_option( '-s', '--scan', dest='scan', default=None, help='URL to <name>.wiff.scan file' )
+    parser.add_option( '-m', '--mtd', dest='mtd', default=None, help='URL to <name>.wiff.mtd file' )
+    parser.add_option( '-n', '--name', dest='name', default=None, help='base name for files' )
+    parser.add_option( '-o', '--output_dir', dest='output_dir', default=None, help='dir to copy files into' )
+    parser.add_option( '-f', '--output_file', dest='output_file', default=None, help='Galaxy dataset file' )
+    (options, args) = parser.parse_args()
+
+    if not (options.archive or options.wiff):
+        stop_err("No wiff input file specified")
+    output_dir = os.getcwd()
+    if options.output_dir:
+        output_dir = options.output_dir
+        if not os.path.exists( output_dir ):
+            os.makedirs(output_dir)
+    basename = options.name
+    rval = ['<html><head><title>Wiff Composite Dataset %s</title></head><body><p/>' % (basename if basename else '')]
+    rval.append('This composite dataset is composed of the following files:<p/><ul>')
+    if options.wiff:
+        file_path = download_from_url (options.wiff, output_dir, basename=basename, ext='wiff')
+        rel_path = os.path.basename(file_path)
+        os.symlink( rel_path, os.path.join(output_dir,'wiff'))
+        rval.append( '<li><a href="%s" type="application/octet-stream">%s</a></li>' % ( rel_path, rel_path ) )
+        print >> sys.stdout, "wiff: %s" % options.wiff
+    if options.scan:
+        file_path = download_from_url (options.scan, output_dir, basename=basename, ext='wiff.scan')
+        rel_path = os.path.basename(file_path)
+        os.symlink( rel_path, os.path.join(output_dir,'wiff_scan'))
+        rval.append( '<li><a href="%s" type="application/octet-stream">%s</a></li>' % ( rel_path, rel_path ) )
+        print >> sys.stdout, "scan: %s" % options.scan
+    if options.mtd:
+        file_path = download_from_url (options.mtd, output_dir, basename=basename, ext='wiff.mtd')
+        rel_path = os.path.basename(file_path)
+        os.symlink( rel_path, os.path.join(output_dir,'wiff_mtd'))
+        rval.append( '<li><a href="%s" type="application/octet-stream">%s</a></li>' % ( rel_path, rel_path ) )
+        print >> sys.stdout, "mtd:  %s" % options.mtd
+    if options.output_file:
+        rval.append( '</ul></div></body></html>' )
+        f = open(options.output_file,'a')
+        f.write("\n".join( rval ))
+        f.close()
+
+if __name__ == '__main__':
+    __main__()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ms_wiff_loader.xml	Tue Mar 10 18:26:36 2015 -0400
@@ -0,0 +1,45 @@
+<tool id="ms_wiff_upload" name="MS Wiff Upload" version="1.0.0">
+  <description>into a galaxy dataset</description>
+  <stdio>
+    <exit_code range="1:" err_level="fatal" />
+  </stdio>
+  <command interpreter="python">ms_wiff_loader.py -w "$wiff"
+  #if len(str($scan)) > 0:
+    -s "$scan"
+  #end if
+  #if len(str($mtd)) > 0:
+    -m "$mtd"
+  #end if
+  -f "$out_file"
+  -o "${out_file.extra_files_path}"
+  </command>
+  <inputs>
+    <param name="wiff" type="text" value="" size="120" label="URL to .wiff file">
+      <validator type="regex" message="Must be a URL">^(ftp://|http://|https://|file:/)?(\\d+\\.\\d+\\.\\d+\\.\\d+|localhost|[a-zA-Z][^/]+)(:\\d+)?/(.*)$</validator>
+    </param>
+    <param name="scan" type="text" value="" size="120" label="URL to .wiff.scan file (optional)" optional="true">
+      <validator type="regex" message="Must be a URL">^(ftp://|http://|https://|file:/)?(\\d+\\.\\d+\\.\\d+\\.\\d+|localhost|[a-zA-Z][^/]+)(:\\d+)?/(.*)$</validator>
+    </param>
+    <param name="mtd" type="text" value="" size="120" label="URL to .wiff.mtd file (optional)" optional="true">
+      <validator type="regex" message="Must be a URL">^(ftp://|http://|https://|file:/)?(\\d+\\.\\d+\\.\\d+\\.\\d+|localhost|[a-zA-Z][^/]+)(:\\d+)?/(.*)$</validator>
+    </param>
+    <param name="name" type="text" value="" size="40" label="Name for dataset (optional)" optional="true">
+    </param>
+  </inputs>
+  <outputs>
+    <data format="wiff" name="out_file" label="$name wiff"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="wiff" value="http://www.ebi.ac.uk/pride/data/archive/2015/01/PXD001010/nselevse_L120327_016.wiff"/>
+      <output name="out_file">
+        <assert_contents>
+          <has_text text="Wiff" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+<help>
+Loads AB SCIEX wiff files into a Galaxy Composite dataset.
+</help>
+</tool>