Migrate in all devteam's DMs

data_managers/data_manager_bowtie2_index_builder/data_manager/bowtie2_index_builder.py

@@ -1,77 +1,81 @@
 #!/usr/bin/env python
-#Dan Blankenberg
+# Dan Blankenberg
+from __future__ import print_function
 
-import sys
-import os
 import optparse
+import os
 import subprocess
-
-from json import loads, dumps
-
+import sys
+from json import dumps, loads
 
 DEFAULT_DATA_TABLE_NAMES = ["bowtie2_indexes"]
 
+
 def get_id_name( params, dbkey, fasta_description=None):
-    #TODO: ensure sequence_id is unique and does not already appear in location file
+    # TODO: ensure sequence_id is unique and does not already appear in location file
     sequence_id = params['param_dict']['sequence_id']
     if not sequence_id:
         sequence_id = dbkey
-    
+
     sequence_name = params['param_dict']['sequence_name']
     if not sequence_name:
         sequence_name = fasta_description
         if not sequence_name:
             sequence_name = dbkey
     return sequence_id, sequence_name
 
+
 def build_bowtie2_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
-    #TODO: allow multiple FASTA input files
+    # TODO: allow multiple FASTA input files
     fasta_base_name = os.path.split( fasta_filename )[-1]
     sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
     os.symlink( fasta_filename, sym_linked_fasta_filename )
     args = [ 'bowtie2-build', sym_linked_fasta_filename, sequence_id ]
     proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
     return_code = proc.wait()
     if return_code:
-        print >> sys.stderr, "Error building index."
+        print("Error building index.", file=sys.stderr)
         sys.exit( return_code )
     data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id )
     for data_table_name in data_table_names:
         _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
 
+
 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
     data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
     data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
     data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
     return data_manager_dict
 
+
 def main():
-    #Parse Command Line
     parser = optparse.OptionParser()
     parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
     parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
     parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
     parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='append', type="string", default=None, help='data_table_name' )
     (options, args) = parser.parse_args()
-    
+
     filename = args[0]
-    
+
     params = loads( open( filename ).read() )
     target_directory = params[ 'output_data' ][0]['extra_files_path']
     os.mkdir( target_directory )
     data_manager_dict = {}
-    
+
     dbkey = options.fasta_dbkey
-    
+
     if dbkey in [ None, '', '?' ]:
         raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
-    
+
     sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
-    
-    #build the index
+
+    # build the index
     build_bowtie2_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES )
-    
-    #save info to json file
+
+    # save info to json file
     open( filename, 'wb' ).write( dumps( data_manager_dict ) )
-
-if __name__ == "__main__": main()
+
+
+if __name__ == "__main__":
+    main()

data_managers/data_manager_bowtie2_index_builder/data_manager/bowtie2_index_builder.xml

@@ -1,30 +1,24 @@
-<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.2.6">
+<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.3.0">
     <description>builder</description>
     <requirements>
-        <requirement type="package" version="2.2.6">bowtie2</requirement>
+        <requirement type="package" version="2.3.0">bowtie2</requirement>
     </requirements>
-    <command interpreter="python">bowtie2_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bowtie2_indexes" ${tophat2}</command>
-    <stdio>
-        <exit_code range=":-1" />
-        <exit_code range="1:" />
-    </stdio>
+    <command detect_errors="exit_code">python '$__tool_directory__/bowtie2_index_builder.py' '${out_file}' --fasta_filename '${all_fasta_source.fields.path}' --fasta_dbkey '${all_fasta_source.fields.dbkey}' --fasta_description '${all_fasta_source.fields.name}' --data_table_name bowtie2_indexes ${tophat2}</command>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta"/>
         </param>
-        <param type="text" name="sequence_name" value="" label="Name of sequence" />
-        <param type="text" name="sequence_id" value="" label="ID for sequence" />
-        <param type="boolean" name="tophat2" label="Also make available for TopHat" checked="True" truevalue="--data_table_name tophat2_indexes" falsevalue="" help="Adds values to tophat2_indexes tool data table." />
+        <param name="sequence_name" type="text" value="" label="Name of sequence" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" />
+        <param name="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
     </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. 
-
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
     </help>
 </tool>

data_managers/data_manager_build_kraken_database/data_manager/kraken_database_builder.xml

@@ -1,49 +1,47 @@
 <?xml version="1.0"?>
-<tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.0.1">
+<tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.0.2">
     <description>database builder</description>
     <requirements>
         <requirement type="package" version="0.10.6-eaf8fb68">kraken</requirement>
-        <requirement type="package" version="1.1.11">jellyfish</requirement>
-        <requirement type="set_environment">KRAKEN_SCRIPT_PATH</requirement>
     </requirements>
-    <stdio>
-        <exit_code description="Error" level="fatal" range="1:" />
-    </stdio>
     <version_command>kraken -version | awk '{print $NF}'</version_command>
-    <command>
+    <command detect_errors="exit_code">
     <![CDATA[
         #set $library_list = str($libraries).split(',')
         mkdir kraken-database && cd kraken-database &&
-        kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db "${database_name}" &&
+        kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' &&
         #for $library in $library_list:
             #if str($library) != 'None':
-                kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}"  &&
+                kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' &&
             #end if
         #end for
         #for $fasta in $input_fasta:
             #if str($fasta) != 'None':
-                kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta"  &&
+                kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' &&
             #end if
         #end for
-        kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len}  &&
-        cd .. && python \$KRAKEN_SCRIPT_PATH/data_manager/make_json.py --db "${database_name}" --out "${out_file}"
+        kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} &&
+        cd .. &&
+        python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
     ]]>
     </command>
     <inputs>
-        <param label="Name for this database" name="database_name" type="text" />
-        <param label="Select partial library to download" multiple="True" name="libraries" type="select">
+        <param name="database_name" type="text" label="Name for this database" />
+        <param name="libraries" type="select" multiple="true" label="Select partial library to download">
             <option value="bacteria">Bacteria</option>
             <option value="plasmids">Plasmids</option>
             <option value="viruses">Viruses</option>
             <option value="human">Human</option>
         </param>
-        <param format="fasta" label="Select history item" multiple="True" name="input_fasta" optional="True" type="data" />
-        <param label="K-mer length in BP" name="kmer_len" type="integer" value="31" />
-        <param label="Minimizer length" name="minimizer_len" type="integer" value="15" />
+        <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" />
+        <param name="kmer_len" type="integer" value="31" label="K-mer length in BP" />
+        <param name="minimizer_len" type="integer" value="15" label="Minimizer length" />
     </inputs>
     <outputs>
-        <data format="data_manager_json" name="out_file" />
+        <data name="out_file" format="data_manager_json" />
     </outputs>
+    <help>
+    </help>
     <citations>
         <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
     </citations>

data_managers/data_manager_build_kraken_database/data_manager/make_json.py

@@ -1,13 +1,8 @@
-import json
 import argparse
+import json
 import os
 import shutil
 
-parser = argparse.ArgumentParser(description='Create data manager json.')
-parser.add_argument('--db', dest='database', action='store', help='Database name')
-parser.add_argument('--out', dest='output', action='store', help='JSON filename')
-
-args = parser.parse_args()
 
 def main(args):
     data_manager_entry = {}
@@ -23,6 +18,10 @@ def main(args):
         shutil.move(os.path.join(output_path, filename), target_directory)
     file(args.output, 'w').write(json.dumps(data_manager_json))
 
+
 if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Create data manager json.')
+    parser.add_argument('--db', dest='database', action='store', help='Database name')
+    parser.add_argument('--out', dest='output', action='store', help='JSON filename')
+    args = parser.parse_args()
     main(args)
-

data_managers/data_manager_fetch_gene_annotation/data_manager/data_manager.py

@@ -1,9 +1,10 @@
+import argparse
+import datetime
+import json
 import os
 import sys
 import uuid
-import json
-import argparse
-import datetime
+
 import requests
 from requests.exceptions import ContentDecodingError
 
@@ -37,8 +38,6 @@ def url_download(url):
 
 
 def main():
-
-    # Generate and parse command line args
     parser = argparse.ArgumentParser(description='Create data manager JSON.')
     parser.add_argument('--out', dest='output', action='store',
                         help='JSON filename')
@@ -70,5 +69,6 @@ def main():
     with open(os.path.join(args.output), "w+") as f:
         f.write(json.dumps(data_manager_entry))
 
+
 if __name__ == '__main__':
     main()

data_managers/data_manager_fetch_gene_annotation/data_manager/gene_annotation_fetcher.xml

@@ -1,25 +1,27 @@
 <?xml version="1.0"?>
-<tool id="gene_annotation_fetcher_data_manager" name="Gene Annotation Fetch" tool_type="manage_data" version="1.0.0">
+<tool id="gene_annotation_fetcher_data_manager" name="Gene Annotation Fetch" tool_type="manage_data" version="1.0.1">
     <description>gene annotation fetcher</description>
-    <stdio>
-        <exit_code description="Error" level="fatal" range="1:" />
-    </stdio>
-    <command interpreter="python">
+    <requirements>
+        <requirement type="package" version="2.13.0">requests</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
     <![CDATA[
-        data_manager.py --out "${out_file}"
+        python '$__tool_directory__/data_manager.py' --out '${out_file}'
         #if $gene_annotation_url:
-            --url "${gene_annotation_url}"
+            --url '${gene_annotation_url}'
         #end if
         #if $database_name:
-            --name "${database_name}"
+            --name '${database_name}'
         #end if
     ]]>
     </command>
     <inputs>
-        <param help="Enter a unique identifier, or leave blank for today's date" label="Name for this database" name="database_name" type="text" optional="True" />
-        <param label="Enter URL for gene annotation files" name="gene_annotation_url" type="text" />
+        <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" />
+        <param name="gene_annotation_url" type="text" label="Enter URL for gene annotation files" />
     </inputs>
     <outputs>
         <data format="data_manager_json" name="out_file" />
     </outputs>
+    <help>
+    </help>
 </tool>