Mercurial > repos > mvdbeek > data_manager_fetch_genome_dbkeys_all_fasta_compressed

changeset 3:addfc494867e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 0b08439873c2278b8116aba51b19718d0ef51482-dirty
author mvdbeek
date Thu, 25 Aug 2016 05:10:22 -0400
parents 0738889ff4d2
children 0007b48a5bb9
files data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml
diffstat 2 files changed, 57 insertions(+), 66 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py	Thu Aug 18 07:34:44 2016 -0400
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py	Thu Aug 25 05:10:22 2016 -0400
@@ -118,7 +118,7 @@
 
 def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ):
     unsorted_fh = open( unsorted_fasta_filename )
-    sorted_fh = open( sorted_fasta_filename, 'wb+' )
+    sorted_fh = open( sorted_fasta_filename, 'w+' )
     
     for name in sorted_names:
         offset = fasta_offsets[ name ]
@@ -183,7 +183,7 @@
     sorted_names = []
     for id_repeat in params['param_dict']['sorting']['sequence_identifiers']:
         sorted_names.append( id_repeat[ 'identifier' ] )
-    handle_not_listed = params['param_dict']['sorting']['handle_not_listed']['handle_not_listed_selector']
+    handle_not_listed = params['param_dict']['sorting']['handle_not_listed_selector']
     if handle_not_listed.startswith( 'keep' ):
         add_list = []
         for name in current_order:
@@ -242,7 +242,7 @@
     """
     UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu'
     UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/'
-    COMPRESSED_EXTENSIONS = ['.tar.gz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2']
+    COMPRESSED_EXTENSIONS = ['.tar.gz', '.tgz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2']
 
     email = params['param_dict']['__user_email__']
     if not email:
@@ -256,7 +256,7 @@
 
     ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey
     path_contents = _get_files_in_ftp_path(ftp, ucsc_path)
-    ftp.close()
+    ftp.quit()
 
     for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES:
         for ext in COMPRESSED_EXTENSIONS:
@@ -328,7 +328,7 @@
 def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ):
     fasta_base_filename = "%s.fa" % sequence_id
     fasta_filename = os.path.join( target_directory, fasta_base_filename )
-    with open( fasta_filename, 'wb+' ) as fasta_writer:
+    with open( fasta_filename, 'w+' ) as fasta_writer:
 
         if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
             fasta_stream = fasta_stream[0]
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml	Thu Aug 18 07:34:44 2016 -0400
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml	Thu Aug 25 05:10:22 2016 -0400
@@ -10,77 +10,68 @@
     ]]></command>
     <inputs>
         <conditional name="dbkey_source">
-          <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one.">
-            <option value="existing" selected="True">Existing</option>
-            <option value="new">New</option>
-          </param>
-          <when value="existing">
-              <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
-          </when>
-          <when value="new">
-              <param type="text" name="dbkey" value="" label="dbkey" optional="False" />
-              <param type="text" name="dbkey_name" value="" label="Display name for dbkey" />
-          </when>
+            <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one.">
+                <option value="existing" selected="True">Existing</option>
+                <option value="new">New</option>
+            </param>
+            <when value="existing">
+                <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
+            </when>
+            <when value="new">
+                <param type="text" name="dbkey" value="" label="dbkey" optional="False" />
+                <param type="text" name="dbkey_name" value="" label="Display name for dbkey" />
+            </when>
         </conditional>
-        
         <param type="text" name="sequence_name" value="" label="Name of sequence" />
         <param type="text" name="sequence_id" value="" label="ID for sequence" />
         <conditional name="reference_source">
-          <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
-            <option value="ucsc" selected="True">UCSC</option>
-            <option value="ncbi">NCBI</option>
-            <option value="url">URL</option>
-            <option value="history">History</option>
-            <option value="directory">Directory on Server</option>
-          </param>
-          <when value="ucsc">
-            <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" />
-          </when>
-          <when value="ncbi">
-              <param type="text" name="requested_identifier" value="" label="NCBI identifier/accession" help="Identifiers (e.g 667699573) or accessions (e.g AC020606.7) may be used" optional="False" />
-          </when>
-          <when value="url">
-            <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
-          </when>
-          <when value="history">
-            <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
-          </when>
-          <when value="directory">
-            <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
-            <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" />
-          </when>
+            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+                <option value="ucsc" selected="True">UCSC</option>
+                <option value="ncbi">NCBI</option>
+                <option value="url">URL</option>
+                <option value="history">History</option>
+                <option value="directory">Directory on Server</option>
+            </param>
+            <when value="ucsc">
+                <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" />
+            </when>
+            <when value="ncbi">
+                <param type="text" name="requested_identifier" value="" label="NCBI identifier/accession" help="Identifiers (e.g 667699573) or accessions (e.g AC020606.7) may be used" optional="False" />
+            </when>
+            <when value="url">
+                <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
+            </when>
+            <when value="history">
+                <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
+            </when>
+            <when value="directory">
+                <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
+                <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" />
+            </when>
         </conditional>
         <conditional name="sorting">
-          <param name="sort_selector" type="select" label="Sort by chromosome name">
-            <option value="as_is" selected="True">As is</option>
-            <option value="lexicographical">Lexicographical</option>
-            <option value="gatk">GATK</option>
-            <option value="custom">Custom</option>
-          </param>
-          <when value="as_is">
-          </when>
-          <when value="lexicographical">
-          </when>
-          <when value="gatk">
-          </when>
-          <when value="custom">
-            <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1">
-                <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" />
-            </repeat>
-            <conditional name="handle_not_listed">
+            <param name="sort_selector" type="select" label="Sort by chromosome name">
+                <option value="as_is" selected="True">As is</option>
+                <option value="lexicographical">Lexicographical</option>
+                <option value="gatk">GATK</option>
+                <option value="custom">Custom</option>
+            </param>
+            <when value="as_is">
+            </when>
+            <when value="lexicographical">
+            </when>
+            <when value="gatk">
+            </when>
+            <when value="custom">
+                <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1">
+                    <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" />
+                </repeat>
                 <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers">
                     <option value="discard" selected="True">Discard</option>
                     <option value="keep_append">Keep and Append</option>
                     <option value="keep_prepend">Keep and Prepend</option>
                 </param>
-                <when value="discard">
-                </when>
-                <when value="keep_append">
-                </when>
-                <when value="keep_prepend">
-                </when>
-            </conditional>
-          </when>
+            </when>
         </conditional>
     </inputs>
     <outputs>
@@ -110,7 +101,7 @@
 
 .. 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>