# HG changeset patch
# User ieguinoa
# Date 1534259989 14400
# Node ID c5dea2080109f5ec3c77bc00a2898284364f2dd8
# Parent  6cd60ba8a842e59a68e093ab74531cf647e06554
Uploaded

diff -r 6cd60ba8a842 -r c5dea2080109 .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Tue Aug 14 11:19:49 2018 -0400
@@ -0,0 +1,19 @@
+categories:
+- Data Managers
+description: Pre-generate indexes for Salmon
+homepage_url: https://github.com/COMBINE-lab/salmon
+long_description: |
+  Salmon is a wicked-fast program to produce a highly-accurate, 
+  transcript-level quantification estimates from RNA-seq data. 
+  Salmon achieves is accuracy and speed via a number of different innovations, 
+  including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), 
+  and massively-parallel stochastic collapsed variational inference. 
+  The result is a versatile tool that fits nicely into many differnt pipelines. 
+  For example, you can choose to make use of our quasi-mapping algorithm by providing 
+  Salmon with raw sequencing reads, or, if it is more convenient, you can provide 
+  Salmon with regular alignments (e.g. an unsorted BAM file produced with your favorite aligner), 
+  and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment.
+name: data_manager_salmon_index_builder
+owner: iuc
+remote_repository_url: https://github.com/ieguinoa/data_manager_salmon_index_builder
+type: unrestricted
diff -r 6cd60ba8a842 -r c5dea2080109 README.md
--- a/README.md	Tue Aug 14 11:14:52 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-# data_manager_fetch_gff
-Galaxy Data Manager to fetch gene annotation files
diff -r 6cd60ba8a842 -r c5dea2080109 data_manager/data_manager_fetch_gff.py
--- a/data_manager/data_manager_fetch_gff.py	Tue Aug 14 11:14:52 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,445 +0,0 @@
-#!/usr/bin/env python
-#Dan Blankenberg
-
-import sys
-import os
-import tempfile
-import shutil
-import optparse
-from ftplib import FTP
-import tarfile
-import zipfile
-import gzip
-import bz2
-try:
-    # For Python 3.0 and later
-    from urllib.request import urlopen
-    from io import BytesIO as StringIO
-    from io import UnsupportedOperation
-except ImportError:
-    # Fall back to Python 2's urllib2
-    from urllib2 import urlopen
-    from StringIO import StringIO
-    UnsupportedOperation = AttributeError
-from json import loads, dumps
-
-
-CHUNK_SIZE = 2**20  # 1mb
-
-DATA_TABLE_NAME = 'all_gff'
-
-def cleanup_before_exit( tmp_dir ):
-    if tmp_dir and os.path.exists( tmp_dir ):
-        shutil.rmtree( tmp_dir )
-
-
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit(1)
-
-
-def get_dbkey_dbname_id_name( params, dbkey_description=None ):
-#    dbkey = params['param_dict']['dbkey_source']['dbkey']
-    #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 #uuid.uuid4() generate and use an uuid instead?
-    
-#    if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new':
-#        dbkey_name = params['param_dict']['dbkey_source']['dbkey_name']
-#        if not dbkey_name:
-#            dbkey_name = dbkey
-#    else:
-#        dbkey_name = None
-    dbkey = params['param_dict']['dbkey'] 
-    dbkey_name = dbkey_description
-    sequence_name = params['param_dict']['sequence_name']
-    if not sequence_name:
-        sequence_name = dbkey_description
-        if not sequence_name:
-            sequence_name = dbkey
-    return dbkey, dbkey_name, sequence_id, sequence_name
-
-
-def _get_files_in_ftp_path( ftp, path ):
-    path_contents = []
-    ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append )
-    return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ]
-
-
-def _get_stream_readers_for_tar( fh, tmp_dir ):
-    fasta_tar = tarfile.open( fileobj=fh, mode='r:*' )
-    return [x for x in [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()] if x]
-
-
-def _get_stream_readers_for_zip( fh, tmp_dir ):
-    """
-    Unpacks all archived files in a zip file.
-    Individual files will be concatenated (in _stream_fasta_to_file)
-    """
-    fasta_zip = zipfile.ZipFile( fh, 'r' )
-    rval = []
-    for member in fasta_zip.namelist():
-        fasta_zip.extract( member, tmp_dir )
-        rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) )
-    return rval
-
-
-def _get_stream_readers_for_gzip( fh, tmp_dir ):
-    return [ gzip.GzipFile( fileobj=fh, mode='rb') ]
-
-
-def _get_stream_readers_for_bz2( fh, tmp_dir ):
-    return [ bz2.BZ2File( fh.name, 'rb') ]
-
-
-def sort_fasta( fasta_filename, sort_method, params ):
-    if sort_method is None:
-        return
-    assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method )
-    return SORTING_METHODS[ sort_method ]( fasta_filename, params )
-
-
-def _move_and_index_fasta_for_sorting( fasta_filename ):
-    unsorted_filename = tempfile.NamedTemporaryFile().name
-    shutil.move( fasta_filename, unsorted_filename )
-    fasta_offsets = {}
-    unsorted_fh = open( unsorted_filename )
-    while True:
-        offset = unsorted_fh.tell()
-        line = unsorted_fh.readline()
-        if not line:
-            break
-        if line.startswith( ">" ):
-            line = line.split( None, 1 )[0][1:]
-            fasta_offsets[ line ] = offset
-    unsorted_fh.close()
-    current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) )
-    return ( unsorted_filename, fasta_offsets, current_order )
-
-
-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+' )
-    
-    for name in sorted_names:
-        offset = fasta_offsets[ name ]
-        unsorted_fh.seek( offset )
-        sorted_fh.write( unsorted_fh.readline() )
-        while True:
-            line = unsorted_fh.readline()
-            if not line or line.startswith( ">" ):
-                break
-            sorted_fh.write( line )
-    unsorted_fh.close()
-    sorted_fh.close()
-
-
-def _sort_fasta_as_is( fasta_filename, params ):
-    return
-
-def _sort_fasta_lexicographical( fasta_filename, params ):
-    ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
-    sorted_names = sorted( fasta_offsets.keys() )
-    if sorted_names == current_order:
-        shutil.move( unsorted_filename, fasta_filename )
-    else:
-        _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )    
-
-
-def _sort_fasta_gatk( fasta_filename, params ):
-    #This method was added by reviewer request.
-    ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
-    sorted_names = map( str, range( 1, 23 ) ) + [ 'X', 'Y' ]
-    #detect if we have chrN, or just N
-    has_chr = False
-    for chrom in sorted_names:
-        if "chr%s" % chrom in current_order:
-            has_chr = True
-            break
-    
-    if has_chr:
-        sorted_names = map( lambda x: "chr%s" % x, sorted_names)
-        sorted_names.insert( 0, "chrM" )
-    else:
-        sorted_names.insert( 0, "MT" )
-    sorted_names.extend( map( lambda x: "%s_random" % x, sorted_names ) )
-    
-    existing_sorted_names = []
-    for name in sorted_names:
-        if name in current_order:
-            existing_sorted_names.append( name )
-    for name in current_order:
-        #TODO: confirm that non-canonical names do not need to be sorted specially
-        if name not in existing_sorted_names:
-            existing_sorted_names.append( name )
-    
-    if existing_sorted_names == current_order:
-        shutil.move( unsorted_filename, fasta_filename )
-    else:
-        _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
-
-
-def _sort_fasta_custom( fasta_filename, params ):
-    ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
-    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_selector']
-    if handle_not_listed.startswith( 'keep' ):
-        add_list = []
-        for name in current_order:
-            if name not in sorted_names:
-                add_list.append( name )
-        if add_list:
-            if handle_not_listed == 'keep_append':
-                sorted_names.extend( add_list )
-            else:
-                add_list.extend( sorted_names )
-                sorted_names = add_list
-    if sorted_names == current_order:
-        shutil.move( unsorted_filename, fasta_filename )
-    else:
-        _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
-
-
-def _download_file(start, fh):
-    tmp = tempfile.NamedTemporaryFile()
-    tmp.write(start)
-    tmp.write(fh.read())
-    tmp.flush()
-    tmp.seek(0)
-    return tmp
-
-
-def get_stream_reader(fh, tmp_dir):
-    """
-    Check if file is compressed and return correct stream reader.
-    If file has to be downloaded, do it now.
-    """
-    magic_dict = {
-        b"\x1f\x8b\x08": _get_stream_readers_for_gzip,
-        b"\x42\x5a\x68": _get_stream_readers_for_bz2,
-        b"\x50\x4b\x03\x04": _get_stream_readers_for_zip,
-    }
-    start_of_file = fh.read(CHUNK_SIZE)
-    try:
-        fh.seek(0)
-    except UnsupportedOperation:  # This is if fh has been created by urlopen
-        fh = _download_file(start_of_file, fh)
-    for k,v in magic_dict.items():
-        if start_of_file.startswith(k):
-            return v(fh, tmp_dir)
-    try:  # Check if file is tar file
-        if tarfile.open(fileobj=StringIO(start_of_file)):
-            return _get_stream_readers_for_tar(fh, tmp_dir)
-    except tarfile.ReadError:
-        pass
-    return fh
-
-
-def _get_ucsc_download_address(params, dbkey):
-    """
-    Check if we can find the correct file for the supplied dbkey on UCSC's FTP server
-    """
-    UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu'
-    UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/'
-    COMPRESSED_EXTENSIONS = ['.tar.gz', '.tgz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2']
-
-    email = params['param_dict']['__user_email__']
-    if not email:
-        email = 'anonymous@example.com'
-
-    ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey
-    UCSC_CHROM_FA_FILENAMES = ['%s.chromFa' % ucsc_dbkey, 'chromFa', ucsc_dbkey]
-
-    ftp = FTP(UCSC_FTP_SERVER)
-    ftp.login('anonymous', email)
-
-    ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey
-    path_contents = _get_files_in_ftp_path(ftp, ucsc_path)
-    ftp.quit()
-
-    for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES:
-        for ext in COMPRESSED_EXTENSIONS:
-            if "%s%s" % (ucsc_chrom_fa_filename, ext) in path_contents:
-                ucsc_file_name = "%s%s%s" % (ucsc_path, ucsc_chrom_fa_filename, ext)
-                return "ftp://%s%s" % (UCSC_FTP_SERVER, ucsc_file_name)
-
-    raise Exception('Unable to determine filename for UCSC Genome for %s: %s' % (ucsc_dbkey, path_contents))
-
-def add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params):
-    for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
-        if data_table_entry:
-            _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
-
-
-def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
-    url = _get_ucsc_download_address(params, dbkey)
-    fasta_readers = get_stream_reader(urlopen(url), tmp_dir)
-    add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
-
-
-def download_from_ncbi( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
-    NCBI_DOWNLOAD_URL = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' #FIXME: taken from dave's genome manager...why some japan site?
-    requested_identifier = params['param_dict']['reference_source']['requested_identifier']
-    url = NCBI_DOWNLOAD_URL % requested_identifier
-    fasta_readers = get_stream_reader(urlopen(url), tmp_dir)
-    add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
-
-
-def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
-    urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
-    fasta_readers = [ get_stream_reader(urlopen( url ), tmp_dir) for url in urls ]
-    add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id,sequence_name, params)
-
-
-def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
-    #TODO: allow multiple FASTA input files
-    input_filename = params['param_dict']['reference_source']['input_fasta']
-    if isinstance( input_filename, list ):
-        fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
-    else:
-        fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
-    add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
-
-
-def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
-    input_filename = params['param_dict']['reference_source']['fasta_filename']
-    create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
-    if create_symlink:
-        data_table_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name )
-    else:
-        if isinstance( input_filename, list ):
-            fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
-        else:
-            fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
-        data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params )
-    for data_table_name, data_table_entry in data_table_entries:
-        if data_table_entry:
-            _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
-
-
-def _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ):
-    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 _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ):
-    fasta_base_filename = "%s.gff" % sequence_id
-    fasta_filename = os.path.join( target_directory, fasta_base_filename )
-    with open( fasta_filename, 'wb+' ) as fasta_writer:
-
-        if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
-            fasta_stream = fasta_stream[0]
-
-        if isinstance( fasta_stream, list ):
-            last_char = None
-            for fh in fasta_stream:
-                if last_char not in [ None, '\n', '\r', b'\n', b'\r' ]:
-                    fasta_writer.write( b'\n' )
-                while True:
-                    data = fh.read( CHUNK_SIZE )
-                    if data:
-                        fasta_writer.write( data )
-                        last_char = data[-1]
-                    else:
-                        break
-                if close_stream:
-                    fh.close()
-        else:
-            while True:
-                data = fasta_stream.read( CHUNK_SIZE )
-                if data:
-                    fasta_writer.write( data )
-                else:
-                    break
-            if close_stream:
-                fasta_stream.close()
-
-    #sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params )
-    
-    
-    return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
-
-
-def compute_fasta_length( fasta_file, out_file, keep_first_word=False ):
-
-    infile = fasta_file
-    out = open( out_file, 'w')
-
-    fasta_title = ''
-    seq_len = 0
-
-    first_entry = True
-
-    for line in open( infile ):
-        line = line.strip()
-        if not line or line.startswith( '#' ):
-            continue
-        if line[0] == '>':
-            if first_entry == False:
-                if keep_first_word:
-                    fasta_title = fasta_title.split()[0]
-                out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
-            else:
-                first_entry = False
-            fasta_title = line
-            seq_len = 0
-        else:
-            seq_len += len(line)
-
-    # last fasta-entry
-    if keep_first_word:
-        fasta_title = fasta_title.split()[0]
-    out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
-    out.close()
-
-
-def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
-    fasta_base_filename = "%s.fa" % sequence_id
-    fasta_filename = os.path.join( target_directory, fasta_base_filename )
-    os.symlink( input_filename, fasta_filename )
-    return [  ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
-
-
-REFERENCE_SOURCE_TO_DOWNLOAD = dict( ucsc=download_from_ucsc, ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )
-
-SORTING_METHODS = dict( as_is=_sort_fasta_as_is, lexicographical=_sort_fasta_lexicographical, gatk=_sort_fasta_gatk, custom=_sort_fasta_custom )
-
-
-def main():
-    #Parse Command Line
-    parser = optparse.OptionParser()
-    parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
-    parser.add_option( '-t', '--type', dest='file_type', action='store', type='string', default=None, help='file_type')
-    (options, args) = parser.parse_args()
-    
-    filename = args[0]
-    global DATA_TABLE_NAME
-    if options.file_type == 'representative':
-       DATA_TABLE_NAME= 'representative_gff'
-    params = loads( open( filename ).read() )
-    target_directory = params[ 'output_data' ][0]['extra_files_path']
-    os.mkdir( target_directory )
-    data_manager_dict = {}
-    
-    dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description ) 
-    
-    if dbkey in [ None, '', '?' ]:
-        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
-
-    # Create a tmp_dir, in case a zip file needs to be uncompressed
-    tmp_dir = tempfile.mkdtemp()
-    #Fetch the FASTA
-    try:
-        REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir )
-    finally:
-        cleanup_before_exit(tmp_dir)
-    #save info to json file
-    open( filename, 'wb' ).write( dumps( data_manager_dict ).encode() )
-        
-if __name__ == "__main__":
-    main()
diff -r 6cd60ba8a842 -r c5dea2080109 data_manager/data_manager_fetch_gff.xml
--- a/data_manager/data_manager_fetch_gff.xml	Tue Aug 14 11:14:52 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-<tool id="data_manager_fetch_gff" name="Create entries in gff data table" version="0.0.1" tool_type="manage_data">
-    <description>fetching</description>
-    <command><![CDATA[
-       python "$__tool_directory__"/data_manager_fetch_gff.py "${out_file}"
-       --type $file_type
-       --dbkey_description ${ dbkey.get_display_text() }
-        
-    ]]></command>
-    <inputs>
-         <param name="file_type" type="select" label="GFF file with only one representative transcript per gene (for htseq-count use) or full features file">
-                <option value="representative">Representative GFF</option>
-                <option value="full">GFF with complete features</option>
-            </param>
- 
-        <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
-        <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="url">URL</option>
-                <option value="history">History</option>
-                <option value="directory">Directory on Server</option>
-            </param>
-            <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>
-    </inputs>
-    <outputs>
-        <data name="out_file" format="data_manager_json"/>
-    </outputs>
-    <tests>
-        <!-- TODO: need some way to test that new entry was added to data table -->
-        <test>
-            <param name="dbkey" value="anoGam1"/>
-            <param name="sequence_name" value=""/>
-            <param name="sequence_desc" value=""/>
-            <param name="sequence_id" value=""/>
-            <param name="reference_source_selector" value="history"/>
-            <param name="input_fasta" value="phiX174.fasta"/>
-            <param name="sort_selector" value="as_is"/>
-            <output name="out_file" file="phiX174.data_manager_json"/>
-        </test>
-    </tests>
-    <help>
-**What it does**
-
-Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table.
-
-------
-
-
-
-.. class:: infomark
-
-**Notice:** If you leave name, description, or id blank, it will be generated automatically.
-
-    </help>
-</tool>
diff -r 6cd60ba8a842 -r c5dea2080109 data_manager/salmon_index_builder.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/salmon_index_builder.py	Tue Aug 14 11:19:49 2018 -0400
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+# Based heavily on the kallisto data manager wrapper script by iuc
+from __future__ import print_function
+
+import argparse
+import os
+import subprocess
+import sys
+from json import dumps, loads
+
+DEFAULT_DATA_TABLE_NAME = "salmon_indexes"
+
+
+def get_id_name( params, dbkey, fasta_description=None):
+    # 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_salmon_index( data_manager_dict, options, params, sequence_id, sequence_name ):
+    data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    if not os.path.exists( target_directory ):
+        os.mkdir( target_directory )
+    if options.kmer_size != '':
+        args.append('-k')
+        args.append(options.kmer_size)
+    args.extend( [ '-t' , options.fasta_filename, '-i', sequence_id ] )
+    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
+    return_code = proc.wait()
+    if return_code:
+        print("Error building index.", file=sys.stderr)
+        sys.exit( return_code )
+    data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id )
+    _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 = argparse.ArgumentParser()
+    parser.add_argument( '--output', dest='output', action='store', type=str, default=None )
+    parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None )
+    parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None )
+    parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None )
+    parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='salmon_indexes' )
+    parser.add_argument( '-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size' )
+    options = parser.parse_args()
+
+    filename = options.output
+
+    params = loads( open( filename ).read() )
+    data_manager_dict = {}
+
+    if options.fasta_dbkey in [ None, '', '?' ]:
+        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )
+
+    sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )
+
+    # build the index
+    build_salmon_index( data_manager_dict, options, params, sequence_id, sequence_name )
+
+    # save info to json file
+    open( filename, 'w' ).write( dumps( data_manager_dict ) )
+
+
+if __name__ == "__main__":
+    main()
diff -r 6cd60ba8a842 -r c5dea2080109 data_manager/salmon_index_builder.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/salmon_index_builder.xml	Tue Aug 14 11:19:49 2018 -0400
@@ -0,0 +1,38 @@
+<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.9.1">
+    <description>index builder</description>
+    <requirements>
+        <requirement type="package" version="0.9.1">salmon</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}'
+            --fasta_filename '${all_fasta_source.fields.path}'
+            --fasta_dbkey '${all_fasta_source.fields.dbkey}'
+            --fasta_description '${all_fasta_source.fields.name}'
+            --kmer_size "${kmer_size}"
+            --data_table_name salmon_indexes
+        ]]>
+    </command>
+    <inputs>
+        <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
+            <options from_data_table="all_fasta" />
+        </param>
+        <param name="sequence_name" type="text" value="" label="Name of sequence" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" />
+        <param name="kmer_size" type="integer" optional='true' value="21" max="32" label="The size of the k-mer on which the index is built"
+                    help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be.  We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE "/>
+
+
+
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <help>
+<![CDATA[
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+]]>
+    </help>
+</tool>
+
diff -r 6cd60ba8a842 -r c5dea2080109 data_manager_conf.xml
--- a/data_manager_conf.xml	Tue Aug 14 11:14:52 2018 -0400
+++ b/data_manager_conf.xml	Tue Aug 14 11:19:49 2018 -0400
@@ -1,32 +1,17 @@
 <?xml version="1.0"?>
 <data_managers>
-<data_manager tool_file="data_manager/data_manager_fetch_gff.xml" id="data_manager_fetch_gff">
-      <data_table name="all_gff">
+    <data_manager tool_file="data_manager/salmon_index_builder.xml" id="salmon_index_builder" version="0.1">
+        <data_table name="salmon_indexes">
             <output>
                 <column name="value" />
                 <column name="dbkey" />
                 <column name="name" />
-                <column name="path" output_ref="out_file">
-                    <move type="file">
-                        <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gff/${path}</target>
+                <column name="path" output_ref="out_file" >
+                    <move type="directory" relativize_symlinks="True">
+                        <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/salmon_index/${value}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/gff/${path}</value_translation>
-                    <value_translation type="function">abspath</value_translation>
-                </column>
-            </output>
-        </data_table>
-     <data_table name="representative_gff">
-            <output>
-                <column name="value" />
-                <column name="dbkey" />
-                <column name="name" />
-                <column name="path" output_ref="out_file">
-                    <move type="file">
-                        <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/representative_gff/${path}</target>
-                    </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/representative_gff/${path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/salmon_index/${value}/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
diff -r 6cd60ba8a842 -r c5dea2080109 tool-data/all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Tue Aug 14 11:19:49 2018 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 6cd60ba8a842 -r c5dea2080109 tool-data/all_gff.loc.sample
--- a/tool-data/all_gff.loc.sample	Tue Aug 14 11:14:52 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#The all_gff.loc file has this format:
-#
-#<unique_build_id>	<dbkey>	<display_name>	<path_to_gff_file>
diff -r 6cd60ba8a842 -r c5dea2080109 tool-data/representative_gff.loc.sample
--- a/tool-data/representative_gff.loc.sample	Tue Aug 14 11:14:52 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#The representative_gff.loc file has this format:
-#
-#<unique_build_id>	<dbkey>	<display_name>	<path_to_gff_file>
diff -r 6cd60ba8a842 -r c5dea2080109 tool-data/salmon_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/salmon_indexes.loc.sample	Tue Aug 14 11:19:49 2018 -0400
@@ -0,0 +1,28 @@
+# salmon_indexes.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Salmon.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a kallisto_indexes.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample), 
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+# So, for example, if you had sacCer3 indexes stored in:
+#
+#    /depot/data2/galaxy/sacCer3/salmon_indexes/
+#
+# then the salmon_indexes.loc entry could look like this:
+#
+#sacCer3	sacCer3	S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)	/depot/data2/galaxy/sacCer3/salmon_indexes
+#
+#More examples:
+#
+#mm10	mm10	Mouse (mm10)	/depot/data2/galaxy/salmon_indexes/mm10
+#dm3	dm3		D. melanogaster (dm3)	/depot/data2/galaxy/salmon_indexes/dm3
+#
+#
diff -r 6cd60ba8a842 -r c5dea2080109 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Tue Aug 14 11:14:52 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Aug 14 11:19:49 2018 -0400
@@ -1,5 +1,12 @@
-<?xml version="1.0"?>
 <tables>
-	<table name="all_gff" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/all_gff.loc" /> </table>
-	<table name="representative_gff" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/representative_gff.loc" /> </table>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of indexes in the kallisto mapper format -->
+    <table name="salmon_indexes" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/salmon_indexes.loc" />
+    </table>
 </tables>