Mercurial > repos > greg > phylogenomics_analysis

--- a/macros.xml	Mon Mar 27 09:57:54 2017 -0400
+++ b/macros.xml	Mon Mar 27 10:42:37 2017 -0400
@@ -346,6 +346,26 @@
             <option value="yes">Yes</option>
         </param>
     </xml>
+    <xml name="output_ptortho">
+        <data name="output_ptortho" format="ptortho">
+            <filter>input_format_cond['input_format'] == 'ptortho'</filter>
+        </data>
+    </xml>
+    <xml name="output_ptorthocs">
+        <data name="output_ptorthocs" format="ptorthocs">
+            <filter>input_format_cond['input_format'] == 'ptorthocs'</filter>
+        </data>
+    </xml>
+    <xml name="output_aln">
+        <data name="output_aln" format="ptalign" label="${tool.name} on ${on_string} (multiple alignments)">
+            <filter>input_format_cond['options_type_cond']['options_type'] == 'advanced' and ((input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes and input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes') or (input_format_cond['options_type_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes and input_format_cond['options_type_cond']['remove_sequences_with_gaps_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'))</filter>
+        </data>
+    </xml>
+    <xml name="output_tree">
+        <data name="output_tree" format="pttree" label="${tool.name} on ${on_string} (phylogenetic trees)">
+            <filter>input_format_cond['options_type_cond']['options_type'] == 'advanced' and input_format_cond['options_type_cond']['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
+        </data>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="bibtex">
--- a/phylogenomics_analysis.py	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,187 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import os
-import shutil
-import subprocess
-import sys
-import tempfile
-
-BUFF_SIZE = 1048576
-OUTPUT_DIR = 'phylogenomicsAnalysis_dir'
-
-parser = argparse.ArgumentParser()
-
-parser.add_argument('--alignments_method', dest='alignments_method', default=None, help='Multiple sequence alignments method')
-parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis')
-parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help="Flag for constructing orthogroup multiple codon alignments")
-parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files')
-parser.add_argument('--gap_trimming', dest='gap_trimming', default=None, type=float, help='Remove sites in alignments with gaps of')
-parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, default=None, help='Maximum number of sequences in orthogroup alignments')
-parser.add_argument('--method', dest='method', help='Protein clustering method')
-parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, default=None, help='Minimum number of sequences in orthogroup alignments')
-parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
-parser.add_argument('--output_aln', dest='output_aln', default=None, help='Output for orthogroups alignments')
-parser.add_argument('--output_aln_dir', dest='output_aln_dir', default=None, help='output_aln.files_path')
-parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Input dataset files_path")
-parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help="Flag for coding sequences associated with orthogroups")
-parser.add_argument('--output_ptortho', dest='output_ptortho', default=None, help='Output for orthogroups')
-parser.add_argument('--output_ptorthocs', dest='output_ptorthocs', default=None, help='Output for orthogroups with corresponding coding sequences')
-parser.add_argument('--output_ptorthocs_dir', dest='output_ptorthocs_dir', default=None, help='output_ptorthocs.files_path')
-parser.add_argument('--output_ptortho_dir', dest='output_ptortho_dir', default=None, help='output_ptortho.files_path')
-parser.add_argument('--output_tree', dest='output_tree', default=None, help='Output for phylogenetic trees')
-parser.add_argument('--output_tree_dir', dest='output_tree_dir', default=None, help='output_tree.files_path')
-parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='"Maximum number of iteration that the PASTA algorithm will execute')
-parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta')
-parser.add_argument('--remove_sequences', dest='remove_sequences', default=None, type=float, help='Remove sequences with gaps of')
-parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees')
-parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold')
-parser.add_argument('--sequence_type', dest='sequence_type', default=None, help="Sequence type used in the phylogenetic inference")
-parser.add_argument('--tree_inference', dest='tree_inference', default=None, help='Phylogenetic trees inference method')
-parser.add_argument('--trim_type', dest='trim_type', default=None, help='Process used for gap trimming')
-
-args = parser.parse_args()
-
-
-def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False):
-    tmp_stderr.close()
-    # Get stderr, allowing for case where it's very large.
-    tmp_stderr = open(tmp_err, 'rb')
-    stderr_str = ''
-    buffsize = BUFF_SIZE
-    try:
-        while True:
-            stderr_str += tmp_stderr.read(buffsize)
-            if not stderr_str or len(stderr_str) % buffsize != 0:
-                break
-    except OverflowError:
-        pass
-    tmp_stderr.close()
-    if include_stdout:
-        tmp_stdout = open(tmp_out, 'rb')
-        stdout_str = ''
-        buffsize = BUFF_SIZE
-        try:
-            while True:
-                stdout_str += tmp_stdout.read(buffsize)
-                if not stdout_str or len(stdout_str) % buffsize != 0:
-                    break
-        except OverflowError:
-            pass
-    tmp_stdout.close()
-    if include_stdout:
-        return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str)
-    return stderr_str
-
-
-def move_directory_files(source_dir, destination_dir):
-    source_directory = os.path.abspath(source_dir)
-    destination_directory = os.path.abspath(destination_dir)
-    if not os.path.isdir(destination_directory):
-        os.makedirs(destination_directory)
-    for dir_entry in os.listdir(source_directory):
-        source_entry = os.path.join(source_directory, dir_entry)
-        shutil.move(source_entry, destination_directory)
-
-
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit(1)
-
-
-def write_html_output(output, title, dir):
-    with open(output, 'w') as fh:
-        fh.write('<html><head><h3>%s</h3></head>\n' % title)
-        fh.write('<body><p/><table cellpadding="2">\n')
-        fh.write('<tr><th>Size</th><th>Name</th></tr>\n')
-        for index, fname in enumerate(sorted(os.listdir(dir))):
-            if index % 2 == 0:
-                bgcolor = '#D8D8D8'
-            else:
-                bgcolor = '#FFFFFF'
-            try:
-                size = str(os.path.getsize(os.path.join(dir, fname)))
-            except:
-                size = 'unknown'
-            link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname)
-            fh.write('<tr bgcolor="%s"><td>%s</td><td>%s</td></tr>\n' % (bgcolor, size, link))
-        fh.write('</table></body></html>\n')
-
-
-# Define command response buffers.
-tmp_out = tempfile.NamedTemporaryFile().name
-tmp_stdout = open(tmp_out, 'wb')
-tmp_err = tempfile.NamedTemporaryFile().name
-tmp_stderr = open(tmp_err, 'wb')
-# Build the command line.
-cmd = 'PhylogenomicsAnalysis'
-cmd += ' --orthogroup_faa %s' % args.orthogroup_faa
-cmd += ' --scaffold %s' % args.scaffold
-cmd += ' --method %s' % args.method
-cmd += ' --config_dir %s' % args.config_dir
-cmd += ' --num_threads %d' % args.num_threads
-
-if args.codon_alignments is not None:
-    cmd += ' --codon_alignments'
-if args.orthogroup_fna is not None:
-    cmd += ' --orthogroup_fna'
-if args.sequence_type is not None:
-    cmd += ' --sequence_type %s' % args.sequence_type
-if args.alignments_method is not None:
-    if args.alignments_method == 'create_alignments':
-        cmd += ' --create_alignments'
-    elif args.alignments_method == 'add_alignments':
-        cmd += ' --add_alignments'
-    elif args.alignments_method == 'pasta_alignments':
-        cmd += ' --pasta_alignments'
-        cmd += ' --pasta_script_path %s' % args.pasta_script_path
-        cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit
-if args.tree_inference is not None:
-    cmd += ' --tree_inference %s' % args.tree_inference
-    if args.tree_inference == 'raxml':
-        if args.rooting_order is not None:
-            cmd += ' --rooting_order %s' % args.rooting_order
-        cmd += ' --bootstrap_replicates %d' % args.bootstrap_replicates
-if args.max_orthogroup_size is not None:
-    cmd += ' --max_orthogroup_size %d' % args.max_orthogroup_size
-if args.min_orthogroup_size is not None:
-    cmd += ' --min_orthogroup_size %d' % args.min_orthogroup_size
-if args.remove_sequences is not None:
-    cmd += ' --remove_sequences %4f' % args.remove_sequences
-if args.trim_type is not None:
-    if args.trim_type == 'automated_trimming':
-        cmd += ' --automated_trimming'
-    else:
-        cmd += ' --gap_trimming %4f' % args.gap_trimming
-# Run the command.
-proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True)
-rc = proc.wait()
-# Handle execution errors.
-if rc != 0:
-    error_message = get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout)
-    stop_err( error_message )
-# Handle phylogenies for orthogroups outputs.
-if args.orthogroup_fna is not None:
-    out_file = args.output_ptorthocs
-    orthogroups_dest_dir = args.output_ptorthocs_dir
-    title = 'Phylogenies files for orthogroups and corresponding coding sequences'
-else:
-    out_file = args.output_ptortho
-    orthogroups_dest_dir = args.output_ptortho_dir
-    title = 'Phylogenies files for orthogroups'
-orthogroups_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
-move_directory_files(orthogroups_src_dir, orthogroups_dest_dir)
-write_html_output(out_file, title, orthogroups_dest_dir)
-# Handle multiple sequences alignments for orthogroups outputs.
-if args.output_aln is not None:
-    alignments_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln')
-    alignments_dest_dir = args.output_aln_dir
-    title = 'Multiple sequence alignments files for orthogroups'
-    move_directory_files(alignments_src_dir, alignments_dest_dir)
-    write_html_output(args.output_aln, title, alignments_dest_dir)
-# Handle phylogenies for orthogroups outputs.
-if args.output_tree is not None:
-    trees_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_tree')
-    trees_dest_dir = args.output_tree_dir
-    title = 'Phylogenetic tree files for orthogroups'
-    move_directory_files(trees_src_dir, trees_dest_dir)
-    write_html_output(args.output_tree, title, trees_dest_dir)
--- a/phylogenomics_analysis.xml	Mon Mar 27 09:57:54 2017 -0400
+++ b/phylogenomics_analysis.xml	Mon Mar 27 10:42:37 2017 -0400
@@ -143,18 +143,10 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output_ptortho" format="ptortho">
-            <filter>input_format_cond['input_format'] == 'ptortho'</filter>
-        </data>
-        <data name="output_ptorthocs" format="ptorthocs">
-            <filter>input_format_cond['input_format'] == 'ptorthocs'</filter>
-        </data>
-        <data name="output_aln" format="ptalign" label="Multiple alignments (method ${options_type_cond['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']}) on ${on_string}">
-            <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
-        </data>
-        <data name="output_tree" format="pttree" label="Phylogenetic trees on ${on_string}">
-            <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
-        </data>
+        <expand macro="output_ptortho" />
+        <expand macro="output_ptorthocs" />
+        <expand macro="output_aln" />
+        <expand macro="output_tree" />
     </outputs>
     <tests>
         <test>
--- a/plant_tribes_scaffolds.loc.sample	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-## Plant Tribes scaffolds
-#Value	Name	Path	Description
-#22Gv1.0	22Gv1.0	/plant_tribes/scaffolds/22Gv1.0	22 plant genomes (Angiosperms clusters, version 1.0; 22Gv1.0)
-#22Gv1.1	22Gv1.1	/plant_tribes/scaffolds/22Gv1.1	22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1)
--- a/rooting_order.config	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-###########################################################################
-## Configuration File for Rooting RAxML Phylogenetic Trees               ##
-## Requirements:                                                         ##
-## A list of string fragments matching sequences identifiers of species  ##
-## in the classification (including scaffold taxa) to be used for        ##
-## determining the most basal taxa in the orthogroups for rooting trees. ##
-## Should be listed in decreasing order from older to younger lineages.  ##
-## If the file is not provided using the "--rooting_order" option, trees ##
-## will be rooted using the oldest lineage scaffold tax0n present in     ##
-## each orthogroup.                                                      ##
-###########################################################################
-## Author: Eric Wafula                                                   ##
-## Email: ekw10@psu.edu                                                  ##
-## Institution: Penn State University, Bio Dept, Claude dePamphilis Lab  ##
-## Date: 01-31-2015                                                      ##
-###########################################################################
-
-[DEFAULT TAXA]
-
-###########################################################################
-## Out Groups                                                            ##
-###########################################################################
-#
-Physcomitrella patens=Phypa
-Selaginella moellendorffii=Selmo
-#
-###########################################################################
-## Basal Angiosperm                                                      ##
-###########################################################################
-#
-Amborella trichopoda=Ambtr
-#
-###########################################################################
-## Monocots                                                              ##
-###########################################################################
-#
-Phoenix dactylifera=Phoda
-Musa acuminata=Musac
-Sorghum bicolor=Sorbi
-Brachypodium distachyon=Bradi
-Oryza sativa=Orysa
-#
-###########################################################################
-## Basal Eudicots                                                        ##
-###########################################################################
-#
-Aquilegia coerulea=Aquco
-Nelumbo nucifera=Nelnu
-#
-###########################################################################
-## Asterids                                                              ##
-###########################################################################
-#
-Mimulus guttatus=Mimgu
-Solanum tuberosum=Soltu
-Solanum lycopersicum=Solly
-#
-###########################################################################
-## Rosids                                                                ##
-###########################################################################
-#
-Vitis vinifera=Vitvi
-Medicago truncatula=Medtr
-Glycine max=Glyma
-Fragaria vesca=Frave
-Populus trichocarpa=Poptr
-Theobroma cacao=Theca
-Carica papaya=Carpa
-Thellungiella parvula=Thepa
-Arabidopsis thaliana=Arath
-#
-###########################################################################
-
-
-
-
-
-
-
-
--- a/run_pasta.py	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-#! /usr/bin/env python
-
-"""Main script of PASTA in command-line mode - this simply invokes the main
-    function found in pasta/mainpasta.py
-"""
-
-# This file is part of PASTA which is forked from SATe
-
-# PASTA like SATe is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-# Jiaye Yu and Mark Holder, University of Kansas
-
-if __name__ == "__main__":
-    import os
-    import sys
-    from pasta.mainpasta import pasta_main
-    from pasta import MESSENGER
-    sys.setrecursionlimit(100000)
-    _PASTA_DEBUG = os.environ.get('PASTA_DEBUG')
-    _DEVELOPER = _PASTA_DEBUG and _PASTA_DEBUG != '0'
-
-    if not _DEVELOPER:
-        _PASTA_DEVELOPER = os.environ.get('PASTA_DEVELOPER')
-        _DEVELOPER = _PASTA_DEVELOPER and _PASTA_DEVELOPER != '0'
-    try:
-        rc, temp_dir, temp_fs = pasta_main()
-        if not rc:
-            raise ValueError("Unknown PASTA execution error")
-        if (temp_dir is not None) and (os.path.exists(temp_dir)):
-            MESSENGER.send_info("Note that temporary files from the run have not been deleted, they can be found in:\n   '%s'\n" % temp_dir)
-            if sys.platform.lower().startswith('darwin') and ("'" not in temp_dir):
-                MESSENGER.send_info('''
-If you cannot see this directory in the Finder application, you may want to use
-the 'open' command executed from a Terminal.  You can do this by launching the
-/Applications/Utilities/Terminal program and then typing
-
-open '%s'
-
-followed by a return at the prompt. If the argument to the open command is a
-directory, then it should open a Finder window in the directory (even if that
-directory is hidden by default).
-''' % temp_dir)
-    except Exception, x:
-        if _DEVELOPER:
-            raise
-        message = "PASTA is exiting because of an error:\n%s " % str(x)
-        try:
-            from pasta import MESSENGER
-            MESSENGER.send_error(message)
-        except:
-            sys.stderr.write(message)
-        sys.exit(1)
--- a/test-data/assembly.fasta	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
->contig_1
-CGATTAACCATGTGTACAACATGACCAATTATGGCCGATCTTGCTTGTTCAGGAGTCTCA
-CTCATCATTCCAAAATCAAGAAAAGCAAGCTTCCCGTCAGGTGTAGCTAAGAGATTCCCT
-GGGTGAGGATCTGCATGAAAATAGCCGTACTCAAGCAGCTGTCGAAGACTGCACTGTATG
-CCGGTATTCACCAGATCCAGAACACTGAGCCCTTGACTCTCAACGGCATCTTGCTCATTT
-AATTTAACACCTTCAACCCACTCCATTGTTAGCACCTTTCCACTCGTGTAATCCCAGAAA
-ATATCTGGGACAAGGATATCTTCCTTGTCTCCATATAATTTTTTAA
->contig_2
-CCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCC
-GGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCAT
-ACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCC
-CGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATG
-GGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCC
-GATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTAC
-AACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTG
-TACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACA
-ACTGTTAAATTATGTGCGCTTTGATGATTAAAAACACGGGGTAATTGAACTCAAGGGATG
-GTTGAGAATTGTAATATTTCTGTAAGTGTCGGGGGATGGTTGAAATGCTTTTTATTATGA
-AGTGTTAAAATGTAAGATAAA
->contig_3
-CGGGGGCAAGGTTTACATGAAAGTACATCTACAGGACCTAGATAAGCATCATCACCTGAC
-AAAAAGCCATACATAGTAACACTTGCTAGTTGATCTGTGAAAATGGTGCACGAGTCGTAA
-CAGACGGCATTAGTTCCTTTCCTGTAACAGCAGATTCGTATGAATGGTTTTCTCGAAATT
-CTTCTTCAAGTGCATCTATAGGCATGGCACGAAGTGACTCTATTGTGCCTTTGCTGGGAA
-TATCCGGCTCGCTCCTAACTGGCGTGGACCCTGTAGGCTCGTAATCCATGTATTTTTGCC
-TGAAAGTATCATTCGTGTGCTGTTCGATACAGGATACCTGCTGGGAATGATCTCTCTTAA
-GGTTCTCAATTGTTTCTGAATGAGCTCTAGCAGTTGTCAGAATTTCAGAAACAGATGCCT
-TCTCCTGCTCTGACAAGCCAGCAACAACAACTCCTTCATCCACA
->contig_4
-CTGACGATGTTCATATTCATGCCACTCTAAATGTATGCCATCCATGTTGAGGAGAAATGC
-TTGTGTAAAGAAGAAACTGGAGTCAAGCGGTCCCGGTTTTACAGTTGAACGTTGCTCTAA
-ATTAGTCAAAGTACCCGACTACCCGCTCATCAAACTGGCGAGCTCGTTTTCCTCGCCGCC
-CTACTCGGTGTCTTGGCGGGGCACATGGGGGTGGCGTGTGGCGTGCGGGGATGCGACAAC
-ATCATAAATTCATAATCGAAGG
->contig_5
-GTGAGAGTGTCGCCTTTTCCATGCTACCCCTTTCCAGATCTGACTTGTTCGAACCTTCCA
-TCATCCGGTTCGACGTCAGCAGTCGGTCCTTCTTCTCCAAGCACGAGAGCAGACGGTGCG
-AGAGCGAGCAAAGACTCGCCTGCCGCGCCTCTCGTGACCTGGCTCGCATCTCCAGGATTC
-ATGGCTCCTTAGCTCGCCCTTCTTCGATACTTCGCTAGACGCCCGAGGACGTCATCGAAG
-GCGAGGGTCGGCACAACGGAGTGCTCCTTGCATGATGTCGGGGCCTGGCATCACGCGGCA
-TCGGCCAAATCGTCCCTCTCGACGTGCGTCACGGAGAGGGCCGAGCGCCGGGACGACCGC
-GTGGAAGAGCCCGCGGGATGCGGGATCCCGCTTGACGTGTGTTTGTGGCGGACCACCG
->contig_6
-TATAACAATTCAAAATATTCCTATGAAAACCAAGACCAGAGGCAACACCGGTATAACCAA
-AGCCAGAGGCAATATCCCTTTATTCTTCGGGAACAGAAAAATACACGATATGCTACAGAC
-AAAAAAATAAATCCAAACCATTCTTCTGTGCATAAACATTGTAAAAGTTTATTAGACCGC
-TGTAAAACTCGTAAATGAAATCCCTGGCAATTGAATCTGTTAAACCTGCTCC
->contig_7
-GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAAT
-AAATCCAATGAAAACGGAACCGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATG
-TTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCATCATCCAATGAAACATGTAGC
-AACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGCG
-AAACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACG
->contig_8
-TGGCATGAAGTCGGCTCGACTCGTGCCCGCTCGTCTATAGACGAATTGAGCTAGATTCAC
-TCATTCCATGAACTCGACTCGTTCATGAGTCGGCTCGTAGTTGTCCGGACTCGCTCCATG
-GCCAGCTCTACAACAGACTGCCTGTATGTAGATGATTGTATTGATTTGTTCTTCTCTTGT
-TTAAATCCAACCAAATATCAACATGATATTTGCAATTTC
->contig_9
-ACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTT
-TGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCC
-TGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAG
-AATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAAC
-AGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAA
-ACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGC
-ACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGA
->contig_10
-GGGGCATTGCCGCCGATTAATTCGAGCGCGAGGTTTCGCGTATCAGGCGGAATTGGGATT
-TGGCGCCACAAAGAGCGCCACCTATGATTTCTGTGGCGGACGACTTCACGAACTCGGACG
-GGACTATCTAACCAATCTTCCAAGTTCATTGCGACATCAGTATAAGGGCGTGATGAAGGT
-TCGCTATCGTCGCTTGAGTTATTGATGGGGCCCAAATTGAGATCGAGGTTCATTGTAGTG
-GTGTTCTCTTCTGCCATTTGAGAATTTCACAAGTTCTAACAAACGAAAACGCAAATCTTC
-GGGACTAATATGCAGAATTTCCCTAAATAGAAGGGGTTTAAAA
--- a/test-data/targetOrthos.ids	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-213
-9300
-752
-4632
-4732
--- a/test-data/transcripts.cds	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->contig_2|m.1 contig_2|g.1 type:5prime_partial len:170 contig_2:2-511(+)
-CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAATTATGTGCGCTTTGATGATTAA
->contig_9|m.2 contig_9|g.2 type:internal len:132 contig_9:2-394(+)
-CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT
--- a/test-data/transcripts.cleaned.cds	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
->contig_2
-CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTA
-CGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCA
-TGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGG
-GTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGA
-GATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGG
-GTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAA
-CTGTTAAATTATGTGCGCTTTGATGAT
->contig_9
-CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGT
-GGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAA
-AACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACA
-GCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGA
-ACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT
--- a/test-data/transcripts.cleaned.nr.cds	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
->contig_2
-CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTA
-CGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCA
-TGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGG
-GTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGA
-GATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGG
-GTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAA
-CTGTTAAATTATGTGCGCTTTGATGAT
->contig_9
-CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGT
-GGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAA
-AACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACA
-GCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGA
-ACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT
--- a/test-data/transcripts.cleaned.nr.pep	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
->contig_2
-LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKW
-VTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQ
-LLNYVRFDD
->contig_9
-LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRT
-AHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV
--- a/test-data/transcripts.cleaned.pep	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
->contig_2
-LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKW
-VTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQ
-LLNYVRFDD
->contig_9
-LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRT
-AHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV
--- a/test-data/transcripts.pep	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->contig_2|m.1 contig_2|g.1 type:5prime_partial len:170 gc:universal contig_2:2-511(+)
-LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD*
->contig_9|m.2 contig_9|g.2 type:internal len:132 gc:universal contig_9:2-394(+)
-LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV
--- a/tool_data_table_conf.xml.sample	Mon Mar 27 09:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<tables>
-    <table name="plant_tribes_scaffolds" comment_char="#">
-        <columns>value, name, path, description</columns>
-        <file path="tool-data/plant_tribes_scaffolds.loc" />
-    </table>
-</tables>