Mercurial > repos > peterjc > seq_filter_by_id
changeset 17:4ae973da053b draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/seq_filter_by_id commit e1865520ff51c7af112dd91af5a0a84cd9fcbdbd
| author | peterjc |
|---|---|
| date | Wed, 13 May 2015 11:01:30 -0400 |
| parents | b5967bd17660 |
| children | 61d381ab8805 |
| files | tools/seq_filter_by_id/README.rst tools/seq_filter_by_id/seq_filter_by_id.py tools/seq_filter_by_id/seq_filter_by_id.py.orig tools/seq_filter_by_id/seq_filter_by_id.py.rej tools/seq_filter_by_id/seq_filter_by_id.xml |
| diffstat | 5 files changed, 49 insertions(+), 464 deletions(-) [+] |
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--- a/tools/seq_filter_by_id/README.rst Thu Nov 27 08:41:36 2014 -0500 +++ b/tools/seq_filter_by_id/README.rst Wed May 13 11:01:30 2015 -0400 @@ -1,7 +1,7 @@ Galaxy tool to filter FASTA, FASTQ or SFF sequences by ID ========================================================= -This tool is copyright 2010-2014 by Peter Cock, The James Hutton Institute +This tool is copyright 2010-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -75,7 +75,7 @@ v0.0.7 - Correct automated dependency definition. v0.0.8 - Simplified XML to apply input format to output data. v0.2.0 - Can supply ID list as a text parameter (instead of in a file) - - Using optparse for command line API. + - Using ``optparse`` for the Python command line API. - Advanced option to ignore paired read suffices. - Updated dependencies to use Biopython 1.64. v0.2.1 - Use Biopython instead of Galaxy for FASTQ handling. @@ -83,6 +83,9 @@ - Include input dataset name in output dataset names. - If white space is found in the requested tabular field then only the first word is used as the identifier (with a warning to stderr). +v0.2.2 - Use the ``format_source=...`` tag. + - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== @@ -96,26 +99,35 @@ Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: + + $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ + ... + +or:: + + $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ + ... - $ tar -czf seq_filter_by_id.tar.gz tools/seq_filter_by_id/README.rst tools/seq_filter_by_id/seq_filter_by_id.* tools/seq_filter_by_id/tool_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical_alt.tabular test-data/k12_hypothetical.tabular test-data/sanger-pairs-mixed.fastq test-data/sanger-pairs-names.tabular test-data/sanger-sample.fastq test-data/empty_file.dat +To just build and check the tar ball, use:: -Check this worked:: - - $ tar -tzf seq_filter_by_id.tar.gz + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/empty_file.dat + test-data/k12_hypothetical.fasta + test-data/k12_hypothetical.tabular + test-data/k12_hypothetical_alt.tabular + test-data/k12_ten_proteins.fasta + test-data/sanger-pairs-mixed.fastq + test-data/sanger-pairs-names.tabular + test-data/sanger-sample.fastq tools/seq_filter_by_id/README.rst tools/seq_filter_by_id/seq_filter_by_id.py tools/seq_filter_by_id/seq_filter_by_id.xml tools/seq_filter_by_id/tool_dependencies.xml - test-data/k12_ten_proteins.fasta - test-data/k12_hypothetical.fasta - test-data/k12_hypothetical.tabular - test-data/k12_hypothetical_alt.tabular - test-data/sanger-pairs-mixed.fastq - test-data/sanger-pairs-names.tabular - test-data/sanger-sample.fastq - test-data/empty_file.dat Licence (MIT)
--- a/tools/seq_filter_by_id/seq_filter_by_id.py Thu Nov 27 08:41:36 2014 -0500 +++ b/tools/seq_filter_by_id/seq_filter_by_id.py Wed May 13 11:01:30 2015 -0400 @@ -32,7 +32,7 @@ import re from optparse import OptionParser -def stop_err(msg, err=1): +def sys_exit(msg, err=1): sys.stderr.write(msg.rstrip() + "\n") sys.exit(err) @@ -89,19 +89,19 @@ drop_suffices = bool(options.suffix) if in_file is None or not os.path.isfile(in_file): - stop_err("Missing input file: %r" % in_file) + sys_exit("Missing input file: %r" % in_file) if out_positive_file is None and out_negative_file is None: - stop_err("Neither output file requested") + sys_exit("Neither output file requested") if seq_format is None: - stop_err("Missing sequence format") + sys_exit("Missing sequence format") if logic not in ["UNION", "INTERSECTION"]: - stop_err("Logic agrument should be 'UNION' or 'INTERSECTION', not %r" % logic) + sys_exit("Logic agrument should be 'UNION' or 'INTERSECTION', not %r" % logic) if options.id_list and args: - stop_err("Cannot accepted IDs via both -t and as tabular files") + sys_exit("Cannot accepted IDs via both -t and as tabular files") elif not options.id_list and not args: - stop_err("Expected matched pairs of tabular files and columns (or -t given)") + sys_exit("Expected matched pairs of tabular files and columns (or -t given)") if len(args) % 2: - stop_err("Expected matched pairs of tabular files and columns, not: %r" % args) + sys_exit("Expected matched pairs of tabular files and columns, not: %r" % args) #Cope with three widely used suffix naming convensions, @@ -128,13 +128,13 @@ tabular_file = args[2*i] cols_arg = args[2*i + 1] if not os.path.isfile(tabular_file): - stop_err("Missing tabular identifier file %r" % tabular_file) + sys_exit("Missing tabular identifier file %r" % tabular_file) try: columns = [int(arg)-1 for arg in cols_arg.split(",")] except ValueError: - stop_err("Expected list of columns (comma separated integers), got %r" % cols_arg) + sys_exit("Expected list of columns (comma separated integers), got %r" % cols_arg) if min(columns) < 0: - stop_err("Expect one-based column numbers (not zero-based counting), got %r" % cols_arg) + sys_exit("Expect one-based column numbers (not zero-based counting), got %r" % cols_arg) identifiers.append((tabular_file, columns)) name_warn = False @@ -345,7 +345,7 @@ try: from Bio.SeqIO.SffIO import SffIterator, SffWriter except ImportError: - stop_err("SFF filtering requires Biopython 1.54 or later") + sys_exit("SFF filtering requires Biopython 1.54 or later") try: from Bio.SeqIO.SffIO import ReadRocheXmlManifest @@ -395,4 +395,4 @@ fastq_filter(in_file, out_positive_file, out_negative_file, ids) # This does not currently track the counts else: - stop_err("Unsupported file type %r" % seq_format) + sys_exit("Unsupported file type %r" % seq_format)
--- a/tools/seq_filter_by_id/seq_filter_by_id.py.orig Thu Nov 27 08:41:36 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,369 +0,0 @@ -#!/usr/bin/env python -"""Filter a FASTA, FASTQ or SSF file with IDs from a tabular file. - -Takes six command line options, tabular filename, ID column numbers (comma -separated list using one based counting), input filename, input type (e.g. -FASTA or SFF) and up to two output filenames (for records with and without -the given IDs, same format as input sequence file). - -When filtering an SFF file, any Roche XML manifest in the input file is -preserved in both output files. - -Note in the default NCBI BLAST+ tabular output, the query sequence ID is -in column one, and the ID of the match from the database is in column two. -Here sensible values for the column numbers would therefore be "1" or "2". - -This tool is a short Python script which requires Biopython 1.54 or later. -If you use this tool in scientific work leading to a publication, please -cite the Biopython application note: - -Cock et al 2009. Biopython: freely available Python tools for computational -molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. -http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. - -This script is copyright 2010-2013 by Peter Cock, The James Hutton Institute -(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved. -See accompanying text file for licence details (MIT license). - -Use -v or --version to get the version, -h or --help for help. -""" -import os -import sys -import re -from optparse import OptionParser - -def stop_err(msg, err=1): - sys.stderr.write(msg.rstrip() + "\n") - sys.exit(err) - -#Parse Command Line -usage = """Use as follows: - -$ python seq_filter_by_id.py [options] tab1 cols1 [, tab2 cols2, ...] - -e.g. Positive matches using column one from tabular file: - -$ seq_filter_by_id.py -i my_seqs.fastq -f fastq -p matches.fastq ids.tabular 1 - -Multiple tabular files and column numbers may be given, or replaced with -the -t or --text option. -""" -parser = OptionParser(usage=usage) -parser.add_option('-i', '--input', dest='input', - default=None, help='Input sequences filename', - metavar="FILE") -parser.add_option('-f', '--format', dest='format', - default=None, - help='Input sequence format (e.g. fasta, fastq, sff)') -parser.add_option('-t', '--text', dest='id_list', - default=None, help="Lists of white space separated IDs (instead of a tabular file)") -parser.add_option('-p', '--positive', dest='output_positive', - default=None, - help='Output filename for matches', - metavar="FILE") -parser.add_option('-n', '--negative', dest='output_negative', - default=None, - help='Output filename for non-matches', - metavar="FILE") -parser.add_option("-l", "--logic", dest="logic", - default="UNION", - help="How to combined multiple ID columns (UNION or INTERSECTION)") -parser.add_option("-s", "--suffix", dest="suffix", - action="store_true", - help="Ignore pair-read suffices for matching names") -parser.add_option("-v", "--version", dest="version", - default=False, action="store_true", - help="Show version and quit") - -options, args = parser.parse_args() - -if options.version: - print "v0.2.1" - sys.exit(0) - -in_file = options.input -seq_format = options.format -out_positive_file = options.output_positive -out_negative_file = options.output_negative -logic = options.logic -drop_suffices = bool(options.suffix) - -if in_file is None or not os.path.isfile(in_file): - stop_err("Missing input file: %r" % in_file) -if out_positive_file is None and out_negative_file is None: - stop_err("Neither output file requested") -if seq_format is None: - stop_err("Missing sequence format") -if logic not in ["UNION", "INTERSECTION"]: - stop_err("Logic agrument should be 'UNION' or 'INTERSECTION', not %r" % logic) -if options.id_list and args: - stop_err("Cannot accepted IDs via both -t and as tabular files") -elif not options.id_list and not args: - stop_err("Expected matched pairs of tabular files and columns (or -t given)") -if len(args) % 2: - stop_err("Expected matched pairs of tabular files and columns, not: %r" % args) - - -#Cope with three widely used suffix naming convensions, -#Illumina: /1 or /2 -#Forward/revered: .f or .r -#Sanger, e.g. .p1k and .q1k -#See http://staden.sourceforge.net/manual/pregap4_unix_50.html -#re_f = re.compile(r"(/1|\.f|\.[sfp]\d\w*)$") -#re_r = re.compile(r"(/2|\.r|\.[rq]\d\w*)$") -re_suffix = re.compile(r"(/1|\.f|\.[sfp]\d\w*|/2|\.r|\.[rq]\d\w*)$") -assert re_suffix.search("demo.f") -assert re_suffix.search("demo.s1") -assert re_suffix.search("demo.f1k") -assert re_suffix.search("demo.p1") -assert re_suffix.search("demo.p1k") -assert re_suffix.search("demo.p1lk") -assert re_suffix.search("demo/2") -assert re_suffix.search("demo.r") -assert re_suffix.search("demo.q1") -assert re_suffix.search("demo.q1lk") - -identifiers = [] -for i in range(len(args) // 2): - tabular_file = args[2*i] - cols_arg = args[2*i + 1] - if not os.path.isfile(tabular_file): - stop_err("Missing tabular identifier file %r" % tabular_file) - try: - columns = [int(arg)-1 for arg in cols_arg.split(",")] - except ValueError: - stop_err("Expected list of columns (comma separated integers), got %r" % cols_arg) - if min(columns) < 0: - stop_err("Expect one-based column numbers (not zero-based counting), got %r" % cols_arg) - identifiers.append((tabular_file, columns)) - -if drop_suffices: - def clean_name(name): - """Remove suffix.""" - match = re_suffix.search(name) - if match: - # Use the fact this is a suffix, and regular expression will be - # anchored to the end of the name: - return name[:match.start()] - else: - # Nothing to do - return name - assert clean_name("foo/1") == "foo" - assert clean_name("foo/2") == "foo" - assert clean_name("bar.f") == "bar" - assert clean_name("bar.r") == "bar" - assert clean_name("baz.p1") == "baz" - assert clean_name("baz.q2") == "baz" -else: - def clean_name(name): - """Do nothing!""" - return name - -mapped_chars = { '>' :'__gt__', - '<' :'__lt__', - "'" :'__sq__', - '"' :'__dq__', - '[' :'__ob__', - ']' :'__cb__', - '{' :'__oc__', - '}' :'__cc__', - '@' : '__at__', - '\n' : '__cn__', - '\r' : '__cr__', - '\t' : '__tc__', - '#' : '__pd__' - } - -#Read tabular file(s) and record all specified identifiers -ids = None #Will be a set -if options.id_list: - assert not identifiers - ids = set() - id_list = options.id_list - #Galaxy turns \r into __cr__ (CR) etc - for k in mapped_chars: - id_list = id_list.replace(mapped_chars[k], k) - for x in options.id_list.split(): - ids.add(clean_name(x.strip())) - print("Have %i unique identifiers from list" % len(ids)) -for tabular_file, columns in identifiers: - file_ids = set() - handle = open(tabular_file, "rU") - if len(columns)>1: - #General case of many columns - for line in handle: - if line.startswith("#"): - #Ignore comments - continue - parts = line.rstrip("\n").split("\t") - for col in columns: - file_ids.add(clean_name(parts[col])) - else: - #Single column, special case speed up - col = columns[0] - for line in handle: - if not line.startswith("#"): - file_ids.add(clean_name(line.rstrip("\n").split("\t")[col])) - print "Using %i IDs from column %s in tabular file" % (len(file_ids), ", ".join(str(col+1) for col in columns)) - if ids is None: - ids = file_ids - if logic == "UNION": - ids.update(file_ids) - else: - ids.intersection_update(file_ids) - handle.close() -if len(identifiers) > 1: - if logic == "UNION": - print "Have %i IDs combined from %i tabular files" % (len(ids), len(identifiers)) - else: - print "Have %i IDs in common from %i tabular files" % (len(ids), len(identifiers)) - - -def crude_fasta_iterator(handle): - """Yields tuples, record ID and the full record as a string.""" - while True: - line = handle.readline() - if line == "": - return # Premature end of file, or just empty? - if line[0] == ">": - break - - no_id_warned = False - while True: - if line[0] != ">": - raise ValueError( - "Records in Fasta files should start with '>' character") - try: - id = line[1:].split(None, 1)[0] - except IndexError: - if not no_id_warned: - sys.stderr.write("WARNING - Malformed FASTA entry with no identifier\n") - no_id_warned = True - id = None - lines = [line] - line = handle.readline() - while True: - if not line: - break - if line[0] == ">": - break - lines.append(line) - line = handle.readline() - yield id, "".join(lines) - if not line: - return # StopIteration - - -def fasta_filter(in_file, pos_file, neg_file, wanted): - """FASTA filter producing 60 character line wrapped outout.""" - pos_count = neg_count = 0 - #Galaxy now requires Python 2.5+ so can use with statements, - with open(in_file) as in_handle: - #Doing the if statement outside the loop for speed - #(with the downside of three very similar loops). - if pos_file is not None and neg_file is not None: - print "Generating two FASTA files" - with open(pos_file, "w") as pos_handle: - with open(neg_file, "w") as neg_handle: - for identifier, record in crude_fasta_iterator(in_handle): - if clean_name(identifier) in wanted: - pos_handle.write(record) - pos_count += 1 - else: - neg_handle.write(record) - neg_count += 1 - elif pos_file is not None: - print "Generating matching FASTA file" - with open(pos_file, "w") as pos_handle: - for identifier, record in crude_fasta_iterator(in_handle): - if clean_name(identifier) in wanted: - pos_handle.write(record) - pos_count += 1 - else: - neg_count += 1 - else: - print "Generating non-matching FASTA file" - assert neg_file is not None - with open(neg_file, "w") as neg_handle: - for identifier, record in crude_fasta_iterator(in_handle): - if clean_name(identifier) in wanted: - pos_count += 1 - else: - neg_handle.write(record) - neg_count += 1 - return pos_count, neg_count - - -if seq_format.lower()=="sff": - #Now write filtered SFF file based on IDs from BLAST file - try: - from Bio.SeqIO.SffIO import SffIterator, SffWriter - except ImportError: - stop_err("SFF filtering requires Biopython 1.54 or later") - - try: - from Bio.SeqIO.SffIO import ReadRocheXmlManifest - except ImportError: - #Prior to Biopython 1.56 this was a private function - from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest - in_handle = open(in_file, "rb") #must be binary mode! - try: - manifest = ReadRocheXmlManifest(in_handle) - except ValueError: - manifest = None - #This makes two passes though the SFF file with isn't so efficient, - #but this makes the code simple. - pos_count = neg_count = 0 - if out_positive_file is not None: - out_handle = open(out_positive_file, "wb") - writer = SffWriter(out_handle, xml=manifest) - in_handle.seek(0) #start again after getting manifest - pos_count = writer.write_file(rec for rec in SffIterator(in_handle) if clean_name(rec.id) in ids) - out_handle.close() - if out_negative_file is not None: - out_handle = open(out_negative_file, "wb") - writer = SffWriter(out_handle, xml=manifest) - in_handle.seek(0) #start again - neg_count = writer.write_file(rec for rec in SffIterator(in_handle) if clean_name(rec.id) not in ids) - out_handle.close() - #And we're done - in_handle.close() - #At the time of writing, Galaxy doesn't show SFF file read counts, - #so it is useful to put them in stdout and thus shown in job info. - print "%i with and %i without specified IDs" % (pos_count, neg_count) -elif seq_format.lower()=="fasta": - #Write filtered FASTA file based on IDs from tabular file - pos_count, neg_count = fasta_filter(in_file, out_positive_file, out_negative_file, ids) - print "%i with and %i without specified IDs" % (pos_count, neg_count) -elif seq_format.lower().startswith("fastq"): - #Write filtered FASTQ file based on IDs from tabular file - from Bio.SeqIO.QualityIO import FastqGeneralIterator - handle = open(in_file, "rU") - if out_positive_file is not None and out_negative_file is not None: - print "Generating two FASTQ files" - positive_handle = open(out_positive_file, "w") - negative_handle = open(out_negative_file, "w") - for title, seq, qual in FastqGeneralIterator(handle): - if clean_name(title.split(None, 1)[0]) in ids: - positive_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) - else: - negative_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) - positive_handle.close() - negative_handle.close() - elif out_positive_file is not None: - print "Generating matching FASTQ file" - positive_handle = open(out_positive_file, "w") - for title, seq, qual in FastqGeneralIterator(handle): - if clean_name(title.split(None, 1)[0]) in ids: - positive_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) - positive_handle.close() - elif out_negative_file is not None: - print "Generating non-matching FASTQ file" - negative_handle = open(out_negative_file, "w") - for title, seq, qual in FastqGeneralIterator(handle): - if clean_name(title.split(None, 1)[0]) not in ids: - negative_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) - negative_handle.close() - handle.close() -else: - stop_err("Unsupported file type %r" % seq_format)
--- a/tools/seq_filter_by_id/seq_filter_by_id.py.rej Thu Nov 27 08:41:36 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ ---- seq_filter_by_mapping.py -+++ seq_filter_by_mapping.py -@@ -301,44 +337,22 @@ - out_handle.close() - #And we're done - in_handle.close() -- #At the time of writing, Galaxy doesn't show SFF file read counts, -- #so it is useful to put them in stdout and thus shown in job info. -+ return pos_count, neg_count -+ -+ -+if seq_format.lower()=="sff": -+ # Now write filtered SFF file based on IDs wanted -+ pos_count, neg_count = sff_filter(in_file, out_positive_file, out_negative_file, ids) -+ # At the time of writing, Galaxy doesn't show SFF file read counts, -+ # so it is useful to put them in stdout and thus shown in job info. - print "%i with and %i without specified IDs" % (pos_count, neg_count) - elif seq_format.lower()=="fasta": -- #Write filtered FASTA file based on IDs from tabular file -+ # Write filtered FASTA file based on IDs from tabular file - pos_count, neg_count = fasta_filter(in_file, out_positive_file, out_negative_file, ids) - print "%i with and %i without specified IDs" % (pos_count, neg_count) - elif seq_format.lower().startswith("fastq"): - #Write filtered FASTQ file based on IDs from mapping file -- from Bio.SeqIO.QualityIO import FastqGeneralIterator -- handle = open(in_file, "r") -- if out_positive_file is not None and out_negative_file is not None: -- print "Generating two FASTQ files" -- positive_handle = open(out_positive_file, "w") -- negative_handle = open(out_negative_file, "w") -- print in_file -- for title, seq, qual in FastqGeneralIterator(handle): -- print("%s --> %s" % (title, clean_name(title.split(None, 1)[0]))) -- if clean_name(title.split(None, 1)[0]) in ids: -- positive_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) -- else: -- negative_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) -- positive_handle.close() -- negative_handle.close() -- elif out_positive_file is not None: -- print "Generating matching FASTQ file" -- positive_handle = open(out_positive_file, "w") -- for title, seq, qual in FastqGeneralIterator(handle): -- if clean_name(title.split(None, 1)[0]) in ids: -- positive_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) -- positive_handle.close() -- elif out_negative_file is not None: -- print "Generating non-matching FASTQ file" -- negative_handle = open(out_negative_file, "w") -- for title, seq, qual in FastqGeneralIterator(handle): -- if clean_name(title.split(None, 1)[0]) not in ids: -- negative_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) -- negative_handle.close() -- handle.close() -+ fastq_filter(in_file, out_positive_file, out_negative_file, ids) -+ # This does not currently track the counts - else: - stop_err("Unsupported file type %r" % seq_format)
--- a/tools/seq_filter_by_id/seq_filter_by_id.xml Thu Nov 27 08:41:36 2014 -0500 +++ b/tools/seq_filter_by_id/seq_filter_by_id.xml Wed May 13 11:01:30 2015 -0400 @@ -1,9 +1,14 @@ -<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.1"> +<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.2"> <description>from a tabular file</description> <requirements> <requirement type="package" version="1.64">biopython</requirement> <requirement type="python-module">Bio</requirement> </requirements> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <version_command interpreter="python">seq_filter_by_id.py --version</version_command> <command interpreter="python"> seq_filter_by_id.py -i "$input_file" -f "$input_file.ext" @@ -25,11 +30,6 @@ -t "$id_opts.id_list" #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." /> <conditional name="id_opts"> @@ -83,10 +83,10 @@ </conditional> </inputs> <outputs> - <data name="output_pos" format="input" metadata_source="input_file" label="$input_file.name with matched ID"> + <data name="output_pos" format_source="input_file" metadata_source="input_file" label="$input_file.name with matched ID"> <filter>output_choice_cond["output_choice"] != "neg"</filter> </data> - <data name="output_neg" format="input" metadata_source="input_file" label="$input_file.name without matched ID"> + <data name="output_neg" format_source="input_file" metadata_source="input_file" label="$input_file.name without matched ID"> <filter>output_choice_cond["output_choice"] != "pos"</filter> </data> </outputs>