| Previous changeset 1:9c8c5079c8af (2013-04-29) Next changeset 3:e1398f2ba9fe (2017-02-02) |
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Commit message:
Uploaded v0.0.4, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence. Includes additional tested added in v0.0.3 |
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added:
tools/seq_rename/README.rst tools/seq_rename/repository_dependencies.xml tools/seq_rename/seq_rename.py tools/seq_rename/seq_rename.xml |
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removed:
tools/filters/seq_rename.py tools/filters/seq_rename.txt tools/filters/seq_rename.xml |
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| diff -r 9c8c5079c8af -r 7c0642fc57ad tools/filters/seq_rename.py --- a/tools/filters/seq_rename.py Mon Apr 29 13:14:23 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,145 +0,0 @@ -#!/usr/bin/env python -"""Rename FASTA, QUAL, FASTQ or SSF sequences with ID mapping from tabular file. - -Takes six command line options, tabular filename, current (old) ID column -number (using one based counting), new ID column number (also using one based -counting), input sequence filename, input type (e.g. FASTA or SFF) and the -output filename (same format as input sequence file). - -When selecting from an SFF file, any Roche XML manifest in the input file is -preserved in both output files. - -This tool is a short Python script which requires Biopython 1.54 or later -for SFF file support. 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 2011-2013 by Peter Cock, The James Hutton Institute UK. -All rights reserved. See accompanying text file for licence details (MIT/BSD -style). - -This is version 0.0.2 of the script. -""" -import sys - -if "-v" in sys.argv or "--version" in sys.argv: - print "v0.0.2" - sys.exit(0) - -def stop_err(msg, err=1): - sys.stderr.write(msg.rstrip() + "\n") - sys.exit(err) - -#Parse Command Line -try: - tabular_file, old_col_arg, new_col_arg, in_file, seq_format, out_file = sys.argv[1:] -except ValueError: - stop_err("Expected six arguments (tabular file, old col, new col, input file, format, output file), got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv))) - -try: - if old_col_arg.startswith("c"): - old_column = int(old_col_arg[1:])-1 - else: - old_column = int(old_col_arg)-1 -except ValueError: - stop_err("Expected column number, got %s" % old_col_arg) -try: - if old_col_arg.startswith("c"): - new_column = int(new_col_arg[1:])-1 - else: - new_column = int(new_col_arg)-1 -except ValueError: - stop_err("Expected column number, got %s" % new_col_arg) -if old_column == new_column: - stop_err("Old and new column arguments are the same!") - -def parse_ids(tabular_file, old_col, new_col): - """Read tabular file and record all specified ID mappings.""" - handle = open(tabular_file, "rU") - for line in handle: - if not line.startswith("#"): - parts = line.rstrip("\n").split("\t") - yield parts[old_col].strip(), parts[new_col].strip() - handle.close() - -#Load the rename mappings -rename = dict(parse_ids(tabular_file, old_column, new_column)) -print "Loaded %i ID mappings" % len(rename) - -#Rewrite the sequence file -if seq_format.lower()=="sff": - #Use Biopython for this format - renamed = 0 - def rename_seqrecords(records, mapping): - global renamed #nasty, but practical! - for record in records: - try: - record.id = mapping[record.id] - renamed += 1 - except KeyError: - pass - yield record - - try: - from Bio.SeqIO.SffIO import SffIterator, SffWriter - except ImportError: - stop_err("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 - out_handle = open(out_file, "wb") - writer = SffWriter(out_handle, xml=manifest) - in_handle.seek(0) #start again after getting manifest - count = writer.write_file(rename_seqrecords(SffIterator(in_handle), rename)) - out_handle.close() - in_handle.close() -else: - #Use Galaxy for FASTA, QUAL or FASTQ - if seq_format.lower() in ["fasta", "csfasta"] \ - or seq_format.lower().startswith("qual"): - from galaxy_utils.sequence.fasta import fastaReader, fastaWriter - reader = fastaReader(open(in_file, "rU")) - writer = fastaWriter(open(out_file, "w")) - marker = ">" - elif seq_format.lower().startswith("fastq"): - from galaxy_utils.sequence.fastq import fastqReader, fastqWriter - reader = fastqReader(open(in_file, "rU")) - writer = fastqWriter(open(out_file, "w")) - marker = "@" - else: - stop_err("Unsupported file type %r" % seq_format) - #Now do the renaming - count = 0 - renamed = 0 - for record in reader: - #The [1:] is because the fastaReader leaves the > on the identifier, - #likewise the fastqReader leaves the @ on the identifier - try: - idn, descr = record.identifier[1:].split(None, 1) - except ValueError: - idn = record.identifier[1:] - descr = None - if idn in rename: - if descr: - record.identifier = "%s%s %s" % (marker, rename[idn], descr) - else: - record.identifier = "%s%s" % (marker, rename[idn]) - renamed += 1 - writer.write(record) - count += 1 - writer.close() - reader.close() - -print "Renamed %i out of %i records" % (renamed, count) |
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| diff -r 9c8c5079c8af -r 7c0642fc57ad tools/filters/seq_rename.txt --- a/tools/filters/seq_rename.txt Mon Apr 29 13:14:23 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,87 +0,0 @@ -Galaxy tool to renamed FASTA, QUAL, FASTQ or SFF sequences -========================================================== - -This tool is copyright 2011 by Peter Cock, The James Hutton Institute -(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. -See the licence text below. - -This tool is a short Python script (using Biopython library functions) to rename -sequences from a FASTA, QUAL, FASTQ, or SFF file based on an ID mapping gives as -two columns of a tabular file. The output order follows that of the sequence file, -and if there are duplicates in the input sequence file, there will be duplicates -in the output sequence file. - -See also the sister tools to filter or select sequence files according to IDs -from column(s) of tabular file. - - -Manual Installation -=================== - -There are just two files to install: - -* seq_rename.py (the Python script) -* seq_rename.xml (the Galaxy tool definition) - -The suggested location is in the Galaxy folder tools/filters next to the tool -for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. - -You will also need to modify the tools_conf.xml file to tell Galaxy to offer the -tool. One suggested location is in the filters section. Simply add the line: - -<tool file="filters/seq_rename.xml" /> - -You will also need to install Biopython 1.54 or later. That's it. - - -History -======= - -v0.0.1 - Initial version. -v0.0.2 - Record script version when run from Galaxy. - - Add unit test. - - Check for errors using Python script's return code. - - -Developers -========== - -This script and related tools are being developed on the following hg branch: -http://bitbucket.org/peterjc/galaxy-central/src/tools - -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder: - -$ tar -czf seq_rename.tar.gz tools/filters/seq_rename.* test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta - -Check this worked: - -$ tar -tzf seq_rename.tar.gz -tools/filter/seq_rename.py -tools/filter/seq_rename.txt -tools/filter/seq_rename.xml -test-data/four_human_proteins.fasta -test-data/four_human_proteins.rename.tabular -test-data/four_human_proteins.rename.fasta - - -Licence (MIT/BSD style) -======================= - -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. - -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE. |
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| diff -r 9c8c5079c8af -r 7c0642fc57ad tools/filters/seq_rename.xml --- a/tools/filters/seq_rename.xml Mon Apr 29 13:14:23 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,68 +0,0 @@ -<tool id="seq_rename" name="Rename sequences" version="0.0.2"> - <description>with ID mapping from a tabular file</description> - <version_commmand interpreter="python">seq_rename.py --version</version_commmand> - <command interpreter="python"> -seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file - </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,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> - <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> - <param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/> - <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/> - </inputs> - <outputs> - <data name="output_file" format="fasta" label="Renamed ${on_string}"> - <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> - <change_format> - <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> - <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> - <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> - <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> - <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> - <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> - <param name="old_column" value="1" /> - <param name="new_column" value="2" /> - <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> - </test> - </tests> - <requirements> - <requirement type="python-module">Bio</requirement> - </requirements> - <help> - -**What it does** - -Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a -new sequence file (of the same format) where the sequence identifiers have been -renamed according two the specified columns a the tabular file. - -WARNING: If you have any duplicates in the intput sequence file, you will still -have duplicate sequences in the output. - -WARNING: If the tabular file has more than one new name for any old ID, the -last one is used. - -**Citation** - -This tool uses Biopython to read and write SFF files. If you use this tool in -scientific work leading to a publication, please cite the Biopython application -note (and Galaxy too of course): - -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. - - </help> -</tool> |
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| diff -r 9c8c5079c8af -r 7c0642fc57ad tools/seq_rename/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/seq_rename/README.rst Fri Oct 11 04:39:16 2013 -0400 |
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| @@ -0,0 +1,121 @@ +Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences +========================================================= + +This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +This tool is a short Python script (using Biopython library functions) to rename +sequences from a FASTA, QUAL, FASTQ, or SFF file based on an ID mapping gives as +two columns of a tabular file. The output order follows that of the sequence file, +and if there are duplicates in the input sequence file, there will be duplicates +in the output sequence file. + +This tool is available from the Galaxy Tool Shed, + +* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename + +See also the sister tools to filter or select sequence files according to IDs +from column(s) of tabular file: + +* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id +* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id + + +Automated Installation +====================== + +This should be straightforward using the Galaxy Tool Shed, which should be +able to automatically install the dependency on Biopython, and then install +this tool and run its unit tests. + + +Manual Installation +=================== + +There are just two files to install to use this tool from within Galaxy: + +* seq_rename.py (the Python script) +* seq_rename.xml (the Galaxy tool definition) + +The suggested location is in a dedicated tools/seq_rename folder. + +You will also need to modify the tools_conf.xml file to tell Galaxy to offer the +tool. One suggested location is in the filters section. Simply add the line:: + + <tool file="seq_rename/seq_rename.xml" /> + +If you wish to run the unit tests, also add this to tools_conf.xml.sample +and move/copy the test-data files under Galaxy's test-data folder. Then:: + + $ ./run_functional_tests.sh -id seq_rename + +You will also need to install Biopython 1.54 or later. That's it. + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial version. +v0.0.2 - Record script version when run from Galaxy. + - Add unit test. + - Check for errors using Python script's return code. +v0.0.3 - Link to Tool Shed added to help text and this documentation. +v0.0.4 - Automated installation of Biopython dependency. + - Use reStructuredText for this README file. + - Adopt standard MIT License. + - Updated citation information (Cock et al. 2013). + - Development moved to GitHub, https://github.com/peterjc/pico_galaxy + - Renamed folder and adopted README.rst naming. +======= ====================================================================== + + +Developers +========== + +This script and related tools were initially developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +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:: + + $ tar -czf seq_rename.tar.gz tools/seq_rename/README.rst tools/seq_rename/seq_rename.* tools/seq_rename/repository_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta + +Check this worked:: + + $ tar -tzf seq_rename.tar.gz + tools/seq_rename/README.rst + tools/seq_rename/seq_rename.py + tools/seq_rename/seq_rename.xml + tools/seq_rename/repository_dependencies.xml + test-data/four_human_proteins.fasta + test-data/four_human_proteins.rename.tabular + test-data/four_human_proteins.rename.fasta + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. |
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| diff -r 9c8c5079c8af -r 7c0642fc57ad tools/seq_rename/repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/seq_rename/repository_dependencies.xml Fri Oct 11 04:39:16 2013 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<repositories description="This requires Biopython as a dependency."> +<!-- Leave out the tool shed and revision to get the current + tool shed and latest revision at the time of upload --> +<repository changeset_revision="3e82cbc44886" name="package_biopython_1_62" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 9c8c5079c8af -r 7c0642fc57ad tools/seq_rename/seq_rename.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/seq_rename/seq_rename.py Fri Oct 11 04:39:16 2013 -0400 |
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| @@ -0,0 +1,145 @@ +#!/usr/bin/env python +"""Rename FASTA, QUAL, FASTQ or SSF sequences with ID mapping from tabular file. + +Takes six command line options, tabular filename, current (old) ID column +number (using one based counting), new ID column number (also using one based +counting), input sequence filename, input type (e.g. FASTA or SFF) and the +output filename (same format as input sequence file). + +When selecting from an SFF file, any Roche XML manifest in the input file is +preserved in both output files. + +This tool is a short Python script which requires Biopython 1.54 or later +for SFF file support. 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 2011-2013 by Peter Cock, The James Hutton Institute UK. +All rights reserved. See accompanying text file for licence details (MIT +license). + +This is version 0.0.4 of the script. +""" +import sys + +if "-v" in sys.argv or "--version" in sys.argv: + print "v0.0.4" + sys.exit(0) + +def stop_err(msg, err=1): + sys.stderr.write(msg.rstrip() + "\n") + sys.exit(err) + +#Parse Command Line +try: + tabular_file, old_col_arg, new_col_arg, in_file, seq_format, out_file = sys.argv[1:] +except ValueError: + stop_err("Expected six arguments (tabular file, old col, new col, input file, format, output file), got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv))) + +try: + if old_col_arg.startswith("c"): + old_column = int(old_col_arg[1:])-1 + else: + old_column = int(old_col_arg)-1 +except ValueError: + stop_err("Expected column number, got %s" % old_col_arg) +try: + if old_col_arg.startswith("c"): + new_column = int(new_col_arg[1:])-1 + else: + new_column = int(new_col_arg)-1 +except ValueError: + stop_err("Expected column number, got %s" % new_col_arg) +if old_column == new_column: + stop_err("Old and new column arguments are the same!") + +def parse_ids(tabular_file, old_col, new_col): + """Read tabular file and record all specified ID mappings.""" + handle = open(tabular_file, "rU") + for line in handle: + if not line.startswith("#"): + parts = line.rstrip("\n").split("\t") + yield parts[old_col].strip(), parts[new_col].strip() + handle.close() + +#Load the rename mappings +rename = dict(parse_ids(tabular_file, old_column, new_column)) +print "Loaded %i ID mappings" % len(rename) + +#Rewrite the sequence file +if seq_format.lower()=="sff": + #Use Biopython for this format + renamed = 0 + def rename_seqrecords(records, mapping): + global renamed #nasty, but practical! + for record in records: + try: + record.id = mapping[record.id] + renamed += 1 + except KeyError: + pass + yield record + + try: + from Bio.SeqIO.SffIO import SffIterator, SffWriter + except ImportError: + stop_err("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 + out_handle = open(out_file, "wb") + writer = SffWriter(out_handle, xml=manifest) + in_handle.seek(0) #start again after getting manifest + count = writer.write_file(rename_seqrecords(SffIterator(in_handle), rename)) + out_handle.close() + in_handle.close() +else: + #Use Galaxy for FASTA, QUAL or FASTQ + if seq_format.lower() in ["fasta", "csfasta"] \ + or seq_format.lower().startswith("qual"): + from galaxy_utils.sequence.fasta import fastaReader, fastaWriter + reader = fastaReader(open(in_file, "rU")) + writer = fastaWriter(open(out_file, "w")) + marker = ">" + elif seq_format.lower().startswith("fastq"): + from galaxy_utils.sequence.fastq import fastqReader, fastqWriter + reader = fastqReader(open(in_file, "rU")) + writer = fastqWriter(open(out_file, "w")) + marker = "@" + else: + stop_err("Unsupported file type %r" % seq_format) + #Now do the renaming + count = 0 + renamed = 0 + for record in reader: + #The [1:] is because the fastaReader leaves the > on the identifier, + #likewise the fastqReader leaves the @ on the identifier + try: + idn, descr = record.identifier[1:].split(None, 1) + except ValueError: + idn = record.identifier[1:] + descr = None + if idn in rename: + if descr: + record.identifier = "%s%s %s" % (marker, rename[idn], descr) + else: + record.identifier = "%s%s" % (marker, rename[idn]) + renamed += 1 + writer.write(record) + count += 1 + writer.close() + reader.close() + +print "Renamed %i out of %i records" % (renamed, count) |
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| diff -r 9c8c5079c8af -r 7c0642fc57ad tools/seq_rename/seq_rename.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/seq_rename/seq_rename.xml Fri Oct 11 04:39:16 2013 -0400 |
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| @@ -0,0 +1,84 @@ +<tool id="seq_rename" name="Rename sequences" version="0.0.4"> + <description>with ID mapping from a tabular file</description> + <requirements> + <requirement type="package" version="1.62">biopython</requirement> + <requirement type="python-module">Bio</requirement> + </requirements> + <version_commmand interpreter="python">seq_rename.py --version</version_commmand> + <command interpreter="python"> +seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file + </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,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> + <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> + <param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/> + <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/> + </inputs> + <outputs> + <data name="output_file" format="fasta" label="Renamed ${on_string}"> + <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> + <change_format> + <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> + <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> + <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> + <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> + <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> + <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> + <param name="old_column" value="1" /> + <param name="new_column" value="2" /> + <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> + </test> + <test> + <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> + <param name="old_column" value="c1" /> + <param name="new_column" value="c2" /> + <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> + </test> + </tests> + <help> +**What it does** + +Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a +new sequence file (of the same format) where the sequence identifiers have been +renamed according to the specified columns in your tabular file. + +WARNING: If you have any duplicates in the input sequence file, you will still +have duplicate sequences in the output. + +WARNING: If the tabular file has more than one new name for any old ID, the +last one is used. + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +This tool uses Biopython to read and write SFF files, so you may also wish to +cite the Biopython application note (and Galaxy too of course): + +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 tool is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename + </help> +</tool> |