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changeset 12:28459eecd18c draft

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author jasper
date Fri, 03 Feb 2017 13:45:14 -0500
parents 680d842fa17a
children 1df4c5372e07
files README.rst align_back_trans.xml shed.yml tool_dependencies.xml
diffstat 4 files changed, 0 insertions(+), 291 deletions(-) [+]
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--- a/README.rst	Fri Feb 03 13:13:17 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-Galaxy tool to back-translate a protein alignment to nucleotides
-================================================================
-
-This tool is copyright 2012-2015 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below (MIT licence).
-
-This tool is a short Python script (using Biopython library functions) to
-load a protein alignment, and matching nucleotide FASTA file of unaligned
-sequences, which are threaded onto the protein alignment in order to produce
-a codon aware nucleotide alignment - which can be viewed as a back translation.
-
-This tool is available from the Galaxy Tool Shed at:
-
-* http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
-
-The underlying Python script can also be used outside of Galaxy, for
-details run::
-
-    $ python align_back_trans.py
-
-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:
-
-* ``align_back_trans.py`` (the Python script)
-* ``align_back_trans.xml`` (the Galaxy tool definition)
-
-The suggested location is in a dedicated ``tools/align_back_trans`` 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 multiple alignments section. Simply
-add the line::
-
-    <tool file="align_back_trans/align_back_trans.xml" />
-
-You will also need to install Biopython 1.62 or later.
-
-If you wish to run the unit tests, also	move/copy the ``test-data/`` files
-under Galaxy's ``test-data/`` folder. Then::
-
-    ./run_tests.sh -id align_back_trans
-
-That's it.
-
-
-History
-=======
-
-======= ======================================================================
-Version Changes
-------- ----------------------------------------------------------------------
-v0.0.1  - Initial version, based on a previously written Python script
-v0.0.2  - Optionally check the translation is consistent
-v0.0.3  - First official release
-v0.0.4  - Simplified XML to apply input format to output data.
-        - Fixed error message when sequence length not a multiple of three.
-v0.0.5  - More explicit error messages when seqences lengths do not match.
-        - Tool definition now embeds citation information.
-v0.0.6  - Reorder XML elements (internal change only).
-        - Use ``format_source=...`` tag.
-        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
-======= ======================================================================
-
-
-Developers
-==========
-
-This script was initially developed on this repository:
-https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
-
-With the addition of a Galaxy wrapper, developement moved here:
-https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
-
-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_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
-    ...
-
-or::
-
-    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
-    ...
-
-To just build and check the tar ball, use::
-
-    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/align_back_trans/
-    ...
-    $ tar -tzf shed_upload.tar.gz 
-    test-data/demo_nucs.fasta
-    test-data/demo_nucs_trailing_stop.fasta
-    test-data/demo_prot_align.fasta
-    test-data/demo_nuc_align.fasta
-    tools/align_back_trans/README.rst
-    tools/align_back_trans/align_back_trans.py
-    tools/align_back_trans/align_back_trans.xml
-    tools/align_back_trans/tool_dependencies.xml
-
-
-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.
--- a/align_back_trans.xml	Fri Feb 03 13:13:17 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,129 +0,0 @@
-<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.6">
-    <description>Gives a codon aware alignment</description>
-    <requirements>
-        <requirement type="package" version="1.63">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">align_back_trans.py --version</version_command>
-    <command interpreter="python">
-align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table"
-    </command>
-    <inputs>
-        <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." />
-        <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
-            <option value="1">1. Standard</option>
-            <option value="2">2. Vertebrate Mitochondrial</option>
-            <option value="3">3. Yeast Mitochondrial</option>
-            <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
-            <option value="5">5. Invertebrate Mitochondrial</option>
-            <option value="6">6. Ciliate Macronuclear and Dasycladacean</option>
-            <option value="9">9. Echinoderm Mitochondrial</option>
-            <option value="10">10. Euplotid Nuclear</option>
-            <option value="11">11. Bacterial</option>
-            <option value="12">12. Alternative Yeast Nuclear</option>
-            <option value="13">13. Ascidian Mitochondrial</option>
-            <option value="14">14. Flatworm Mitochondrial</option>
-            <option value="15">15. Blepharisma Macronuclear</option>
-            <option value="16">16. Chlorophycean Mitochondrial</option>
-            <option value="21">21. Trematode Mitochondrial</option>
-            <option value="22">22. Scenedesmus obliquus</option>
-            <option value="23">23. Thraustochytrium Mitochondrial</option>
-            <option value="0">Don't check the translation</option>
-        </param>
-        <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" />
-    </inputs>
-    <outputs>
-        <data name="out_nuc_align" format_source="prot_align" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="prot_align" value="demo_prot_align.fasta" />
-            <param name="nuc_file" value="demo_nucs.fasta" />
-            <param name="table" value="0" />
-            <output name="out_nuc_align" file="demo_nuc_align.fasta" />
-        </test>
-        <test>
-            <param name="prot_align" value="demo_prot_align.fasta" />
-            <param name="nuc_file" value="demo_nucs_trailing_stop.fasta" />
-            <param name="table" value="11" />
-            <output name="out_nuc_align" file="demo_nuc_align.fasta" />
-        </test>
-    </tests>
-    <help>
-**What it does**
-
-Takes an input file of aligned protein sequences (typically FASTA or Clustal
-format), and a matching file of unaligned nucleotide sequences (FASTA format,
-using the same identifiers), and threads the nucleotide sequences onto the
-protein alignment to produce a codon aware nucleotide alignment - which can
-be viewed as a back translation.
-
-If you specify one of the standard NCBI genetic codes (recommended), then the
-translation is verified. This will allow fuzzy matching if stop codons in the
-protein sequence have been reprented as X, and will allow for a trailing stop
-codon present in the nucleotide sequences but not the protein.
-
-Note - the protein and nucleotide sequences must use the same identifers.
-
-Note - If no translation table is specified, the provided nucleotide sequences
-should be exactly three times the length of the protein sequences (exluding the gaps).
-
-Note - the nucleotide FASTA file may contain extra sequences not in the
-protein alignment, they will be ignored. This can be useful if for example
-you have a nucleotide FASTA file containing all the genes in an organism,
-while the protein alignment is for a specific gene family.
-
-**Example**
-
-Given this protein alignment in FASTA format::
-
-    >Alpha
-    DEER
-    >Beta
-    DE-R
-    >Gamma
-    D--R
-
-and this matching unaligned nucleotide FASTA file::
-
-    >Alpha
-    GATGAGGAACGA
-    >Beta
-    GATGAGCGU
-    >Gamma
-    GATCGG
-
-the tool would return this nucleotide alignment::
-
-    >Alpha
-    GATGAGGAACGA
-    >Beta
-    GATGAG---CGU
-    >Gamma
-    GAT------CGG
-
-Notice that all the gaps are multiples of three in length.
-
-
-**Citation**
-
-This tool uses Biopython, so if you use this Galaxy tool in work leading to a
-scientific publication please cite the following paper:
-
-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/align_back_trans
-    </help>
-    <citations>
-        <citation type="doi">10.7717/peerj.167</citation>
-        <citation type="doi">10.1093/bioinformatics/btp163</citation>
-    </citations>
-</tool>
--- a/shed.yml	Fri Feb 03 13:13:17 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-name: align_back_trans
-owner: peterjc
-homepage_url: https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
-remote_repository_url: https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
-description: Thread nucleotides onto a protein alignment (back-translation)
-long_description: |
-  Takes an input file of aligned protein sequences (typically FASTA or Clustal
-  format), and a matching file of unaligned nucleotide sequences (FASTA format,
-  using the same identifiers), and threads the nucleotide sequences onto the
-  protein alignment to produce a codon aware nucleotide alignment - which can
-  be viewed as a back translation.
-categories:
-- Fasta Manipulation
-- Sequence Analysis
-type: unrestricted
-include:
-- strip_components: 2
-  source:
-  - ../../test-data/demo_nuc_align.fasta
-  - ../../test-data/demo_nucs.fasta
-  - ../../test-data/demo_nucs_trailing_stop.fasta
-  - ../../test-data/demo_prot_align.fasta
-  - ../../tools/align_back_trans/README.rst
-  - ../../tools/align_back_trans/align_back_trans.py
-  - ../../tools/align_back_trans/align_back_trans.xml
-  - ../../tools/align_back_trans/tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Feb 03 13:13:17 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="biopython" version="1.63">
-        <repository changeset_revision="a5c49b83e983" name="package_biopython_1_63" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>