Mercurial > repos > lparsons > htseq_count
changeset 18:737cda668bdd draft
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 7ed7ce73afea50d212c9470fd3b98a232e312502
| author | lparsons |
|---|---|
| date | Mon, 22 Jun 2015 12:42:30 -0400 |
| parents | 3102bfcac0d6 |
| children | 8bc865a85024 |
| files | README.md README.rst fabfile.py htseq-count.xml test-data/htseq-test-paired_counts.tsv test-data/htseq-test-paired_othercounts.tsv tool_dependencies.xml |
| diffstat | 7 files changed, 145 insertions(+), 118 deletions(-) [+] |
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--- a/README.md Fri Apr 11 15:54:58 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -htseq-count wrapper for Galaxy -============================== - -Galaxy wrapper for -[htseq-count](http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) -script from python -[HTSeq](http://www-huber.embl.de/users/anders/HTSeq/doc/index.html) package. - -Installation ------------- - -Installation directly from the [Galaxy -Toolshed](http://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) is -recommended. - -Development ------------ - -Repository-Maintainer: Lance Parsons <lparsons@princeton.edu> - -Repository-Development: <https://bitbucket.org/lance_parsons/htseq_count_galaxy_wrapper> - - -License -------- - -Copyright (c) 2012-2014, Lance R. Parsons <lparsons@princeton.edu> -All rights reserved. - -Licensed under the BSD 2-Clause License: <http://opensource.org/licenses/BSD-2-Clause> - - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions are met: - - * Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimer. - - * Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND - ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED - WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE - FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL - DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR - SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER - CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, - OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Jun 22 12:42:30 2015 -0400 @@ -0,0 +1,49 @@ +htseq-count wrapper for Galaxy +============================== + +Galaxy wrapper for +`htseq-count <http://www-huber.embl.de/users/anders/HTSeq/doc/count.html>`_ +script from python +`HTSeq <http://www-huber.embl.de/users/anders/HTSeq/doc/index.html>`_ package. + +Installation +------------ + +Installation directly from the `Galaxy Toolshed <http://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count>`_ is +recommended. + +Development +----------- + +Repository-Maintainer: Lance Parsons <lparsons@princeton.edu> + +Repository-Development: `https://bitbucket.org/lance_parsons/htseq_count_galaxy_wrapper <https://bitbucket.org/lance_parsons/htseq_count_galaxy_wrapper>`_ + +License +------- + +Copyright (c) 2012-2014, Lance R. Parsons <lparsons@princeton.edu> +All rights reserved. + +Licensed under the BSD 2-Clause License: <http://opensource.org/licenses/BSD-2-Clause> + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE + FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL + DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR + SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER + CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fabfile.py Mon Jun 22 12:42:30 2015 -0400 @@ -0,0 +1,26 @@ +from fabric.api import local +from fabric.operations import prompt +import os + + +def package(): + ''' + Pacakge for upload to toolshed + packaging 'test' version (default) uses local directory + otherwise, specify a mercurial tag to package + ''' + package_dir = 'package' + base_filename = os.path.join(package_dir, 'htseq-count') + version = prompt("Enter version number for package [test]:") + revision_option = '' + if version != '': + revision_option = '-r "%s"' % version + else: + version = 'test' + version_filename = '%s_%s.tar.gz' % (base_filename, version) + local('mkdir -p %s' % package_dir) + local('rm -f %s' % version_filename) + if version == 'test': + local('tar czvf %s --exclude "fabfile.*" --exclude "%s" --exclude ".hg*" --exclude ".DS_Store" --exclude "*.pyc" --exclude "*.swp" *' % (version_filename, package_dir)) + else: + local('hg archive -t tgz %s -X "fabfile.*" -X "package" -X ".hg*" -p . "%s"' % (revision_option, version_filename))
--- a/htseq-count.xml Fri Apr 11 15:54:58 2014 -0400 +++ b/htseq-count.xml Mon Jun 22 12:42:30 2015 -0400 @@ -1,12 +1,23 @@ <tool id="htseq_count" name="htseq-count" version="0.4.1"> <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> - <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command> <requirements> - <requirement type="package" version="1.7.1">numpy</requirement> <requirement type="package" version="0.6.1">htseq</requirement> <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="0.7.7">pysam</requirement> </requirements> + + <stdio> + <exit_code range="1:" level="fatal" description="Unknown error occurred" /> + <regex match="htseq-count: (command ){0,1}not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" /> + <regex match="samtools: (command ){0,1}not found" source="stderr" level="fatal" description="The samtools package is not properly installed, contact Galaxy administrators" /> + <regex match="Error: Feature (.+) does not contain a '(.+)' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified 'Feature type' does not have a value for the specified 'ID Attribute'" /> + <regex match="Error occured in line (\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" /> + <regex match="Error" source="stderr" level="fatal" description="Unknown error occured" /> + <regex match="Warning: Read (.+) claims to have an aligned mate which could not be found. \(Is the SAM file properly sorted\?\)" source="stderr" level="warning" description="PAIRED DATA MISSING OR NOT PROPERLY SORTED. Try reruning and selecting the paired-end option. See stderr output of this dataset for more information." /> + </stdio> + + <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command> + <command> ##set up input files #set $reference_fasta_filename = "localref.fa" @@ -18,23 +29,24 @@ #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path ) #end if #end if - htseq-count + htseq-count --format=$samfile.extension --order=pos - --mode=$mode - --stranded=$stranded - --minaqual=$minaqual - --type=$featuretype - --idattr=$idattr + --mode=$mode + --stranded=$stranded + --minaqual=$minaqual + --type=$featuretype + --idattr=$idattr #if $samout_conditional.samout: --samout=$__new_file_path__/${samoutfile.id}_tmp #end if $samfile - $gfffile + $gfffile | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}' > $counts 2>$othercounts #if $samout_conditional.samout: && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile #end if</command> + <inputs> <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/> <param format="gff" name="gfffile" type="data" label="GFF File"/> @@ -63,7 +75,7 @@ <param name="samout" type="boolean" value="False" truevalue="True" falsevalue="False" label="Additional BAM Output"> <help>Write out all SAM alignment records into an output BAM file, annotating each line with its assignment to a feature or a special counter (as an optional field with tag ‘XF’).</help> </param> - <when value="True"> + <when value="True"> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> <option value="cached">Locally cached</option> @@ -93,16 +105,6 @@ </data> </outputs> - <stdio> - <exit_code range="1:" level="fatal" description="Unknown error occurred" /> - <regex match="htseq-count: command not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" /> - <regex match="samtools: command not found" source="stderr" level="fatal" description="The samtools package is not properly installed, contact Galaxy administrators" /> - <regex match="Error: Feature (.+) does not contain a '(.+)' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified 'Feature type' does not have a value for the specified 'ID Attribute'" /> - <regex match="Error occured in line (\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" /> - <regex match="Error" source="stderr" level="fatal" description="Unknown error occured" /> - <regex match="Warning: Read (.+) claims to have an aligned mate which could not be found. \(Is the SAM file properly sorted\?\)" source="stderr" level="warning" description="PAIRED DATA MISSING OR NOT PROPERLY SORTED. Try reruning and selecting the paired-end option. See stderr output of this dataset for more information." /> - </stdio> - <tests> <test> <param name="samfile" value="htseq-test.sam" /> @@ -145,22 +147,22 @@ -------- This tool takes an alignment file in SAM or BAM format and feature file in GFF format -and calculates the number of reads mapping to each feature. It uses the *htseq-count* +and calculates the number of reads mapping to each feature. It uses the *htseq-count* script that is part of the HTSeq python module. See http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details. A feature is an interval (i.e., a range of positions) on a chromosome or a union of -such intervals. In the case of RNA-Seq, the features are typically genes, where -each gene is considered here as the union of all its exons. One may also consider -each exon as a feature, e.g., in order to check for alternative splicing. For -comparative ChIP-Seq, the features might be binding regions from a pre-determined +such intervals. In the case of RNA-Seq, the features are typically genes, where +each gene is considered here as the union of all its exons. One may also consider +each exon as a feature, e.g., in order to check for alternative splicing. For +comparative ChIP-Seq, the features might be binding regions from a pre-determined list. Overlap Modes ------------- -Special care must be taken to decide how to deal with reads that overlap more than one feature. +Special care must be taken to decide how to deal with reads that overlap more than one feature. The htseq-count script allows to choose between three modes: *union*, *intersection-strict*, and *intersection-nonempty*. @@ -231,4 +233,29 @@ Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General Public License v3. Part of the 'HTSeq' framework. </help> + <citations> + <citation type="bibtex"> +@article{anders_htseqpython_2015, + title = {{HTSeq}—a {Python} framework to work with high-throughput sequencing data}, + volume = {31}, + issn = {1367-4803, 1460-2059}, + url = {http://bioinformatics.oxfordjournals.org/content/31/2/166}, + doi = {10.1093/bioinformatics/btu638}, + abstract = {Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. +Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. +Availability and implementation: HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. +Contact: sanders\{at\}fs.tum.de}, + language = {en}, + number = {2}, + urldate = {2015-04-21}, + journal = {Bioinformatics}, + author = {Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang}, + month = jan, + year = {2015}, + pmid = {25260700}, + pages = {166--169}, + file = {Full Text PDF:/Users/lparsons/Library/Application Support/Firefox/Profiles/thd2t4je.default/zotero/storage/84XQB8V6/Anders et al. - 2015 - HTSeq—a Python framework to work with high-through.pdf:application/pdf;Snapshot:/Users/lparsons/Library/Application Support/Firefox/Profiles/thd2t4je.default/zotero/storage/JKUAUCKB/166.html:text/html} +} + </citation> + </citations> </tool>
--- a/test-data/htseq-test-paired_counts.tsv Fri Apr 11 15:54:58 2014 -0400 +++ b/test-data/htseq-test-paired_counts.tsv Mon Jun 22 12:42:30 2015 -0400 @@ -2,8 +2,8 @@ YAL001C 12 YAL002W 6 YAL003W 5 -YAL004W 3 -YAL005C 5 +YAL004W 2 +YAL005C 2 YAL007C 1 YAL008W 0 YAL009W 2 @@ -76,11 +76,11 @@ YAL064C-A 0 YAL064W 0 YAL064W-B 0 -YAL065C 2 +YAL065C 1 YAL066W 0 YAL067C 8 YAL067W-A 1 -YAL068C 1 +YAL068C 0 YAL068W-A 0 YAL069W 0 YAR002C-A 0 @@ -88,7 +88,7 @@ YAR003W 4 YAR007C 7 YAR008W 0 -YAR009C 1 +YAR009C 0 YAR010C 0 YAR014C 4 YAR015W 4 @@ -101,7 +101,7 @@ YAR028W 3 YAR029W 0 YAR030C 2 -YAR031W 4 +YAR031W 3 YAR033W 0 YAR035C-A 0 YAR035W 3 @@ -109,15 +109,15 @@ YAR047C 0 YAR050W 4 YAR053W 0 -YAR060C 2 +YAR060C 0 YAR061W 0 -YAR062W 2 +YAR062W 1 YAR064W 1 YAR066W 2 -YAR068W 2 -YAR069C 1 +YAR068W 1 +YAR069C 0 YAR070C 0 -YAR071W 4 +YAR071W 2 YAR073W 1 YAR075W 0 snR18 0
--- a/test-data/htseq-test-paired_othercounts.tsv Fri Apr 11 15:54:58 2014 -0400 +++ b/test-data/htseq-test-paired_othercounts.tsv Mon Jun 22 12:42:30 2015 -0400 @@ -1,5 +1,5 @@ -_feature 755 -__ambiguous 0 -__too_low_aQual 96 +__no_feature 480 +__ambiguous 1 +__too_low_aQual 68 __not_aligned 0 __alignment_not_unique 0
--- a/tool_dependencies.xml Fri Apr 11 15:54:58 2014 -0400 +++ b/tool_dependencies.xml Mon Jun 22 12:42:30 2015 -0400 @@ -1,40 +1,16 @@ <?xml version="1.0"?> <tool_dependency> - <package name="numpy" version="1.7.1"> - <repository changeset_revision="55a7a5e9d63f" name="package_numpy_1_7" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="pysam" version="0.7.7"> - <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="htseq" version="0.6.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz</action> - <!-- populate the environment variables from the dependend repos --> - <action type="set_environment_for_install"> - <repository changeset_revision="55a7a5e9d63f" name="package_numpy_1_7" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="numpy" version="1.7.1" /> - </repository> - </action> - <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> - <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise --> - <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> - <action type="set_environment"> - <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package. - </readme> + <repository changeset_revision="025da27a2bb2" name="package_htseq_0_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>