Mercurial > repos > lparsons > htseq_count
changeset 14:265ca0f35789
Merge multiple heads.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Mon, 27 Jan 2014 14:12:09 -0500 |
| parents | 30bb8acb77a4 (diff) 14e18dc9ed13 (current diff) |
| children | 3ffe4e2572a7 |
| files | tool_dependencies.xml |
| diffstat | 11 files changed, 303 insertions(+), 7058 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgignore Mon Jan 27 14:12:09 2014 -0500 @@ -0,0 +1,3 @@ +^package$ +syntax: glob +*.pyc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.hgtags Mon Jan 27 14:12:09 2014 -0500 @@ -0,0 +1,3 @@ +142ec9462fa644cd29642ea0ad10e9889ce75619 0.3 +3e7b1e8a69f9d79b8de603f24e466deb7b192100 0.3.release2 +496a7dc0786f8367264520dfff6e8e8e744de3b2 0.3.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Jan 27 14:12:09 2014 -0500 @@ -0,0 +1,51 @@ +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 +------------ + +Installtion 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) 2012-2013, 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 Jan 27 14:12:09 2014 -0500 @@ -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*" *' % (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 Tue Sep 04 14:00:14 2012 -0400 +++ b/htseq-count.xml Mon Jan 27 14:12:09 2014 -0500 @@ -1,9 +1,11 @@ -<tool id="htseq_count" name="htseq-count" version="0.1"> +<tool id="htseq_count" name="htseq-count" version="0.3.2"> <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="0.5.3p9">htseq</requirement> - <requirement type="package" version="0.1.18">samtools</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="0.5.4p5">htseq</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="1.56.0">picard</requirement> </requirements> <command> ##set up input files @@ -16,32 +18,46 @@ #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path ) #end if #end if - - #if $samfile.extension == "bam": - samtools view $samfile | + #if str($singlepaired) == "paired": + ln -s $samfile local_input.sam && + java -Xmx2G -jar "\$JAVA_JAR_PATH/SortSam.jar" VALIDATION_STRINGENCY=LENIENT SORT_ORDER=queryname O=prepared_input.sam I=local_input.sam TMP_DIR="${__new_file_path__}" + || echo "Error running Picard MergeSamFiles" >&2 && + #else: + #if $samfile.extension == "bam": + samtools view $samfile | + #else + ln -s $samfile prepared_input.sam && + #end if #end if htseq-count --mode=$mode --stranded=$stranded --minaqual=$minaqual - --type=$type + --type=$featuretype --idattr=$idattr #if $samout_conditional.samout: --samout=$__new_file_path__/${samoutfile.id}_tmp #end if - #if $samfile.extension == "bam": - - - #else - $samfile - #end if + #if str($singlepaired) == "paired": + prepared_input.sam + #else: + #if $samfile.extension == "bam": + - + #else: + prepared_input.sam + #end if + #end if $gfffile - > $counts + | 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 File"> - <help>Paired-End data must be sorted by QUERY NAME, use Picard Read Mate Fixer and Query name sort order before using this tool on paired data</help> + <param format="sam, bam" name="samfile" type="data" label="Aligned SAM/BAM File"/> + <param name="singlepaired" type="select" label="Is this library mate-paired?"> + <help>Paired libraries will be sorted by read name prior to counting.</help> + <option value="single" selected="true">single-end</option> + <option value="paired">paired-end</option> </param> <param format="gff" name="gfffile" type="data" label="GFF File"/> <param name="mode" type="select" label="Mode"> @@ -59,11 +75,11 @@ <param name="minaqual" type="integer" value="0" label="Minimum alignment quality"> <help>Skip all reads with alignment quality lower than the given minimum value</help> </param> - <param name="type" type="text" value="exon" label="Feature type"> + <param name="featuretype" type="text" value="exon" label="Feature type"> <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon.</help> </param> <param name="idattr" type="text" value="gene_id" label="ID Attribute"> - <help>GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. The default, suitable for RNA-SEq and Ensembl GTF files, is gene_id.</help> + <help>GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. All features of the specified type MUST have a value for this attribute. The default, suitable for RNA-SEq and Ensembl GTF files, is gene_id.</help> </param> <conditional name="samout_conditional"> <param name="samout" type="boolean" value="False" truevalue="True" falsevalue="False" label="Additional BAM Output"> @@ -78,7 +94,7 @@ <when value="cached"> <param name="ref_file" type="select" label="Using reference genome"> <options from_data_table="sam_fa_indexes"> - <filter type="data_meta" key="dbkey" ref="samfile" column="3"/> + <filter type="data_meta" key="dbkey" ref="samfile" column="1"/> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> @@ -92,14 +108,21 @@ </inputs> <outputs> - <data format="tabular" name="counts" label="${tool.name} on ${on_string}"/> - <data format="bam" name="samoutfile" label="${tool.name} on ${on_string} (BAM)"> + <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}"/> + <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/> + <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)"> <filter>samout_conditional['samout']</filter> </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> @@ -108,12 +131,22 @@ <param name="gfffile" value="htseq-test.gff" /> <param name="samout" value="False" /> <output name="counts" file="htseq-test_counts.tsv" /> + <output name="othercounts" file="htseq-test_othercounts.tsv" /> </test> <test> <param name="samfile" value="htseq-test.bam" /> <param name="gfffile" value="htseq-test.gff" /> <param name="samout" value="False" /> <output name="counts" file="htseq-test_counts.tsv" /> + <output name="othercounts" file="htseq-test_othercounts.tsv" /> + </test> + <test> + <param name="samfile" value="htseq-test-paired.bam" /> + <param name="singlepaired" value="paired" /> + <param name="gfffile" value="htseq-test.gff" /> + <param name="samout" value="False" /> + <output name="counts" file="htseq-test-paired_counts.tsv" /> + <output name="othercounts" file="htseq-test-paired_othercounts.tsv" /> </test> <!-- Seems to be an issue setting the $reference_fasta_filename variable during test <test> @@ -123,6 +156,7 @@ <param name="reference_source_selector" value="history" /> <param name="ref_file" value="htseq-test_reference.fasta" /> <output name="counts" file="htseq-test_counts.tsv" /> + <output name="othercounts" file="htseq-test_othercounts.tsv" /> <output name="samoutfile" file="htseq-test_samout.bam" /> </test> --> @@ -144,10 +178,6 @@ comparative ChIP-Seq, the features might be binding regions from a pre-determined list. -**Paired-end Data MUST be sorted by QUERY NAME first** - -This tool requires that paired-end data be sorted by query name, which is NOT the default for Galaxy. Using the Picard Paired Read Mate Fixer with Query name sort FIRST is required for paired end data. - Overlap Modes ------------- @@ -158,14 +188,16 @@ The following figure illustrates the effect of these three modes: -.. image:: /static/images/count_modes.png +.. image:: $PATH_TO_IMAGES/count_modes.png :width: 500 + Strandedness ------------ **Important**: The default for strandedness is yes. If your RNA-Seq data has not been made with a strand-specific protocol, this causes half of the reads to be lost. Hence, make sure to set the option Stranded to 'No' unless you have strand-specific data! + Output ------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/htseq-test-paired_counts.tsv Mon Jan 27 14:12:09 2014 -0500 @@ -0,0 +1,127 @@ +HRA1 2 +YAL001C 12 +YAL002W 6 +YAL003W 5 +YAL004W 3 +YAL005C 5 +YAL007C 1 +YAL008W 0 +YAL009W 2 +YAL010C 3 +YAL011W 2 +YAL012W 3 +YAL013W 3 +YAL014C 5 +YAL015C 5 +YAL016C-A 0 +YAL016C-B 1 +YAL016W 2 +YAL017W 8 +YAL018C 5 +YAL019W 1 +YAL019W-A 0 +YAL020C 0 +YAL021C 10 +YAL022C 4 +YAL023C 5 +YAL024C 13 +YAL025C 1 +YAL026C 6 +YAL026C-A 0 +YAL027W 3 +YAL028W 3 +YAL029C 10 +YAL030W 1 +YAL031C 4 +YAL031W-A 2 +YAL032C 3 +YAL033W 2 +YAL034C 0 +YAL034C-B 2 +YAL034W-A 2 +YAL035W 7 +YAL036C 4 +YAL037C-A 0 +YAL037C-B 3 +YAL037W 1 +YAL038W 4 +YAL039C 1 +YAL040C 3 +YAL041W 8 +YAL042C-A 1 +YAL042W 5 +YAL043C 9 +YAL044C 0 +YAL044W-A 0 +YAL045C 0 +YAL046C 2 +YAL047C 2 +YAL047W-A 0 +YAL048C 7 +YAL049C 1 +YAL051W 3 +YAL053W 5 +YAL054C 2 +YAL055W 3 +YAL056C-A 0 +YAL056W 7 +YAL058W 4 +YAL059C-A 6 +YAL059W 4 +YAL060W 1 +YAL061W 4 +YAL062W 4 +YAL063C 0 +YAL063C-A 0 +YAL064C-A 0 +YAL064W 0 +YAL064W-B 0 +YAL065C 2 +YAL066W 0 +YAL067C 8 +YAL067W-A 1 +YAL068C 1 +YAL068W-A 0 +YAL069W 0 +YAR002C-A 0 +YAR002W 1 +YAR003W 4 +YAR007C 7 +YAR008W 0 +YAR009C 1 +YAR010C 0 +YAR014C 4 +YAR015W 4 +YAR018C 4 +YAR019C 4 +YAR019W-A 3 +YAR020C 0 +YAR023C 1 +YAR027W 0 +YAR028W 3 +YAR029W 0 +YAR030C 2 +YAR031W 4 +YAR033W 0 +YAR035C-A 0 +YAR035W 3 +YAR042W 4 +YAR047C 0 +YAR050W 4 +YAR053W 0 +YAR060C 2 +YAR061W 0 +YAR062W 2 +YAR064W 1 +YAR066W 2 +YAR068W 2 +YAR069C 1 +YAR070C 0 +YAR071W 4 +YAR073W 1 +YAR075W 0 +snR18 0 +tA(UGC)A 0 +tL(CAA)A 1 +tP(UGG)A 2 +tS(AGA)A 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/htseq-test-paired_othercounts.tsv Mon Jan 27 14:12:09 2014 -0500 @@ -0,0 +1,5 @@ +no_feature 533 +ambiguous 1 +too_low_aQual 0 +not_aligned 0 +alignment_not_unique 0
--- a/test-data/htseq-test_counts.tsv Tue Sep 04 14:00:14 2012 -0400 +++ b/test-data/htseq-test_counts.tsv Mon Jan 27 14:12:09 2014 -0500 @@ -1,60 +1,4 @@ -15S_rRNA 0 -21S_rRNA 0 HRA1 0 -LSR1 0 -NME1 0 -Q0010 0 -Q0017 0 -Q0032 0 -Q0045 0 -Q0050 0 -Q0055 0 -Q0060 0 -Q0065 0 -Q0070 0 -Q0075 0 -Q0080 0 -Q0085 0 -Q0092 0 -Q0105 0 -Q0110 0 -Q0115 0 -Q0120 0 -Q0130 0 -Q0140 0 -Q0142 0 -Q0143 0 -Q0144 0 -Q0160 0 -Q0182 0 -Q0250 0 -Q0255 0 -Q0275 0 -Q0297 0 -R0010W 3 -R0020C 14 -R0030W 1 -R0040C 20 -RDN18-1 205 -RDN18-2 2 -RDN25-1 1408 -RDN25-2 59 -RDN5-1 0 -RDN5-2 1 -RDN5-3 0 -RDN5-4 0 -RDN5-5 3 -RDN5-6 0 -RDN58-1 85 -RDN58-2 1 -RNA170 0 -RPM1 0 -RPR1 0 -RUF5-1 0 -RUF5-2 0 -SCR1 0 -SRG1 1 -TLC1 0 YAL001C 3 YAL002W 2 YAL003W 31 @@ -176,6954 +120,8 @@ YAR071W 1 YAR073W 0 YAR075W 0 -YBL001C 2 -YBL002W 6 -YBL003C 20 -YBL004W 8 -YBL005W 2 -YBL005W-A 0 -YBL005W-B 3 -YBL006C 1 -YBL006W-A 0 -YBL007C 4 -YBL008W 2 -YBL008W-A 0 -YBL009W 3 -YBL010C 1 -YBL011W 4 -YBL012C 0 -YBL013W 0 -YBL014C 0 -YBL015W 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/htseq-test_othercounts.tsv Mon Jan 27 14:12:09 2014 -0500 @@ -0,0 +1,5 @@ +no_feature 19 +ambiguous 0 +too_low_aQual 0 +not_aligned 1336 +alignment_not_unique 0
--- a/tool_dependencies.xml Tue Sep 04 14:00:14 2012 -0400 +++ b/tool_dependencies.xml Mon Jan 27 14:12:09 2014 -0500 @@ -1,17 +1,34 @@ <?xml version="1.0"?> <tool_dependency> - <package name="htseq" version="0.5.3p9"> + + <package name="numpy" version="1.7.1"> + <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="samtools" version="0.1.19"> + <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="picard" version="1.56.0"> + <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="htseq" version="0.5.4p5"> <install version="1.0"> <actions> - <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action> - <action type="shell_command">mkdir -p $INSTALL_DIR/lib/python</action> - <action type="set_environment"> - <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> + <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action> + <!-- populate the environment variables from the dependend repos --> + <action type="set_environment_for_install"> + <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.7.1" /> + </repository> </action> - <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py build</action> - <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> + <action type="make_directory">$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 $INSTALL_DIR/bin</action> <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> @@ -19,27 +36,5 @@ Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package. </readme> </package> - <package name="samtools" version="0.1.18"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> - <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>misc/maq2sam-long</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Compiling SAMtools requires the ncurses and zlib development libraries. - </readme> - </package> + </tool_dependency>