# HG changeset patch # User Dave Bouvier # Date 1390849929 18000 # Node ID 265ca0f35789ba11dfb0855395d153db39c6df1e # Parent 30bb8acb77a4ea09b5a1166de04e437babb4f29d# Parent 14e18dc9ed13ea6d0b1c7db86bcd87c0d482eced Merge multiple heads. diff -r 14e18dc9ed13 -r 265ca0f35789 .hgignore --- /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 diff -r 14e18dc9ed13 -r 265ca0f35789 .hgtags --- /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 diff -r 14e18dc9ed13 -r 265ca0f35789 README.md --- /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 + +Repository-Development: + + +License +------- + +Copyright (c) 2012-2013, Lance R. Parsons +All rights reserved. + +Licensed under the BSD 2-Clause License: + + 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. diff -r 14e18dc9ed13 -r 265ca0f35789 fabfile.py --- /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)) diff -r 14e18dc9ed13 -r 265ca0f35789 htseq-count.xml --- 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 @@ - + - Count aligned reads in a BAM file that overlap features in a GFF file htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/' - htseq - samtools + numpy + htseq + samtools + picard ##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 - - 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 + + + Paired libraries will be sorted by read name prior to counting. + + @@ -59,11 +75,11 @@ Skip all reads with alignment quality lower than the given minimum value - + 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. - 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. + 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. @@ -78,7 +94,7 @@ - + @@ -92,14 +108,21 @@ - - + + + samout_conditional['samout'] + + + + + + @@ -108,12 +131,22 @@ + + + + + + + + + + @@ -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 ------ diff -r 14e18dc9ed13 -r 265ca0f35789 test-data/htseq-test-paired.bam Binary file test-data/htseq-test-paired.bam has changed diff -r 14e18dc9ed13 -r 265ca0f35789 test-data/htseq-test-paired_counts.tsv --- /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 diff -r 14e18dc9ed13 -r 265ca0f35789 test-data/htseq-test-paired_othercounts.tsv --- /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 diff -r 14e18dc9ed13 -r 265ca0f35789 test-data/htseq-test_counts.tsv --- 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 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-tT(AGU)N1 0 -tT(AGU)N2 0 -tT(AGU)O1 0 -tT(AGU)O2 0 -tT(CGU)K 0 -tT(UGU)G1 0 -tT(UGU)G2 0 -tT(UGU)H 0 -tT(UGU)P 0 -tT(UGU)Q1 0 -tT(XXX)Q2 0 -tV(AAC)E1 0 -tV(AAC)E2 0 -tV(AAC)G1 0 -tV(AAC)G2 0 -tV(AAC)G3 0 -tV(AAC)H 0 -tV(AAC)J 0 -tV(AAC)K1 0 -tV(AAC)K2 0 -tV(AAC)L 0 -tV(AAC)M1 0 -tV(AAC)M2 0 -tV(AAC)M3 0 -tV(AAC)O 0 -tV(CAC)D 0 -tV(CAC)H 0 -tV(UAC)B 0 -tV(UAC)D 0 -tV(UAC)Q 0 -tW(CCA)G1 0 -tW(CCA)G2 0 -tW(CCA)J 0 -tW(CCA)K 0 -tW(CCA)M 0 -tW(CCA)P 0 -tW(UCA)Q 0 -tX(XXX)D 0 -tY(GUA)D 0 -tY(GUA)F1 0 -tY(GUA)F2 0 -tY(GUA)J1 0 -tY(GUA)J2 0 -tY(GUA)M1 0 -tY(GUA)M2 0 -tY(GUA)O 0 -tY(GUA)Q 0 -no_feature 1437 -ambiguous 67 -too_low_aQual 0 -not_aligned 1336 -alignment_not_unique 0 diff -r 14e18dc9ed13 -r 265ca0f35789 test-data/htseq-test_othercounts.tsv --- /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 diff -r 14e18dc9ed13 -r 265ca0f35789 tool_dependencies.xml --- 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 @@ - + + + + + + + + + + + + + + - http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz - mkdir -p $INSTALL_DIR/lib/python - - $INSTALL_DIR/lib/python + https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz + + + + + - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py build - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin + $INSTALL_DIR/lib/python + $INSTALL_DIR/lib64/python + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin - $INSTALL_DIR/bin + $INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python + $INSTALL_DIR/bin @@ -19,27 +36,5 @@ Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package. - - - - http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2 - sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile - make - - samtools - $INSTALL_DIR/bin - - - misc/maq2sam-long - $INSTALL_DIR/bin - - - $INSTALL_DIR/bin - - - - - Compiling SAMtools requires the ncurses and zlib development libraries. - - +