# HG changeset patch # User lparsons # Date 1397236417 14400 # Node ID c86659f03e98922c6727c637ef471d67cc9a406b # Parent 1a69449ae02599ae719077b916f877fa32d15c2a Uploaded test version diff -r 1a69449ae025 -r c86659f03e98 .hgignore --- a/.hgignore Tue Nov 05 11:07:33 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -^package$ -syntax: glob -*.pyc diff -r 1a69449ae025 -r c86659f03e98 .hgtags --- a/.hgtags Tue Nov 05 11:07:33 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -142ec9462fa644cd29642ea0ad10e9889ce75619 0.3 -3e7b1e8a69f9d79b8de603f24e466deb7b192100 0.3.release2 -496a7dc0786f8367264520dfff6e8e8e744de3b2 0.3.1 diff -r 1a69449ae025 -r c86659f03e98 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Apr 11 13:13:37 2014 -0400 @@ -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 +------------ + +Installation 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) 2012-2014, 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 1a69449ae025 -r c86659f03e98 fabfile.py --- a/fabfile.py Tue Nov 05 11:07:33 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -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 1a69449ae025 -r c86659f03e98 htseq-count.xml --- a/htseq-count.xml Tue Nov 05 11:07:33 2013 -0500 +++ b/htseq-count.xml Fri Apr 11 13:13:37 2014 -0400 @@ -1,11 +1,10 @@ - + - Count aligned reads in a BAM file that overlap features in a GFF file htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/' numpy - htseq + htseq samtools - picard ##set up input files @@ -18,18 +17,9 @@ #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path ) #end if #end if - #if str($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 $samfile prepared_input.sam && - #end if - #end if htseq-count + --format=$samfile.extension + --order=pos --mode=$mode --stranded=$stranded --minaqual=$minaqual @@ -38,15 +28,7 @@ #if $samout_conditional.samout: --samout=$__new_file_path__/${samoutfile.id}_tmp #end if - #if str($singlepaired) == "paired": - prepared_input.sam - #else: - #if $samfile.extension == "bam": - - - #else: - prepared_input.sam - #end if - #end if + $samfile $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: @@ -54,11 +36,6 @@ #end if - - Paired libraries will be sorted by read name prior to counting. - - - Mode to handle reads overlapping more than one feature. @@ -72,7 +49,7 @@ - + Skip all reads with alignment quality lower than the given minimum value diff -r 1a69449ae025 -r c86659f03e98 tool_dependencies.xml --- a/tool_dependencies.xml Tue Nov 05 11:07:33 2013 -0500 +++ b/tool_dependencies.xml Fri Apr 11 13:13:37 2014 -0400 @@ -6,17 +6,13 @@ - + - - - - - + - https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz + https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz