Mercurial > repos > lparsons > htseq_count
changeset 16:227f9d3f0e32 draft
Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions
| author | lparsons |
|---|---|
| date | Fri, 11 Apr 2014 15:05:28 -0400 |
| parents | 3ffe4e2572a7 |
| children | d5edaf8dc974 |
| files | .hgignore .hgtags README.md fabfile.py htseq-count.xml tool_dependencies.xml |
| diffstat | 6 files changed, 15 insertions(+), 75 deletions(-) [+] |
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--- a/.hgignore Mon Jan 27 14:12:46 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -^package$ -syntax: glob -*.pyc
--- a/.hgtags Mon Jan 27 14:12:46 2014 -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
--- a/README.md Mon Jan 27 14:12:46 2014 -0500 +++ b/README.md Fri Apr 11 15:05:28 2014 -0400 @@ -9,7 +9,7 @@ Installation ------------ -Installtion directly from the [Galaxy +Installation directly from the [Galaxy Toolshed](http://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) is recommended. @@ -24,7 +24,7 @@ License ------- -Copyright (c) 2012-2013, Lance R. Parsons <lparsons@princeton.edu> +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>
--- a/fabfile.py Mon Jan 27 14:12:46 2014 -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))
--- a/htseq-count.xml Mon Jan 27 14:12:46 2014 -0500 +++ b/htseq-count.xml Fri Apr 11 15:05:28 2014 -0400 @@ -1,11 +1,10 @@ -<tool id="htseq_count" name="htseq-count" version="0.3.2"> +<tool id="htseq_count" name="htseq-count" version="0.4"> <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="0.5.4p5">htseq</requirement> + <requirement type="package" version="0.6.1">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 @@ -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 @@ -38,27 +28,14 @@ #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: && 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 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="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/> <param format="gff" name="gfffile" type="data" label="GFF File"/> <param name="mode" type="select" label="Mode"> <help>Mode to handle reads overlapping more than one feature.</help> @@ -72,7 +49,7 @@ <option value="no">No</option> <option value="reverse">Reverse</option> </param> - <param name="minaqual" type="integer" value="0" label="Minimum alignment quality"> + <param name="minaqual" type="integer" value="10" label="Minimum alignment quality"> <help>Skip all reads with alignment quality lower than the given minimum value</help> </param> <param name="featuretype" type="text" value="exon" label="Feature type"> @@ -188,8 +165,7 @@ The following figure illustrates the effect of these three modes: -.. image:: $PATH_TO_IMAGES/count_modes.png - :width: 500 +.. image:: count_modes.png Strandedness
--- a/tool_dependencies.xml Mon Jan 27 14:12:46 2014 -0500 +++ b/tool_dependencies.xml Fri Apr 11 15:05:28 2014 -0400 @@ -2,24 +2,20 @@ <tool_dependency> <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" /> + <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" 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" /> + <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> - <package name="htseq" version="0.5.4p5"> + <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-0.5.4p5.tar.gz</action> + <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="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"> <package name="numpy" version="1.7.1" /> </repository> </action>