| Previous changeset 2:f5d08224af89 (2012-09-04) Next changeset 4:14bec14f4290 (2012-09-11) |
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Commit message:
Split feature and non-feature counts, removed tool_dependencies.xml (for now) |
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modified:
htseq-count.xml test-data/htseq-test_counts.tsv |
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added:
test-data/htseq-test_othercounts.tsv |
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removed:
tool_dependencies.xml |
| b |
| diff -r f5d08224af89 -r f7a5b54a8d4f htseq-count.xml --- a/htseq-count.xml Tue Sep 04 14:16:33 2012 -0400 +++ b/htseq-count.xml Mon Sep 10 17:30:10 2012 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="htseq_count" name="htseq-count" version="0.1"> +<tool id="htseq_count" name="htseq-count" version="0.2"> <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> @@ -35,7 +35,7 @@ $samfile #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 > $samoutfile #end if</command> @@ -93,6 +93,7 @@ <outputs> <data format="tabular" name="counts" label="${tool.name} on ${on_string}"/> + <data format="tabular" name="othercounts" label="${tool.name} on ${on_string} (no feature)"/> <data format="bam" name="samoutfile" label="${tool.name} on ${on_string} (BAM)"> <filter>samout_conditional['samout']</filter> </data> @@ -108,12 +109,14 @@ <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> <!-- Seems to be an issue setting the $reference_fasta_filename variable during test <test> @@ -123,6 +126,7 @@ <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> --> |
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| diff -r f5d08224af89 -r f7a5b54a8d4f test-data/htseq-test_counts.tsv --- a/test-data/htseq-test_counts.tsv Tue Sep 04 14:16:33 2012 -0400 +++ b/test-data/htseq-test_counts.tsv Mon Sep 10 17:30:10 2012 -0400 |
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| @@ -7122,8 +7122,3 @@ 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 |
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| diff -r f5d08224af89 -r f7a5b54a8d4f test-data/htseq-test_othercounts.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/htseq-test_othercounts.tsv Mon Sep 10 17:30:10 2012 -0400 |
| b |
| @@ -0,0 +1,5 @@ +no_feature 1437 +ambiguous 67 +too_low_aQual 0 +not_aligned 1336 +alignment_not_unique 0 |
| b |
| diff -r f5d08224af89 -r f7a5b54a8d4f tool_dependencies.xml --- a/tool_dependencies.xml Tue Sep 04 14:16:33 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,45 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="htseq" version="0.5.3p9"> - <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> - <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 $INSTALL_DIR/bin</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$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> - </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> |