1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/63bc46cc73b7/ changeset: 63bc46cc73b7 user: jgoecks date: 2012-01-18 15:48:32 summary: Update Tophat tests for v1.4.0 affected #: 6 files
diff -r 6d2729e0cf8cda6413aefdbdbbc71eb4c00d48e0 -r 63bc46cc73b770a081f657534fd21ebf423f4e49 test-data/tophat_out1j.bed --- a/test-data/tophat_out1j.bed +++ b/test-data/tophat_out1j.bed @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 180 400 JUNC00000001 26 + 180 400 255,0,0 2 70,50 0,170 -test_chromosome 349 550 JUNC00000002 22 + 349 550 255,0,0 2 51,50 0,151 +test_chromosome 180 400 JUNC00000001 23 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 350 550 JUNC00000002 24 + 350 550 255,0,0 2 50,50 0,150
diff -r 6d2729e0cf8cda6413aefdbdbbc71eb4c00d48e0 -r 63bc46cc73b770a081f657534fd21ebf423f4e49 test-data/tophat_out2j.bed --- a/test-data/tophat_out2j.bed +++ b/test-data/tophat_out2j.bed @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 177 400 JUNC00000001 61 + 177 400 255,0,0 2 73,50 0,173 -test_chromosome 350 550 JUNC00000002 45 + 350 550 255,0,0 2 50,50 0,150 +test_chromosome 179 400 JUNC00000001 38 + 179 400 255,0,0 2 71,50 0,171 +test_chromosome 350 549 JUNC00000002 30 + 350 549 255,0,0 2 50,49 0,150
diff -r 6d2729e0cf8cda6413aefdbdbbc71eb4c00d48e0 -r 63bc46cc73b770a081f657534fd21ebf423f4e49 test-data/tophat_out3j.bed --- a/test-data/tophat_out3j.bed +++ b/test-data/tophat_out3j.bed @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 177 400 JUNC00000001 32 + 177 400 255,0,0 2 73,50 0,173 -test_chromosome 350 550 JUNC00000002 26 + 350 550 255,0,0 2 50,50 0,150 +test_chromosome 180 400 JUNC00000001 23 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 350 550 JUNC00000002 24 + 350 550 255,0,0 2 50,50 0,150
diff -r 6d2729e0cf8cda6413aefdbdbbc71eb4c00d48e0 -r 63bc46cc73b770a081f657534fd21ebf423f4e49 test-data/tophat_out4j.bed --- a/test-data/tophat_out4j.bed +++ b/test-data/tophat_out4j.bed @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 180 402 JUNC00000001 49 + 180 402 255,0,0 2 70,52 0,170 -test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 +test_chromosome 179 400 JUNC00000001 38 + 179 400 255,0,0 2 71,50 0,171 +test_chromosome 350 549 JUNC00000002 30 + 350 549 255,0,0 2 50,49 0,150
diff -r 6d2729e0cf8cda6413aefdbdbbc71eb4c00d48e0 -r 63bc46cc73b770a081f657534fd21ebf423f4e49 tools/ngs_rna/tophat_wrapper.py --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -210,6 +210,7 @@ tmp_stdout = open( tmp_out, 'wb' ) tmp_err = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_err, 'wb' ) + print cmd proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr ) returncode = proc.wait() tmp_stderr.close()
diff -r 6d2729e0cf8cda6413aefdbdbbc71eb4c00d48e0 -r 63bc46cc73b770a081f657534fd21ebf423f4e49 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -518,7 +518,7 @@ <test><!-- Tophat commands: bowtie-build -f test-data/tophat_in1.fasta tophat_in1 - tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +allow-indels +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger + tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger Replace the + with double-dash Rename the files in tmp_dir appropriately --> @@ -561,7 +561,7 @@ <!-- Test base-space paired-end reads with user-supplied reference fasta and full parameters --><test><!-- TopHat commands: - tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger + tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger Replace the + with double-dash Rename the files in tmp_dir appropriately --> @@ -589,13 +589,7 @@ <param name="use_annotations" value="No" /><param name="use_juncs" value="No" /><param name="no_novel_juncs" value="No" /> - <param name="use_search" value="Yes" /> - <param name="min_closure_exon" value="50" /> - <param name="min_closure_intron" value="50" /> - <param name="max_closure_intron" value="5000" /> - <param name="use_search" value="Yes" /> - <param name="min_coverage_intron" value="50" /> - <param name="max_coverage_intron" value="20000" /> + <param name="use_search" value="No" /><param name="microexon_search" value="Yes" /><output name="junctions" file="tophat_out4j.bed" /><output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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