Mercurial > repos > iuc > slamdunk
changeset 5:8b62f89924a7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 64bbe6ec9a3f3cd6241fa4cf0e0548e0e67629a0"
| author | iuc |
|---|---|
| date | Sat, 18 Jan 2020 12:59:37 -0500 |
| parents | fe3fe68b09a7 |
| children | 141f65f7c7c8 |
| files | macros.xml slamdunk.xml test-data/reads1_overallrates.csv test-data/reads_slamdunk_mapped_filtered_tcount.tsv test-data/summary.txt |
| diffstat | 5 files changed, 11 insertions(+), 8 deletions(-) [+] |
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--- a/macros.xml Fri May 24 13:30:30 2019 -0400 +++ b/macros.xml Sat Jan 18 12:59:37 2020 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.3.3</token> + <token name="@TOOL_VERSION@">0.4.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">slamdunk</requirement> @@ -29,7 +29,7 @@ </xml> <xml name="citations"> <citation type="doi"> - 10.1186/s12859-019-2849-7 + 10.1186/s12859-019-2849-7 </citation> </xml> -</macros> \ No newline at end of file +</macros>
--- a/slamdunk.xml Fri May 24 13:30:30 2019 -0400 +++ b/slamdunk.xml Sat Jan 18 12:59:37 2020 -0500 @@ -125,7 +125,7 @@ </output_collection> <output_collection name="outputTsv"> <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" - lines_diff="2" /> + compare="re_match" /> </output_collection> <output_collection name="outputVcf"> <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" /> @@ -134,6 +134,7 @@ <test> <!--Ensure built-in fasta works --> <param name="reference_source_selector" value="cached" /> + <param name="ref_file" value="hg38full" /> <param name="Reference" value="actb.bed" /> <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" /> <param name="readLength" value="100" /> @@ -148,7 +149,7 @@ </output_collection> <output_collection name="outputTsv"> <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" - lines_diff="2" /> + compare="re_match" /> </output_collection> <output_collection name="outputVcf"> <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
--- a/test-data/reads1_overallrates.csv Fri May 24 13:30:30 2019 -0400 +++ b/test-data/reads1_overallrates.csv Sat Jan 18 12:59:37 2020 -0500 @@ -1,4 +1,4 @@ -# slamdunk rates v0.3.3 +# slamdunk rates v0.4.1 A a C c G g T t N n A 93 20 0 0 0 1 0 0 0 0 C 0 0 106 12 0 0 0 0 0 0
--- a/test-data/reads_slamdunk_mapped_filtered_tcount.tsv Fri May 24 13:30:30 2019 -0400 +++ b/test-data/reads_slamdunk_mapped_filtered_tcount.tsv Sat Jan 18 12:59:37 2020 -0500 @@ -1,2 +1,4 @@ +#slamdunk v0.4.1 3 sample info: sample_0 0 NA -1 +#annotation: dataset_.*.dat .* Chromosome Start End Name Length Strand ConversionRate ReadsCPM Tcontent CoverageOnTs ConversionsOnTs ReadCount TcReadCount multimapCount ConversionRateLower ConversionRateUpper -chr5 120498 122492 Actb 1994 + 0.0222222222222 666666.666667 445 90 2 8 4 0 -1.0 -1.0 +chr5 120498 122492 Actb 1994 \+ 0.022\d* 666666.66\d* 445 90 2 8 4 0 -1\.0 -1\.0
--- a/test-data/summary.txt Fri May 24 13:30:30 2019 -0400 +++ b/test-data/summary.txt Sat Jan 18 12:59:37 2020 -0500 @@ -1,4 +1,4 @@ -# slamdunk summary v0.3.3 +# slamdunk summary v0.4.1 FileName SampleName SampleType SampleTime Sequenced Mapped Deduplicated MQ-Filtered Identity-Filtered NM-Filtered Multimap-Filtered Retained Counted Annotation ./filter/reads1.bam sample_1 NA -1 12 12 0 0 0 0 0 12 16 ./filter/reads2.bam sample_2 NA -1 6 6 0 0 0 0 0 6 12