| Previous changeset 3:8157a81f511c (2022-02-01) Next changeset 5:81cbb6a4c1ca (2022-03-17) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" |
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modified:
bbmap.xml macros.xml |
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removed:
test-data/output1.bam test-data/output2.bam test-data/output3.bam |
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| diff -r 8157a81f511c -r 6d44c9f1a42b bbmap.xml --- a/bbmap.xml Tue Feb 01 23:01:08 2022 +0000 +++ b/bbmap.xml Thu Feb 03 21:13:25 2022 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+<tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy3" profile="@PROFILE@">\n <description>short-read aligner</description>\n <macros>\n <import>macros.xml</import>\n@@ -44,59 +44,274 @@\n ln -s \'${read2}\' \'${read2_file}\' &&\n #end if\n \n-bbmap.sh t=\\${GALAXY_SLOTS:-4} ref=\'${ref}\'\n+bbmap.sh\n+\n+#### Indexing Parameters\n+nodisk=f\n+ref=\'${ref}\'\n+k=13\n+usemodulo=f\n+rebuild=f\n+\n+#### Input Parameters\n #if str($input_type_cond.input_type) == \'single\':\n in=\'${read1_file}\'\n #else:\n- in1=\'${read1_file}\' in2=\'${read2_file}\'\n+ in=\'${read1_file}\' in2=\'${read2_file}\'\n #end if\n-#if str($output_sort) == \'coordinate\':\n- out=\'mapped.bam\'; samtools sort -@\\${GALAXY_SLOTS:-4} -T "\\${TMPDIR:-.}" -O bam -o \'$output\' \'mapped.bam\'\n-#elif str($output_sort) == \'name\':\n- out=\'mapped.bam\'; samtools sort -n -@\\${GALAXY_SLOTS:-4} -T \'\\${TMPDIR:-.}\' -O bam -o \'$output\' \'mapped.bam\'\n+fastareadlen=500\n+unpigz=f\n+touppercase=t\n+\n+#### Sampling Parameters\n+reads=-1\n+samplerate=1\n+skipreads=0\n+\n+#### Mapping Parameters\n+maxindel=$mapping_options.maxindel\n+strictmaxindel=\'$mapping_options.strictmaxindel\'\n+tipsearch=$mapping_options.tipsearch\n+minid=$mapping_options.minid\n+minhits=$mapping_options.minhits\n+local=\'$mapping_options.local\'\n+perfectmode=\'$mapping_options.perfectmode\'\n+semiperfectmode=\'$mapping_options.semiperfectmode\'\n+threads=\\${GALAXY_SLOTS:-4}\n+ambiguous=\'$mapping_options.ambiguous\'\n+samestrandpairs=\'$mapping_options.samestrandpairs\'\n+requirecorrectstrand=\'$mapping_options.requirecorrectstrand\'\n+killbadpairs=\'$mapping_options.killbadpairs\'\n+pairedonly=\'$mapping_options.pairedonly\'\n+rcomp=\'$mapping_options.rcomp\'\n+rcompmate=\'$mapping_options.rcompmate\'\n+pairlen=$mapping_options.pairlen\n+rescuedist=$mapping_options.rescuedist\n+rescuemismatches=$mapping_options.rescuemismatches\n+averagepairdist=$mapping_options.averagepairdist\n+deterministic=\'$mapping_options.deterministic\'\n+bandwidthratio=\'$mapping_options.bandwidthratio\'\n+bandwidth=\'$mapping_options.bandwidth\'\n+usejni=\'f\'\n+maxsites2=$mapping_options.maxsites2\n+ignorefrequentkmers=\'$mapping_options.ignorefrequentkmers\'\n+excludefraction=$mapping_options.excludefraction\n+greedy=\'$mapping_options.greedy\'\n+kfilter=$mapping_options.kfilter\n+\n+#### Quality and Trimming Parameters\n+qin=\'auto\'\n+qout=\'auto\'\n+qtrim=\'$qt_options.qtrim\'\n+untrim=\'$qt_options.untrim\'\n+trimq=$qt_options.trimq\n+mintrimlength=$qt_options.mintrimlength\n+fakefastaquality=$qt_options.fakefastaquality\n+ignorebadquality=\'$qt_options.ignorebadquality\'\n+usequality=\'$qt_options.usequality\'\n+minaveragequality=$qt_options.minaveragequality\n+maqb=$qt_options.maqb\n+\n+#### Post-Filtering options\n+idfilter=$pf_options.idfilter\n+subfilter=$pf_options.subfilter\n+insfilter=$pf_options.insfilter\n+delfilter=$pf_options.delfilter\n+indelfilter=$pf_options.indelfilter\n+editfilter=$pf_options.editfilter\n+inslenfilter=$pf_options.inslenfilter\n+dellenfilter=$pf_options.dellenfilter\n+nfilter=$pf_options.nfilter\n+\n+#### Output parameters\n+secondary=\'$output_options.secondary\'\n+maxsites=$output_options.maxsites\n+sssr=$output_options.sssr\n+ssao=\'$output_options.ssao\'\n+quickmatch=\'$output_options.quickmatch\'\n+trimreaddescriptions=\'$output_options.trimreaddescriptions\'\n+machineout=\'$output_options.machineout\'\n+printunmappedcount=\'$output_options.printunmappedcount\'\n+renamebyinsert=\'$output_options.renamebyinsert\'\n+#if str($output_options.output_sort) == \'coordinate\':\n+ out=\'all_reads.bam\'\n+ outu=\'unmapped_reads.bam\'\n+ outm=\'mapped_reads.bam\'\n+ && samtools sort -@\\${GALAXY_SLOTS:-4} -T "\\${TMPDIR:-.}" -O bam -o \'$output_all_reads\' \'all_reads.bam\'\n+ && samtools sort -@\\${GALAXY_SLOTS:-4} -T "\\${TMPDIR:-.}" -O bam -o \'$output_unmapped_reads\' \'unmapped_reads.bam\'\n+ && samtools sort -@\\${GALAXY_SLOTS:-4} -T "\\${TMPDIR:-.}" -O bam -o \'$output_mapped_reads\' \'m'..b'put name="output" file="output1.bam" ftype="bam" lines_diff="4">\n- <metadata name="dbkey" value="89" />\n+ <param name="output_sort" value="coordinate"/>\n+ <output name="output_all_reads" ftype="bam">\n+ <metadata name="dbkey" value="89"/>\n+ <assert_contents>\n+ <has_size value="9433" delta="300"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_unmapped_reads" ftype="bam">\n+ <metadata name="dbkey" value="89"/>\n+ <assert_contents>\n+ <has_size value="9432" delta="300"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_mapped_reads" ftype="bam">\n+ <metadata name="dbkey" value="89"/>\n+ <assert_contents>\n+ <has_size value="938" delta="100"/>\n+ </assert_contents>\n </output>\n </test>\n <!-- Paired reads in separate datasets, cached reference, output name sorted -->\n- <test expect_num_outputs="1">\n+ <test expect_num_outputs="3">\n <param name="input_type" value="pair"/>\n <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>\n <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>\n <param name="output_sort" value="name"/>\n- <output name="output" file="output2.bam" ftype="qname_sorted.bam" lines_diff="4">\n- <metadata name="dbkey" value="89" />\n+ <output name="output_all_reads" ftype="qname_sorted.bam">\n+ <metadata name="dbkey" value="89"/>\n+ <assert_contents>\n+ <has_size value="17103" delta="600"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_unmapped_reads" ftype="qname_sorted.bam">\n+ <metadata name="dbkey" value="89"/>\n+ <assert_contents>\n+ <has_size value="17105" delta="600"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_mapped_reads" ftype="qname_sorted.bam">\n+ <metadata name="dbkey" value="89"/>\n+ <assert_contents>\n+ <has_size value="967" delta="100"/>\n+ </assert_contents>\n </output>\n </test>\n <!-- Collection of Paired reads, history reference, output unsorted -->\n- <test expect_num_outputs="1">\n+ <test expect_num_outputs="3">\n <param name="input_type" value="paired"/>\n <param name="reads_collection">\n <collection type="paired">\n@@ -107,8 +322,23 @@\n <param name="ref_source" value="history"/>\n <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/>\n <param name="output_sort" value="unsorted"/>\n- <output name="output" file="output3.bam" ftype="qname_input_sorted.bam" lines_diff="4">\n- <metadata name="dbkey" value="89" />\n+ <output name="output_all_reads" ftype="qname_input_sorted.bam">\n+ <metadata name="dbkey" value="89"/>\n+ <assert_contents>\n+ <has_size value="17059" delta="600"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_unmapped_reads" ftype="qname_input_sorted.bam">\n+ <metadata name="dbkey" value="89"/>\n+ <assert_contents>\n+ <has_size value="17059" delta="600"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_mapped_reads" ftype="qname_input_sorted.bam">\n+ <metadata name="dbkey" value="89"/>\n+ <assert_contents>\n+ <has_size value="906" delta="100"/>\n+ </assert_contents>\n </output>\n </test>\n </tests>\n' |
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| diff -r 8157a81f511c -r 6d44c9f1a42b macros.xml --- a/macros.xml Tue Feb 01 23:01:08 2022 +0000 +++ b/macros.xml Thu Feb 03 21:13:25 2022 +0000 |
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| @@ -1,10 +1,10 @@ <macros> <token name="@WRAPPER_VERSION@">1.0.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">20.09</token> <xml name="requirements"> <requirements> - <requirement type="package" version="38.92">bbmap</requirement> + <requirement type="package" version="38.93">bbmap</requirement> </requirements> </xml> <macro name="dbKeyActionsBBMap"> |
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| diff -r 8157a81f511c -r 6d44c9f1a42b test-data/output1.bam |
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| Binary file test-data/output1.bam has changed |
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| diff -r 8157a81f511c -r 6d44c9f1a42b test-data/output2.bam |
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| Binary file test-data/output2.bam has changed |
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| diff -r 8157a81f511c -r 6d44c9f1a42b test-data/output3.bam |
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| Binary file test-data/output3.bam has changed |