| Previous changeset 2:07d36bc47eaf (2021-12-07) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0" |
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modified:
blast2lca.xml macros.xml |
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added:
test-data/input1.sam test-data/input2.sam |
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| diff -r 07d36bc47eaf -r a80281b0172e blast2lca.xml --- a/blast2lca.xml Tue Dec 07 10:18:20 2021 +0000 +++ b/blast2lca.xml Sat Dec 11 11:53:22 2021 +0000 |
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| @@ -76,7 +76,10 @@ <param argument="--showRanks" type="boolean" truevalue="--showRanks" falsevalue="" checked="true" label="Show taxonomic ranks?"/> <param argument="--officialRanksOnly" type="boolean" truevalue="--officialRanksOnly" falsevalue="" checked="true" label="Report only taxa that have an official rank?"/> <param argument="--showTaxIds" type="boolean" truevalue="--showTaxIds" falsevalue="" checked="false" label="Report taxon ids rather than taxon names?"/> - <expand macro="blast_params"/> + <expand macro="min_score_param"/> + <expand macro="max_expected_param"/> + <expand macro="min_percent_identity_param"/> + <expand macro="top_percent_param"/> <param argument="--maxKeggPerRead" type="integer" value="4" label="Maximum number of KEGG assignments to report for a read"/> <param argument="--applyTopPercentKegg" type="boolean" truevalue="--applyTopPercentKegg" falsevalue="" checked="true" label="Apply top percent filter in KEGG KO analysis?"/> <param argument="--parseTaxonNames" type="boolean" truevalue="--parseTaxonNames" falsevalue="" checked="true" label="Apply top percent filter in KEGG KO analysis?"/> |
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| diff -r 07d36bc47eaf -r a80281b0172e macros.xml --- a/macros.xml Tue Dec 07 10:18:20 2021 +0000 +++ b/macros.xml Sat Dec 11 11:53:22 2021 +0000 |
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| @@ -79,10 +79,16 @@ <macro name="classify_param"> <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/> </macro> - <macro name="blast_params"> + <macro name="min_score_param"> <param argument="--minScore" type="float" value="50.0" label="Minimum score"/> + </macro> + <macro name="max_expected_param"> <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/> + </macro> + <macro name="min_percent_identity_param"> <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/> + </macro> + <macro name="top_percent_param"> <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/> </macro> <macro name="min_max_params"> |
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| diff -r 07d36bc47eaf -r a80281b0172e test-data/input1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.sam Sat Dec 11 11:53:22 2021 +0000 |
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| @@ -0,0 +1,5 @@ +@HD VN:1.5 SO:unsorted GO:query +@PG ID:1 PN:MALT CL:--mode BlastN --matchScore 2 --mismatchScore -3 --setLambda 0.625 --setK 0.41 --alignmentType Local --inFile 13-1941-6_S4_L001_R1_600000_fastq_gz.fastq.gz --index /home/galaxy/tool-data/malt_index/AF2122-1 --output ./output.rma6 --numThreads 1 --memoryMode load --maxTables 0 --minBitScore 50.0 --maxExpected 1.0 --minPercentIdentity 0.0 --maxAlignmentsPerQuery 25 --maxAlignmentsPerRef 1 --topPercent 10.0 --minSupportPercent 0.001 --minSupport 0 --minPercentIdentityLCA 0.0 --maxSeedsPerFrame 100 --maxSeedsPerRef 20 --seedShift 1 --gapOpen 11 --gapExtend 1 --band 4 --alignments ./alignments_output.SAM.gz --format SAM --outAligned ./aligned_output.fna.gz --outUnaligned ./unaligned_output.fna.gz DS:BlastN +@RG ID:1 PL:unknown SM:unknown +@CO BlastN-like alignments +@CO Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length |
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| diff -r 07d36bc47eaf -r a80281b0172e test-data/input2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input2.sam Sat Dec 11 11:53:22 2021 +0000 |
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| @@ -0,0 +1,5 @@ +@HD VN:1.5 SO:unsorted GO:query +@PG ID:1 PN:MALT CL:--mode BlastN --matchScore 2 --mismatchScore -3 --setLambda 0.625 --setK 0.41 --alignmentType Local --inFile 13-1941-6_S4_L001_R2_600000_fastq_gz.fastq.gz --index /home/galaxy/tool-data/malt_index/AF2122-1 --output ./output.rma6 --numThreads 1 --memoryMode load --maxTables 0 --minBitScore 50.0 --maxExpected 1.0 --minPercentIdentity 0.0 --maxAlignmentsPerQuery 25 --maxAlignmentsPerRef 1 --topPercent 10.0 --minSupportPercent 0.001 --minSupport 0 --minPercentIdentityLCA 0.0 --maxSeedsPerFrame 100 --maxSeedsPerRef 20 --seedShift 1 --gapOpen 11 --gapExtend 1 --band 4 --alignments ./alignments_output.SAM.gz --format SAM --outAligned ./aligned_output.fna.gz --outUnaligned ./unaligned_output.fna.gz DS:BlastN +@RG ID:1 PL:unknown SM:unknown +@CO BlastN-like alignments +@CO Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length |