| Previous changeset 1:f1b6527ba952 (2021-12-07) Next changeset 3:6ca88053665c (2022-08-27) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0" |
|
modified:
daa_meganizer.xml macros.xml |
|
added:
test-data/input1.sam test-data/input2.sam |
| b |
| diff -r f1b6527ba952 -r bb2a8bd85c85 daa_meganizer.xml --- a/daa_meganizer.xml Tue Dec 07 10:17:41 2021 +0000 +++ b/daa_meganizer.xml Sat Dec 11 11:52:14 2021 +0000 |
| b |
| @@ -52,7 +52,10 @@ <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in the output files"/> <expand macro="long_reads_param"/> <expand macro="classify_param"/> - <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"/> <expand macro="min_max_params"/> <expand macro="lca_params"/> <expand macro="read_assignment_mode_param"/> @@ -65,7 +68,7 @@ <data name="output" format="daa"/> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="in" ftype="daa" value="input.daa"/> <output name="output" ftype="daa"> <assert_contents> |
| b |
| diff -r f1b6527ba952 -r bb2a8bd85c85 macros.xml --- a/macros.xml Tue Dec 07 10:17:41 2021 +0000 +++ b/macros.xml Sat Dec 11 11:52:14 2021 +0000 |
| b |
| @@ -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"> |
| b |
| diff -r f1b6527ba952 -r bb2a8bd85c85 test-data/input1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.sam Sat Dec 11 11:52:14 2021 +0000 |
| b |
| @@ -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 |
| b |
| diff -r f1b6527ba952 -r bb2a8bd85c85 test-data/input2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input2.sam Sat Dec 11 11:52:14 2021 +0000 |
| b |
| @@ -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 |