| Previous changeset 0:fa3c3a64c993 (2021-11-24) Next changeset 2:5be253dd3e08 (2021-12-07) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d" |
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modified:
blast2rma.xml macros.xml |
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added:
test-data/daa2info_output1.txt test-data/daa2info_output2.txt test-data/daa2info_output_summary2.txt test-data/input.daa test-data/input_meganized.daa test-data/read_extractor_input.rma6 test-data/read_extractor_output.txt |
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| diff -r fa3c3a64c993 -r 2f8d3924bb3b blast2rma.xml --- a/blast2rma.xml Wed Nov 24 21:52:14 2021 +0000 +++ b/blast2rma.xml Fri Dec 03 23:09:53 2021 +0000 |
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| @@ -114,8 +114,8 @@ --lcaAlgorithm '$advanced_options.lcaAlgorithm' --lcaCoveragePercent $advanced_options.lcaCoveragePercent --readAssignmentMode '$advanced_options.readAssignmentMode' -#if str($advanced_options.con_file_cond.conFile) == 'yes': - --conFile '$advanced_options.con_file_cond.conFile' +#if $advanced_options.conFile: + --conFile '$advanced_options.conFile' #end if #if str($input_type_cond.input_type) == 'paired': && mv './tmp.rma6' '$rma6_output' @@ -127,35 +127,14 @@ <expand macro="blast_mode_options"/> </param> <section name="advanced_options" title="Advanced options" expanded="false"> - <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/> + <expand macro="long_reads_param"/> <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/> - <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/> - <expand macro="common_blast_params"/> - <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/> - <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/> - <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/> - <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/> - <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/> - <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment"> - <option value="naive" selected="true">naive</option> - <option value="weighted">weighted</option> - <option value="longReads">longReads</option> - </param> - <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/> - <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode"> - <option value="alignedBases" selected="true">alignedBases</option> - <option value="readCount">readCount</option> - </param> - <conditional name="con_file_cond"> - <param argument="--conFile" type="select" label="Process a file of contaminant taxa" help="One id or name per line"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"/> - <when value="yes"> - <param argument="conFile" type="data" format="txt" label="File of contaminant taxa"/> - </when> - </conditional> + <expand macro="classify_param"/> + <expand macro="blast_params"/> + <expand macro="min_max_params"/> + <expand macro="lca_params"/> + <expand macro="read_assignment_mode_param"/> + <expand macro="con_file_param"/> </section> </inputs> <outputs> @@ -178,7 +157,6 @@ <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/> <param name="blast1" value="blast_R1.txt" ftype="txt"/> <param name="blastMode" value="BlastN"/> - <param name="conFile" value="yes"/> <param name="conFile" value="contaminants.txt" ftype="txt"/> <output name="rma6_output" ftype="rma6"> <assert_contents> @@ -239,8 +217,6 @@ This tool outputs a RealMedia Audio (RMA) file. MEGAN uses an update of the original RMA file format known as RMA6. This update requires less disk space for files. </help> - <citations> - <citation type="doi">https://doi.org/10.1101/050559</citation> - </citations> + <expand macro="citations"/> </tool> |
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| diff -r fa3c3a64c993 -r 2f8d3924bb3b macros.xml --- a/macros.xml Wed Nov 24 21:52:14 2021 +0000 +++ b/macros.xml Fri Dec 03 23:09:53 2021 +0000 |
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| @@ -38,6 +38,18 @@ </when> </conditional> </macro> + <macro name="long_reads_param"> + <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/> + </macro> + <macro name="classification_options"> + <option value="EC" selected="true">EC</option> + <option value="EGGNOG">EGGNOG</option> + <option value="GTDB">GTDB</option> + <option value="INTERPRO2GO">INTERPRO2GO</option> + <option value="KEGG">KEGG</option> + <option value="SEED">SEED</option> + <option value="Taxonomy">Taxonomy</option> + </macro> <macro name="blast_mode_options"> <option value="Unknown" selected="true">Unknown</option> <option value="BlastN">BlastN</option> @@ -45,12 +57,42 @@ <option value="BlastX">BlastX</option> <option value="Classifier">Classifier</option> </macro> - <macro name="common_blast_params"> + <macro name="classify_param"> + <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/> + </macro> + <macro name="blast_params"> <param argument="--minScore" type="float" value="50.0" label="Minimum score"/> <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/> <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/> <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/> </macro> + <macro name="min_max_params"> + <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/> + <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/> + <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/> + <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/> + <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/> + </macro> + <macro name="lca_params"> + <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment"> + <option value="naive" selected="true">naive</option> + <option value="weighted">weighted</option> + <option value="longReads">longReads</option> + </param> + <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/> + </macro> + <macro name="read_assignment_mode_param"> + <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode"> + <option value="alignedBases" selected="true">alignedBases</option> + <option value="readCount">readCount</option> + </param> + </macro> + <macro name="con_file_param"> + <param argument="--conFile" type="data" format="txt" optional="true" label="File of contaminant taxa (one id or name per line)" help="Optional, no selection ignores"/> + </macro> + <macro name="mapdb_param"> + <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db" help="Optional, no selection ignores"/> + </macro> <xml name="sanitize_query" token_validinitial="string.printable"> <sanitizer> <valid initial="@VALIDINITIAL@"> @@ -64,6 +106,8 @@ </xml> <xml name="citations"> <citations> + <citation type="doi">10.1038/nmeth.3176</citation> + <citation type="doi">10.1101/gr.120618.111</citation> <citation type="doi">10.1101/gr.5969107</citation> </citations> </xml> |
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| diff -r fa3c3a64c993 -r 2f8d3924bb3b test-data/daa2info_output1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/daa2info_output1.txt Fri Dec 03 23:09:53 2021 +0000 |
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| @@ -0,0 +1,3 @@ +# Number of reads: 1 +# Alignment mode: BLASTP +# Is meganized: false |
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| diff -r fa3c3a64c993 -r 2f8d3924bb3b test-data/daa2info_output2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/daa2info_output2.txt Fri Dec 03 23:09:53 2021 +0000 |
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| @@ -0,0 +1,19 @@ +# Number of reads: 1 +# Alignment mode: BLASTP +# Is meganized: true +# Classifications: Taxonomy +# Meganization summary: +## @Creator DAA2Info +## @CreationDate +## @ContentType Summary4 +## @Names input +## @BlastMode BlastP +## @Uids +## @Sizes 1.0 +## @TotalReads 1 +## @AdditionalReads 0 +## Classifications: +## Taxonomy (1 classes) +## @Algorithm Taxonomy merge +## @Parameters +## |
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| diff -r fa3c3a64c993 -r 2f8d3924bb3b test-data/daa2info_output_summary2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/daa2info_output_summary2.txt Fri Dec 03 23:09:53 2021 +0000 |
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| @@ -0,0 +1,16 @@ +@Creator DAA2Info +@CreationDate +@ContentType Summary4 +@Names input +@BlastMode BlastP +@Uids +@Sizes 1 +@TotalReads 1 +@AdditionalReads 0 +@Algorithm Taxonomy merge +@Parameters +@ColorTable Fews8 White-Green +TAX -2 1 +END_OF_DATA_TABLE +#SampleID @Source +input.daa input.DAA |
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| diff -r fa3c3a64c993 -r 2f8d3924bb3b test-data/input.daa |
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| Binary file test-data/input.daa has changed |
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| diff -r fa3c3a64c993 -r 2f8d3924bb3b test-data/input_meganized.daa |
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| Binary file test-data/input_meganized.daa has changed |
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| diff -r fa3c3a64c993 -r 2f8d3924bb3b test-data/read_extractor_input.rma6 |
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| Binary file test-data/read_extractor_input.rma6 has changed |
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| diff -r fa3c3a64c993 -r 2f8d3924bb3b test-data/read_extractor_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read_extractor_output.txt Fri Dec 03 23:09:53 2021 +0000 |
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| @@ -0,0 +1,2 @@ +>sequence +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY |