| Previous changeset 1:77289957d47b (2020-02-26) Next changeset 3:43f9ca23c132 (2021-04-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67" |
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modified:
macros.xml mash_sketch.xml |
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added:
test-data/test_01_mash_sketch.msh test-data/test_02_mash_sketch.msh test-data/test_03_mash_sketch.msh test-data/test_04_mash_sketch.msh test-data/test_05_mash_sketch.msh test-data/test_06_mash_sketch.msh test-data/test_07_mash_sketch.msh |
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removed:
test-data/ERR024951_seqtk_sample_1000_1.sketch.msh test-data/test_assembly.sketch.msh |
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| diff -r 77289957d47b -r 91ee99b4f05a macros.xml --- a/macros.xml Wed Feb 26 15:48:46 2020 -0500 +++ b/macros.xml Sat Apr 24 11:29:14 2021 +0000 |
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| @@ -1,23 +1,19 @@ <macros> - <token name="@TOOL_VERSION@">2.1</token> + <token name="@TOOL_VERSION@">2.3</token> <token name="@INTYPES@"> fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz </token> - + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mash</requirement> + </requirements> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1186/s13059-016-0997-x</citation> </citations> </xml> - - <xml name="requirements"> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">mash</requirement> - </requirements> - </xml> - <xml name="version_command"> <version_command>mash --version</version_command> </xml> - </macros> |
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| diff -r 77289957d47b -r 91ee99b4f05a mash_sketch.xml --- a/mash_sketch.xml Wed Feb 26 15:48:46 2020 -0500 +++ b/mash_sketch.xml Sat Apr 24 11:29:14 2021 +0000 |
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| b'@@ -11,22 +11,29 @@\n mash sketch\n -s \'${sketch_size}\'\n -k \'${kmer_size}\'\n+ -w \'${prob_threshold}\'\n #if str ( $reads_assembly.reads_assembly_selector ) == "reads"\n- -m \'${reads_assembly.minimum_kmer_copies}\'\n- -r\n- #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"\n- \'$reads_assembly.reads_input.reads_1\' \'$reads_assembly.reads_input.reads_2\'\n- #end if\n- #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection"\n- \'$reads_assembly.reads_input.reads.forward\' \'$reads_assembly.reads_input.reads.reverse\'\n- #end if\n- #if str( $reads_assembly.reads_input.reads_input_selector ) == "single"\n- \'$reads_assembly.reads_input.reads\'\n- #end if\n+ -m \'${reads_assembly.minimum_kmer_copies}\'\n+ -r\n+ #if $reads_assembly.target_coverage\n+ -c \'${reads_assembly.target_coverage}\'\n+ #end if\n+ #if $reads_assembly.genome_size\n+ -g \'${reads_assembly.genome_size}\'\n+ #end if\n+ #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"\n+ \'$reads_assembly.reads_input.reads_1\' \'$reads_assembly.reads_input.reads_2\'\n+ #end if\n+ #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection"\n+ \'$reads_assembly.reads_input.reads.forward\' \'$reads_assembly.reads_input.reads.reverse\'\n+ #end if\n+ #if str( $reads_assembly.reads_input.reads_input_selector ) == "single"\n+ \'$reads_assembly.reads_input.reads\'\n+ #end if\n #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly"\n- -p \\${GALAXY_SLOTS:-1}\n- \'${assembly}\'\n- ${reads_assembly.individual_sequences}\n+ -p \\${GALAXY_SLOTS:-1}\n+ \'${assembly}\'\n+ ${reads_assembly.individual_sequences}\n #end if\n -o \'sketch\'\n ]]></command>\n@@ -55,29 +62,104 @@\n </when>\n </conditional>\n <param type="integer" name="minimum_kmer_copies" argument="-m" value="1" min="1" max="1000" label="Minimum copies of each k-mer required to pass noise filter"/>\n+ <param type="integer" name="target_coverage" argument="-c" value="" min="0" max="500" optional="true" label="Target coverage" help="If specified, sketching will conclude if this coverage is reached before the end of the input file (estimated by average k-mer multiplicity)"/>\n+ <param type="integer" name="genome_size" argument="-g" value="" min="1000" max="10 0000000000" optional="true" label="Genome size" help="If specified, will be used for p-value calculation instead of an estimated size from k-mer content"/>\n </when>\n <when value="assembly">\n <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/>\n- <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences"/>\n+ <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences" help="Sketch individual sequences, rather than whole files, e.g. for multi-fastas of single-chromosome genomes or pair-wise gene comparisons"/>\n </when>\n </conditional>\n- <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" label="Sketch size" />\n+ <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" label="Sketch size" help="Each sketch will have at most this many non-redundant min-hashes"/>\n <param type='..b' <conditional name="reads_assembly">\n+ <param name="reads_assembly_selector" value="reads"/>\n+ <conditional name="reads_input">\n+ <param name="reads_input_selector" value="single"/>\n+ <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>\n+ <param name="minimum_kmer_copies" value="10"/>\n+ </conditional>\n+ </conditional>\n+ <output name="sketch" file="test_02_mash_sketch.msh" compare="sim_size" />\n+ </test>\n+ <test>\n+ <conditional name="reads_assembly">\n+ <param name="reads_assembly_selector" value="reads"/>\n+ <conditional name="reads_input">\n+ <param name="reads_input_selector" value="single"/>\n+ <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>\n+ <param name="target_coverage" value="1"/>\n+ </conditional>\n+ </conditional>\n+ <output name="sketch" file="test_03_mash_sketch.msh" compare="sim_size" />\n </test>\n <test>\n- <param name="reads_assembly_selector" value="assembly" />\n- <param name="assembly" value="test_assembly.fasta"/>\n- <output name="sketch" file="test_assembly.sketch.msh" compare="sim_size" />\n+ <conditional name="reads_assembly">\n+ <param name="reads_assembly_selector" value="reads"/>\n+ <conditional name="reads_input">\n+ <param name="reads_input_selector" value="single"/>\n+ <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>\n+ <param name="genome_size" value="1000"/>\n+ </conditional>\n+ </conditional>\n+ <output name="sketch" file="test_04_mash_sketch.msh" compare="sim_size" />\n+ </test>\n+ <test>\n+ <conditional name="reads_assembly">\n+ <param name="reads_assembly_selector" value="reads"/>\n+ <conditional name="reads_input">\n+ <param name="reads_input_selector" value="single"/>\n+ <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>\n+ </conditional>\n+ </conditional>\n+ <param name="sketch_size" value="500"/>\n+ <output name="sketch" file="test_05_mash_sketch.msh" compare="sim_size" />\n+ </test>\n+ <test>\n+ <conditional name="reads_assembly">\n+ <param name="reads_assembly_selector" value="reads"/>\n+ <conditional name="reads_input">\n+ <param name="reads_input_selector" value="single"/>\n+ <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>\n+ </conditional>\n+ </conditional>\n+ <param name="kmer_size" value="17"/>\n+ <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" />\n+ </test>\n+ <test>\n+ <conditional name="reads_assembly">\n+ <param name="reads_assembly_selector" value="reads"/>\n+ <conditional name="reads_input">\n+ <param name="reads_input_selector" value="single"/>\n+ <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>\n+ </conditional>\n+ </conditional>\n+ <param name="prob_threshold" value="0.1"/>\n+ <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" />\n+ </test>\n+ <test>\n+ <conditional name="reads_assembly">\n+ <param name="reads_assembly_selector" value="assembly"/>\n+ <param name="assembly" value="test_assembly.fasta"/>\n+ </conditional>\n+ <output name="sketch" file="test_07_mash_sketch.msh" compare="sim_size" />\n </test>\n </tests>\n <help><![CDATA[\n' |
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