Mercurial > repos > iuc > meryl_filter_kmers
changeset 1:4f5b7b30ed7d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
| author | iuc |
|---|---|
| date | Sun, 09 Nov 2025 18:34:21 +0000 |
| parents | 956142499a02 |
| children | |
| files | filter-kmers.xml macros.xml |
| diffstat | 2 files changed, 23 insertions(+), 3 deletions(-) [+] |
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--- a/filter-kmers.xml Tue Oct 08 16:43:18 2024 +0000 +++ b/filter-kmers.xml Sun Nov 09 18:34:21 2025 +0000 @@ -19,7 +19,7 @@ #if $filter_type.type == 'times' $filter_type.N #elif $filter_type.type == 'frequency' - distinct=${operation_type.filter_type.distinct} + distinct=$filter_type.distinct #end if tmp.meryl output read-db.meryl && @@ -52,6 +52,7 @@ <tests> <test expect_num_outputs="1"> <conditional name="filter_type"> + <param name="type" value="times"/> <param name="N" value="100"/> </conditional> <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/> @@ -65,6 +66,7 @@ </test> <test expect_num_outputs="1"> <conditional name="filter_type"> + <param name="type" value="times"/> <param name="N" value="80"/> </conditional> <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/> @@ -78,6 +80,7 @@ </test> <test expect_num_outputs="1"> <conditional name="filter_type"> + <param name="type" value="frequency"/> <param name="distinct" value="0.9998"/> </conditional> <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb"/> @@ -91,6 +94,7 @@ </test> <test expect_num_outputs="1"> <conditional name="filter_type"> + <param name="type" value="times"/> <param name="N" value="100"/> </conditional> <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/> @@ -104,6 +108,7 @@ </test> <test expect_num_outputs="1"> <conditional name="filter_type"> + <param name="type" value="times"/> <param name="N" value="100"/> </conditional> <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
--- a/macros.xml Tue Oct 08 16:43:18 2024 +0000 +++ b/macros.xml Sun Nov 09 18:34:21 2025 +0000 @@ -1,7 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">1.3</token> + <token name="@TOOL_VERSION@">1.4.1</token> <token name="@GALAXY_TOOL_VERSION@">galaxy</token> - <token name="@SUFFIX_VERSION@">7</token> + <token name="@SUFFIX_VERSION@">0</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics> @@ -19,6 +19,21 @@ <requirement type="package" version="2.8">pigz</requirement> </requirements> </xml> + <xml name="kmer_param"> + <conditional name="options_kmer_size"> + <param name="kmer_size" type="select" label="K-mer size selector"> + <option value="provide">Set a k-mer size</option> + <option value="estimate">Estimate the best k-mer size</option> + </param> + <when value="provide"> + <param name="input_kmer_size" type="integer" min="1" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G).."/> + </when> + <when value="estimate"> + <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided."/> + <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001."/> + </when> + </conditional> + </xml> <xml name="meryldb_archive_assumptions"> <has_archive_member path="^[^/]+.meryl$" n="1"/> <!-- folder also counts --> <has_archive_member path="[^/]+.meryl/merylIndex" n="1" all="true">