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Changeset 0:2b3df62a3b6b (2022-08-29)

Next changeset 1:f40e6da10c03 (2023-01-13)

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

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qiime2__feature_classifier__classify_consensus_vsearch.xml
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diff -r 000000000000 -r 2b3df62a3b6b qiime2__feature_classifier__classify_consensus_vsearch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__feature_classifier__classify_consensus_vsearch.xml Mon Aug 29 19:52:15 2022 +0000

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b'@@ -0,0 +1,129 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+\n+\n+<tool name="qiime2 feature-classifier classify-consensus-vsearch" id="qiime2__feature_classifier__classify_consensus_vsearch" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">\n+ <description>VSEARCH-based consensus taxonomy classifier</description>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/core:2022.8</container>\n+ </requirements>\n+ <version_command>q2galaxy version feature_classifier</version_command>\n+ <command detect_errors="aggressive">q2galaxy run feature_classifier classify_consensus_vsearch \'$inputs\'</command>\n+ <configfiles>\n+ <inputs name="inputs" data_style="paths"/>\n+ </configfiles>\n+ <inputs>\n+ <param name="query" type="data" format="qza" label="query: FeatureData[Sequence]" help="[required] Query Sequences.">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="FeatureData[Sequence]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'FeatureData[Sequence]\']</validator>\n+ </param>\n+ <param name="reference_reads" type="data" format="qza" label="reference_reads: FeatureData[Sequence]" help="[required] Reference sequences.">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="FeatureData[Sequence]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'FeatureData[Sequence]\']</validator>\n+ </param>\n+ <param name="reference_taxonomy" type="data" format="qza" label="reference_taxonomy: FeatureData[Taxonomy]" help="[required] Reference taxonomy labels.">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="FeatureData[Taxonomy]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'FeatureData[Taxonomy]\']</validator>\n+ </param>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <conditional name="__q2galaxy__GUI__conditional__maxaccepts__">\n+ <param name="__q2galaxy__GUI__select__" type="select" label="maxaccepts: Int % Range(1, None) | Str % Choices(\'all\')" help="[default: 10] Maximum number of hits to keep for each query. Set to "all" to keep all hits > perc_identity similarity. Note that if strand=both, maxaccepts will keep N hits for each direction (if searches in the opposite direction yield results that exceed the minimum perc_identity). In those cases use maxhits to control the total number of hits returned. This option works in pair with maxrejects. The search process sorts target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if the first target sequence passes the acceptation criteria, it is accepted as best hit and the search process stops for that query. If maxaccepts is set to a higher value, more hits are accepted. If maxaccepts and maxrejects are both set to "all", the complete database is searched.">\n+ <option value="all">all (Str)</option>\n+ <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide'..b'(Int % Range(1, None))</option>\n+ </param>\n+ <when value="all">\n+ <param name="maxrejects" type="hidden" value="all"/>\n+ </when>\n+ <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">\n+ <param name="maxrejects" type="integer" min="1" value="" label="maxrejects: Int % Range(1, None)" help="[required] Maximum number of non-matching target sequences to consider before stopping the search. This option works in pair with maxaccepts (see maxaccepts description for details)."/>\n+ </when>\n+ </conditional>\n+ <param name="output_no_hits" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="output_no_hits: Bool" help="[default: Yes] Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs."/>\n+ <param name="weak_id" type="float" min="0.0" max="1.0" value="0.0" label="weak_id: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.0] Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc_identity). As weak_id reports weak hits that are not deduced from maxaccepts, high perc_identity values can be used, hence preserving both speed and sensitivity. Logically, weak_id must be smaller than the value indicated by perc_identity, otherwise this option will be ignored."/>\n+ <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1] Number of threads to use for job parallelization."/>\n+ <param name="min_consensus" type="float" min="0.500001" max="1.0" value="0.51" label="min_consensus: Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True)" help="[default: 0.51] Minimum fraction of assignments must match top hit to be accepted as consensus assignment."/>\n+ <param name="unassignable_label" type="text" value="Unassigned" label="unassignable_label: Str" help="[default: \'Unassigned\'] Annotation given to sequences without any hits.">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="classification" format="qza" label="${tool.name} on ${on_string}: classification.qza" from_work_dir="classification.qza"/>\n+ <data name="search_results" format="qza" label="${tool.name} on ${on_string}: search_results.qza" from_work_dir="search_results.qza"/>\n+ </outputs>\n+ <tests/>\n+ <help>\n+QIIME 2: feature-classifier classify-consensus-vsearch\n+======================================================\n+VSEARCH-based consensus taxonomy classifier\n+\n+\n+Outputs:\n+--------\n+:classification.qza: Taxonomy classifications of query sequences.\n+:search_results.qza: Top hits for each query.\n+\n+| \n+\n+Description:\n+------------\n+Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global alignment between query and reference_reads, then assigns consensus taxonomy to each query sequence from among maxaccepts top hits, min_consensus of which share that taxonomic assignment. Unlike classify-consensus-blast, this method searches the entire reference database before choosing the top N hits, not the first N hits.\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="doi">10.7717/peerj.2584</citation>\n+ <citation type="doi">10.1186/s40168-018-0470-z</citation>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n'