Mercurial > repos > iuc > megan_read_extractor
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
author | iuc |
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date | Fri, 03 Dec 2021 23:10:39 +0000 |
parents | |
children | 72fe1fcc2108 |
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<macros> <token name="@TOOL_VERSION@">6.21.7</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">20.09</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">megan</xref> </xrefs> </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">megan</requirement> </requirements> </xml> <macro name="input_type_cond"> <conditional name="input_type_cond"> <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed"> <option value="single" selected="true">Single dataset</option> <option value="pair">Dataset pair</option> <option value="paired">List of dataset pairs</option> </param> <when value="single"> <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/> <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/> </when> <when value="pair"> <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/> <param name="read2" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Reverse read file" help="This read file should be the one used by Blast to generate the Blast file below"/> <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/> <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/> <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input reverse read file"/> </when> <when value="paired"> <param name="reads_collection" type="data_collection" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of paired read files"/> <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/> <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for forward read"/> <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for reverse read"/> </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> <option value="BlastP">BlastP</option> <option value="BlastX">BlastX</option> <option value="Classifier">Classifier</option> </macro> <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@"> <remove value="'" /> <add value="|" /> </valid> <mapping initial="none"> <add source="'" target="'"'"'" /> </mapping> </sanitizer> </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> </macros>