Mercurial > repos > iuc > megan_sam2rma
diff macros.xml @ 0:4f0a8e401e2e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
| author | iuc |
|---|---|
| date | Sat, 11 Dec 2021 11:52:57 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Dec 11 11:52:57 2021 +0000 @@ -0,0 +1,140 @@ +<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="input_daa_param"> + <param argument="--in" type="data" format="daa" label="Input DAA file"/> + </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="max_matches_per_read_param"> + <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/> + </macro> + <macro name="only_named_classifications_param"> + <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications"> + <sanitizer> + <valid initial="@VALIDINITIAL@"> + <remove value="'" /> + <add value="|" /> + </valid> + <mapping initial="none"> + <add source="'" target="'"'"'" /> + </mapping> + </sanitizer> + </param> + </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="min_score_param"> + <param argument="--minScore" type="float" value="50.0" label="Minimum score"/> + </macro> + <macro name="max_expected_param"> + <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/> + </macro> + <macro name="min_percent_identity_param"> + <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/> + </macro> + <macro name="top_percent_param"> + <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> +