Mercurial > repos > iuc > megan_blast2rma

comparison macros.xml @ 1:2f8d3924bb3b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
author iuc
date Fri, 03 Dec 2021 23:09:53 +0000
parents fa3c3a64c993
children 5be253dd3e08
comparison
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0:fa3c3a64c993 1:2f8d3924bb3b
36 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for forward read"/> 36 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for forward read"/>
37 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for reverse read"/> 37 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for reverse read"/>
38 </when> 38 </when>
39 </conditional> 39 </conditional>
40 </macro> 40 </macro>
41 <macro name="long_reads_param">
42 <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
43 </macro>
44 <macro name="classification_options">
45 <option value="EC" selected="true">EC</option>
46 <option value="EGGNOG">EGGNOG</option>
47 <option value="GTDB">GTDB</option>
48 <option value="INTERPRO2GO">INTERPRO2GO</option>
49 <option value="KEGG">KEGG</option>
50 <option value="SEED">SEED</option>
51 <option value="Taxonomy">Taxonomy</option>
52 </macro>
41 <macro name="blast_mode_options"> 53 <macro name="blast_mode_options">
42 <option value="Unknown" selected="true">Unknown</option> 54 <option value="Unknown" selected="true">Unknown</option>
43 <option value="BlastN">BlastN</option> 55 <option value="BlastN">BlastN</option>
44 <option value="BlastP">BlastP</option> 56 <option value="BlastP">BlastP</option>
45 <option value="BlastX">BlastX</option> 57 <option value="BlastX">BlastX</option>
46 <option value="Classifier">Classifier</option> 58 <option value="Classifier">Classifier</option>
47 </macro> 59 </macro>
48 <macro name="common_blast_params"> 60 <macro name="classify_param">
61 <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
62 </macro>
63 <macro name="blast_params">
49 <param argument="--minScore" type="float" value="50.0" label="Minimum score"/> 64 <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
50 <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/> 65 <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
51 <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/> 66 <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
52 <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/> 67 <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
68 </macro>
69 <macro name="min_max_params">
70 <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"/>
71 <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>
72 <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"/>
73 <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"/>
74 <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
75 </macro>
76 <macro name="lca_params">
77 <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
78 <option value="naive" selected="true">naive</option>
79 <option value="weighted">weighted</option>
80 <option value="longReads">longReads</option>
81 </param>
82 <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
83 </macro>
84 <macro name="read_assignment_mode_param">
85 <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
86 <option value="alignedBases" selected="true">alignedBases</option>
87 <option value="readCount">readCount</option>
88 </param>
89 </macro>
90 <macro name="con_file_param">
91 <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"/>
92 </macro>
93 <macro name="mapdb_param">
94 <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db" help="Optional, no selection ignores"/>
53 </macro> 95 </macro>
54 <xml name="sanitize_query" token_validinitial="string.printable"> 96 <xml name="sanitize_query" token_validinitial="string.printable">
55 <sanitizer> 97 <sanitizer>
56 <valid initial="@VALIDINITIAL@"> 98 <valid initial="@VALIDINITIAL@">
57 <remove value="&apos;" /> 99 <remove value="&apos;" />
62 </mapping> 104 </mapping>
63 </sanitizer> 105 </sanitizer>
64 </xml> 106 </xml>
65 <xml name="citations"> 107 <xml name="citations">
66 <citations> 108 <citations>
109 <citation type="doi">10.1038/nmeth.3176</citation>
110 <citation type="doi">10.1101/gr.120618.111</citation>
67 <citation type="doi">10.1101/gr.5969107</citation> 111 <citation type="doi">10.1101/gr.5969107</citation>
68 </citations> 112 </citations>
69 </xml> 113 </xml>
70 </macros> 114 </macros>
71 115