Mercurial > repos > iuc > megan_read_extractor

comparison macros.xml @ 0:abcec2e77d6c 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 23:08:01 +0000
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children 8c3f478eb916
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-1:000000000000 0:abcec2e77d6c
1 <macros>
2 <token name="@TOOL_VERSION@">6.21.7</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">20.09</token>
5 <xml name="bio_tools">
6 <xrefs>
7 <xref type="bio.tools">megan</xref>
8 </xrefs>
9 </xml>
10 <xml name="requirements">
11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">megan</requirement>
13 </requirements>
14 </xml>
15 <macro name="input_type_cond">
16 <conditional name="input_type_cond">
17 <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed">
18 <option value="single" selected="true">Single dataset</option>
19 <option value="pair">Dataset pair</option>
20 <option value="paired">List of dataset pairs</option>
21 </param>
22 <when value="single">
23 <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"/>
24 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
25 </when>
26 <when value="pair">
27 <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"/>
28 <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"/>
29 <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"/>
30 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
31 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input reverse read file"/>
32 </when>
33 <when value="paired">
34 <param name="reads_collection" type="data_collection" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of paired read files"/>
35 <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"/>
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"/>
38 </when>
39 </conditional>
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>
53 <macro name="blast_mode_options">
54 <option value="Unknown" selected="true">Unknown</option>
55 <option value="BlastN">BlastN</option>
56 <option value="BlastP">BlastP</option>
57 <option value="BlastX">BlastX</option>
58 <option value="Classifier">Classifier</option>
59 </macro>
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">
64 <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
65 <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
66 <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
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"/>
95 </macro>
96 <xml name="sanitize_query" token_validinitial="string.printable">
97 <sanitizer>
98 <valid initial="@VALIDINITIAL@">
99 <remove value="&apos;" />
100 <add value="|" />
101 </valid>
102 <mapping initial="none">
103 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
104 </mapping>
105 </sanitizer>
106 </xml>
107 <xml name="citations">
108 <citations>
109 <citation type="doi">10.1038/nmeth.3176</citation>
110 <citation type="doi">10.1101/gr.120618.111</citation>
111 <citation type="doi">10.1101/gr.5969107</citation>
112 </citations>
113 </xml>
114 </macros>
115