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comparison macros.xml @ 0:4f0a8e401e2e draft

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"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
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-1:000000000000 0:4f0a8e401e2e
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="input_daa_param">
42 <param argument="--in" type="data" format="daa" label="Input DAA file"/>
43 </macro>
44 <macro name="long_reads_param">
45 <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
46 </macro>
47 <macro name="max_matches_per_read_param">
48 <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/>
49 </macro>
50 <macro name="only_named_classifications_param">
51 <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">
52 <sanitizer>
53 <valid initial="@VALIDINITIAL@">
54 <remove value="&apos;" />
55 <add value="|" />
56 </valid>
57 <mapping initial="none">
58 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
59 </mapping>
60 </sanitizer>
61 </param>
62 </macro>
63 <macro name="classification_options">
64 <option value="EC" selected="true">EC</option>
65 <option value="EGGNOG">EGGNOG</option>
66 <option value="GTDB">GTDB</option>
67 <option value="INTERPRO2GO">INTERPRO2GO</option>
68 <option value="KEGG">KEGG</option>
69 <option value="SEED">SEED</option>
70 <option value="Taxonomy">Taxonomy</option>
71 </macro>
72 <macro name="blast_mode_options">
73 <option value="Unknown" selected="true">Unknown</option>
74 <option value="BlastN">BlastN</option>
75 <option value="BlastP">BlastP</option>
76 <option value="BlastX">BlastX</option>
77 <option value="Classifier">Classifier</option>
78 </macro>
79 <macro name="classify_param">
80 <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
81 </macro>
82 <macro name="min_score_param">
83 <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
84 </macro>
85 <macro name="max_expected_param">
86 <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
87 </macro>
88 <macro name="min_percent_identity_param">
89 <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
90 </macro>
91 <macro name="top_percent_param">
92 <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
93 </macro>
94 <macro name="min_max_params">
95 <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"/>
96 <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>
97 <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"/>
98 <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"/>
99 <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
100 </macro>
101 <macro name="lca_params">
102 <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
103 <option value="naive" selected="true">naive</option>
104 <option value="weighted">weighted</option>
105 <option value="longReads">longReads</option>
106 </param>
107 <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
108 </macro>
109 <macro name="read_assignment_mode_param">
110 <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
111 <option value="alignedBases" selected="true">alignedBases</option>
112 <option value="readCount">readCount</option>
113 </param>
114 </macro>
115 <macro name="con_file_param">
116 <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"/>
117 </macro>
118 <macro name="mapdb_param">
119 <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db" help="Optional, no selection ignores"/>
120 </macro>
121 <xml name="sanitize_query" token_validinitial="string.printable">
122 <sanitizer>
123 <valid initial="@VALIDINITIAL@">
124 <remove value="&apos;" />
125 <add value="|" />
126 </valid>
127 <mapping initial="none">
128 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
129 </mapping>
130 </sanitizer>
131 </xml>
132 <xml name="citations">
133 <citations>
134 <citation type="doi">10.1038/nmeth.3176</citation>
135 <citation type="doi">10.1101/gr.120618.111</citation>
136 <citation type="doi">10.1101/gr.5969107</citation>
137 </citations>
138 </xml>
139 </macros>
140