comparison macros.xml @ 0:fa3c3a64c993 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
author iuc
date Wed, 24 Nov 2021 21:52:14 +0000
parents
children 2f8d3924bb3b
comparison
equal deleted inserted replaced
-1:000000000000 0:fa3c3a64c993
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="blast_mode_options">
42 <option value="Unknown" selected="true">Unknown</option>
43 <option value="BlastN">BlastN</option>
44 <option value="BlastP">BlastP</option>
45 <option value="BlastX">BlastX</option>
46 <option value="Classifier">Classifier</option>
47 </macro>
48 <macro name="common_blast_params">
49 <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
50 <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"/>
52 <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
53 </macro>
54 <xml name="sanitize_query" token_validinitial="string.printable">
55 <sanitizer>
56 <valid initial="@VALIDINITIAL@">
57 <remove value="&apos;" />
58 <add value="|" />
59 </valid>
60 <mapping initial="none">
61 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
62 </mapping>
63 </sanitizer>
64 </xml>
65 <xml name="citations">
66 <citations>
67 <citation type="doi">10.1101/gr.5969107</citation>
68 </citations>
69 </xml>
70 </macros>
71