Mercurial > repos > iuc > megan_sam2rma

annotate macros.xml @ 1:ef0443c0eaba draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 6b0c3dbd5bdf9c272cf32f39e0004d504f953ff0
author iuc
date Sat, 27 Aug 2022 17:07:04 +0000
parents 4f0a8e401e2e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
1 <macros>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
2 <token name="@TOOL_VERSION@">6.21.7</token>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
4 <token name="@PROFILE@">20.09</token>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
5 <xml name="bio_tools">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
6 <xrefs>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
7 <xref type="bio.tools">megan</xref>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
8 </xrefs>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
9 </xml>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
10 <xml name="requirements">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
11 <requirements>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
12 <requirement type="package" version="@TOOL_VERSION@">megan</requirement>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
13 </requirements>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
14 </xml>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
15 <macro name="input_type_cond">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
16 <conditional name="input_type_cond">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
17 <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
18 <option value="single" selected="true">Single dataset</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
19 <option value="pair">Dataset pair</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
20 <option value="paired">List of dataset pairs</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
21 </param>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
22 <when value="single">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
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"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
24 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
25 </when>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
26 <when value="pair">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
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"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
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"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
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"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
30 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
31 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input reverse read file"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
32 </when>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
33 <when value="paired">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
34 <param name="reads_collection" type="data_collection" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of paired read files"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
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"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
36 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for forward read"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
37 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for reverse read"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
38 </when>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
39 </conditional>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
40 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
41 <macro name="input_daa_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
42 <param argument="--in" type="data" format="daa" label="Input DAA file"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
43 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
44 <macro name="long_reads_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
45 <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
46 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
47 <macro name="max_matches_per_read_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
48 <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
49 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
50 <macro name="only_named_classifications_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
51 <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
52 <sanitizer>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
53 <valid initial="@VALIDINITIAL@">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
54 <remove value="&apos;" />
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
55 <add value="|" />
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
56 </valid>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
57 <mapping initial="none">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
58 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
59 </mapping>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
60 </sanitizer>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
61 </param>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
62 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
63 <macro name="classification_options">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
64 <option value="EC" selected="true">EC</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
65 <option value="EGGNOG">EGGNOG</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
66 <option value="GTDB">GTDB</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
67 <option value="INTERPRO2GO">INTERPRO2GO</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
68 <option value="KEGG">KEGG</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
69 <option value="SEED">SEED</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
70 <option value="Taxonomy">Taxonomy</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
71 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
72 <macro name="blast_mode_options">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
73 <option value="Unknown" selected="true">Unknown</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
74 <option value="BlastN">BlastN</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
75 <option value="BlastP">BlastP</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
76 <option value="BlastX">BlastX</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
77 <option value="Classifier">Classifier</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
78 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
79 <macro name="classify_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
80 <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
81 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
82 <macro name="min_score_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
83 <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
84 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
85 <macro name="max_expected_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
86 <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
87 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
88 <macro name="min_percent_identity_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
89 <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
90 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
91 <macro name="top_percent_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
92 <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
93 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
94 <macro name="min_max_params">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
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"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
96 <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
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"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
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"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
99 <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
100 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
101 <macro name="lca_params">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
102 <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
103 <option value="naive" selected="true">naive</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
104 <option value="weighted">weighted</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
105 <option value="longReads">longReads</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
106 </param>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
107 <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
108 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
109 <macro name="read_assignment_mode_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
110 <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
111 <option value="alignedBases" selected="true">alignedBases</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
112 <option value="readCount">readCount</option>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
113 </param>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
114 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
115 <macro name="con_file_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
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"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
117 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
118 <macro name="mapdb_param">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
119 <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db" help="Optional, no selection ignores"/>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
120 </macro>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
121 <xml name="sanitize_query" token_validinitial="string.printable">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
122 <sanitizer>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
123 <valid initial="@VALIDINITIAL@">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
124 <remove value="&apos;" />
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
125 <add value="|" />
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
126 </valid>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
127 <mapping initial="none">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
128 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
129 </mapping>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
130 </sanitizer>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
131 </xml>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
132 <xml name="citations">
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
133 <citations>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
134 <citation type="doi">10.1038/nmeth.3176</citation>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
135 <citation type="doi">10.1101/gr.120618.111</citation>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
136 <citation type="doi">10.1101/gr.5969107</citation>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
137 </citations>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
138 </xml>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
139 </macros>
4f0a8e401e2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
iuc
parents:
diff changeset
140