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comparison macros.xml @ 0:242462fc608b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
author iuc
date Mon, 10 Jul 2017 16:38:55 -0400
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-1:000000000000 0:242462fc608b
1 <?xml version="1.0" ?>
2 <macros>
3 <token name="@WRAPPER_VERSION@">1.9.1</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@WRAPPER_VERSION@">qiime</requirement>
7 <yield/>
8 </requirements>
9 </xml>
10 <xml name="citations">
11 <citation type="doi">10.1038/nmeth.f.303</citation>
12 </xml>
13 <xml name="pick_otus_reference_source">
14 <conditional name="references">
15 <param name="source_selector" type="select" label="Use reference sequences from">
16 <option value="cached">Local cache</option>
17 <option value="history">History</option>
18 </param>
19 <when value="cached">
20 <param argument="--refseqs_fp" label="Reference sequences" type="select">
21 <options from_data_table="qiime_rep_set"/>
22 </param>
23 </when>
24 <when value="history">
25 <param argument="--refseqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
26 </when>
27 </conditional>
28 </xml>
29 <xml name="assign_taxonomy_reference_source">
30 <conditional name="references">
31 <param name="source_selector" type="select" label="Select a reference sequence file from">
32 <option value="cached">The local cache</option>
33 <option value="history">The active history</option>
34 </param>
35 <when value="cached">
36 <param argument="--reference_seqs_fp" label="Reference sequences either used to generate a blast database (Blast) or used as training sequences for the selected classifier (RDP, Mothur)" type="select">
37 <options from_data_table="qiime_rep_set"/>
38 </param>
39 </when>
40 <when value="history">
41 <param argument="--reference_seqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
42 </when>
43 </conditional>
44 </xml>
45 <xml name="pick_otus_similarity">
46 <param argument="--similarity" type="float" value="0.97" label="Sequence similarity threshold"/>
47 </xml>
48 <xml name="pick_otus_denovo_otu_id_prefix">
49 <param argument="--denovo_otu_id_prefix" type="text" value="denovo" label="OTU identifier prefix for the de novo OTU pickers"/>
50 </xml>
51 <xml name="pick_otus_enable_rev_strand_match">
52 <param argument="--enable_rev_strand_match" type="boolean" truevalue="--enable_rev_strand_match" falsevalue="" checked="false" label="Enable reverse strand matching?" help="Will double the amount of memory used"/>
53 </xml>
54 <xml name="pick_otus_suppress_presort_by_abundance_uclust">
55 <param argument="--suppress_presort_by_abundance_uclust" type="boolean" truevalue="--suppress_presort_by_abundance_uclust" falsevalue="" checked="false" label="Suppress presorting of sequences by abundance?"/>
56 </xml>
57 <xml name="pick_otus_max">
58 <param argument="--max_accepts" type="integer" value="1" label="Max_accepts value"/>
59 <param argument="--max_rejects" type="integer" value="8" label="Max_rejects value"/>
60 </xml>
61 <xml name="pick_otus_stepwords">
62 <param argument="--stepwords" type="integer" value="8" label="Stepwords value"/>
63 </xml>
64 <xml name="pick_otus_word_length">
65 <param argument="--word_length" type="integer" value="8" label="Word length value"/>
66 </xml>
67 <xml name="pick_otus_suppress_prefilter_exact_match">
68 <param argument="--suppress_prefilter_exact_match" type="boolean" truevalue="--suppress_prefilter_exact_match" falsevalue="" checked="false" label="Don't collapse exact matches before calling?"/>
69 </xml>
70 </macros>