Mercurial > repos > iuc > qiime_pick_rep_set

comparison macros.xml @ 0:6ebade612aa0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:32:11 -0400
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children c95abbb6ebb3
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-1:000000000000 0:6ebade612aa0
1 <?xml version="1.0" ?>
2 <macros>
3 <token name="@WRAPPER_VERSION@">1.9.1</token>
4
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@WRAPPER_VERSION@">qiime</requirement>
8 <yield/>
9 </requirements>
10 </xml>
11
12 <xml name="citations">
13 <citation type="doi">10.1038/nmeth.f.303</citation>
14 </xml>
15
16 <xml name="pick_otus_reference_source">
17 <conditional name="references">
18 <param name="source_selector" type="select" label="Use reference sequences from">
19 <option value="cached">Local cache</option>
20 <option value="history">History</option>
21 </param>
22 <when value="cached">
23 <param argument="--refseqs_fp" label="Reference sequences" type="select">
24 <options from_data_table="qiime_rep_set"/>
25 </param>
26 </when>
27 <when value="history">
28 <param argument="--refseqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
29 </when>
30 </conditional>
31 </xml>
32 <xml name="pick_otus_similarity">
33 <param argument="--similarity" type="float" value="0.97" label="Sequence similarity threshold"/>
34 </xml>
35 <xml name="pick_otus_denovo_otu_id_prefix">
36 <param argument="--denovo_otu_id_prefix" type="text" value="denovo" label="OTU identifier prefix for the de novo OTU pickers"/>
37 </xml>
38 <xml name="pick_otus_enable_rev_strand_match">
39 <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"/>
40 </xml>
41 <xml name="pick_otus_suppress_presort_by_abundance_uclust">
42 <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?"/>
43 </xml>
44 <xml name="pick_otus_max">
45 <param argument="--max_accepts" type="integer" value="1" label="Max_accepts value"/>
46 <param argument="--max_rejects" type="integer" value="8" label="Max_rejects value"/>
47 </xml>
48 <xml name="pick_otus_stepwords">
49 <param argument="--stepwords" type="integer" value="8" label="Stepwords value"/>
50 </xml>
51 <xml name="pick_otus_word_length">
52 <param argument="--word_length" type="integer" value="8" label="Word length value"/>
53 </xml>
54 <xml name="pick_otus_suppress_prefilter_exact_match">
55 <param argument="--suppress_prefilter_exact_match" type="boolean" truevalue="--suppress_prefilter_exact_match" falsevalue="" checked="false" label="Don't collapse exact matches before calling?"/>
56 </xml>
57 </macros>