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comparison tn93_cluster.xml @ 0:af03f3398f03 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
author iuc
date Fri, 23 Apr 2021 03:04:15 +0000
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children 112d80c9ccca
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-1:000000000000 0:af03f3398f03
1 <tool id="tn93_cluster" name="TN93 Cluster" version="@VERSION@">
2 <description>sequences that lie within a specific distance of each other</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@VERSION@">tn93</requirement>
8 <requirement type="package" version="3.9">python</requirement>
9 </requirements>
10 <version_command><![CDATA[tn93 --version]]></version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 python '$__tool_directory__/tn93_cluster.py' --input '$input_fasta' --reference '$reference' --output '$tn93_clusters'
13 --threshold $threshold
14 --ambigs $ambigs
15 --cluster-type $cluster_type
16 --overlap $overlap
17 --fraction $fraction
18 --cluster-count $cluster_count
19 #if $compress:
20 --compressed '$tn93_compressed_clusters'
21 #end if
22 ]]></command>
23 <inputs>
24 <param name="input_fasta" type="data" format="fasta" label="Input in FASTA format" />
25 <param name="reference" type="data" format="fasta" label="Reference in FASTA format" />
26 <param argument="--compress" type="boolean" truevalue="--compress" falsevalue="" label="Output additional fasta dataset with compressed clusters" />
27 <param argument="--cluster-count" type="integer" value="200" label="Only retain this many clusters" />
28 <param argument="--threshold" type="float" min="0" value="0.0005" label="Distance threshold" help="Sequences which lie within this distance will be clustered" />
29 <param argument="--ambigs" type="select" label="Strategy for ambiguous nucleotides">
30 <option value="resolve" selected="true">resolve</option>
31 <option value="average">average</option>
32 <option value="skip">skip</option>
33 <option value="gapmm">gapmm</option>
34 </param>
35 <param argument="--cluster_type" type="select" label="Clustering rules" help="&quot;All&quot;: Each sequence within the cluster must be within the specified distance of every other sequence in the cluster. &quot;Any&quot;: Each sequence within the cluster must be within the specified distance of at least one other sequence.">
36 <option value="all">All</option>
37 <option value="any">Any</option>
38 </param>
39 <param name="overlap" argument="-l" type="integer" value="100"
40 label="Only process pairs that overlap by at least N bases" />
41 <param name="fraction" argument="-g" type="float" value="1.0"
42 label="Maximum tolerated fraction of ambiguous characters" />
43 </inputs>
44 <outputs>
45 <data format="json" name="tn93_clusters" />
46 <data format="fasta" name="tn93_compressed_clusters">
47 <filter>compress</filter>
48 </data>
49 </outputs>
50 <tests>
51 <test expect_num_outputs="2">
52 <param name="input_fasta" value="cluster-in1-1.fa" />
53 <param name="reference" value="cluster-in1-2.fa" />
54 <param name="threshold" value="0.35" />
55 <param name="compress" value="true" />
56 <output file="cluster-out1.json" ftype="json" name="tn93_clusters" />
57 <output file="cluster-out1.fa" ftype="fasta" name="tn93_compressed_clusters" />
58 </test>
59 </tests>
60 <help><![CDATA[
61 TN93-Cluster
62 ============
63
64 Clusters sequences within a minimum distance of each other using the 1993
65 Tamura-Nei distance calculation.
66
67 ]]></help>
68 <expand macro="citations">
69 <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
70 </expand>
71 </tool>