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comparison tn93_cluster.xml @ 1:112d80c9ccca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
author iuc
date Wed, 20 Apr 2022 17:00:11 +0000
parents af03f3398f03
children eb6f0ec5b95e
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0:af03f3398f03 1:112d80c9ccca
1 <tool id="tn93_cluster" name="TN93 Cluster" version="@VERSION@"> 1 <tool id="tn93_cluster" name="TN93 Cluster" version="@TOOL_VERSION@+galaxy1">
2 <description>sequences that lie within a specific distance of each other</description> 2 <description>sequences that lie within a specific distance of each other</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="requirements">
7 <requirement type="package" version="@VERSION@">tn93</requirement>
8 <requirement type="package" version="3.9">python</requirement> 7 <requirement type="package" version="3.9">python</requirement>
9 </requirements> 8 </expand>
10 <version_command><![CDATA[tn93 --version]]></version_command> 9 <version_command><![CDATA[tn93 --version]]></version_command>
11 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
12 python '$__tool_directory__/tn93_cluster.py' --input '$input_fasta' --reference '$reference' --output '$tn93_clusters' 11 python '$__tool_directory__/tn93_cluster.py' --input '$input_fasta' --reference '$reference' --output '$tn93_clusters'
13 --threshold $threshold 12 --threshold $threshold
14 --ambigs $ambigs 13 --ambigs $ambigs
23 <inputs> 22 <inputs>
24 <param name="input_fasta" type="data" format="fasta" label="Input in FASTA format" /> 23 <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" /> 24 <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" /> 25 <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" /> 26 <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" /> 27 <param argument="--threshold" type="float" value="0.0005" min="0" max="1" label="Distance threshold" help="Sequences which lie within this distance will be clustered" />
29 <param argument="--ambigs" type="select" label="Strategy for ambiguous nucleotides"> 28 <param argument="--ambigs" type="select" label="Strategy for ambiguous nucleotides">
30 <option value="resolve" selected="true">resolve</option> 29 <option value="resolve" selected="true">resolve</option>
31 <option value="average">average</option> 30 <option value="average">average</option>
32 <option value="skip">skip</option> 31 <option value="skip">skip</option>
33 <option value="gapmm">gapmm</option> 32 <option value="gapmm">gapmm</option>
40 label="Only process pairs that overlap by at least N bases" /> 39 label="Only process pairs that overlap by at least N bases" />
41 <param name="fraction" argument="-g" type="float" value="1.0" 40 <param name="fraction" argument="-g" type="float" value="1.0"
42 label="Maximum tolerated fraction of ambiguous characters" /> 41 label="Maximum tolerated fraction of ambiguous characters" />
43 </inputs> 42 </inputs>
44 <outputs> 43 <outputs>
45 <data format="json" name="tn93_clusters" /> 44 <data format="json" name="tn93_clusters" from_work_dir="clusters.json" />
46 <data format="fasta" name="tn93_compressed_clusters"> 45 <data format="fasta" name="tn93_compressed_clusters" from_work_dir="clusters.fa">
47 <filter>compress</filter> 46 <filter>compress</filter>
48 </data> 47 </data>
49 </outputs> 48 </outputs>
50 <tests> 49 <tests>
51 <test expect_num_outputs="2"> 50 <test expect_num_outputs="2">