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comparison nonpareil.xml @ 1:45210df786b9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil commit 46f7675fa6e17042965d1a8e5e368ed1c482f08c
author iuc
date Wed, 27 Jul 2022 09:26:36 +0000
parents 280386b252a5
children cef64c36c89e
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0:280386b252a5 1:45210df786b9
1 <tool id="nonpareil" name="Nonpareil" version="@WRAPPER_VERSION@.0"> 1 <tool id="nonpareil" name="Nonpareil" version="@TOOL_VERSION@.1" profile="21.01">
2 <description>to estimate average coverage and generate Nonpareil curves</description> 2 <description>to estimate average coverage and generate Nonpareil curves</description>
3 <macros> 3 <macros>
4 <token name="@WRAPPER_VERSION@">3.1.1</token> 4 <token name="@TOOL_VERSION@">3.1.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@WRAPPER_VERSION@">nonpareil</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">nonpareil</requirement>
8 </requirements> 8 </requirements>
9 <version_command>nonpareil -V</version_command> 9 <version_command>nonpareil -V</version_command>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 ln -s '$input' input &&
13
12 nonpareil 14 nonpareil
13 -s '$input' 15 -s input
14 -T '$algo' 16 -T '$algo'
15 #if $input.is_of_type("fasta") 17 #if $input.is_of_type("fasta")
16 -f 'fasta' 18 -f 'fasta'
17 #else if $input.is_of_type("fastq") 19 #else if $input.is_of_type("fastq")
18 -f 'fastq' 20 -f 'fastq'
42 -k '$mating.kmer_size' 44 -k '$mating.kmer_size'
43 #if str($mating.proba) != '' 45 #if str($mating.proba) != ''
44 -x '$mating.proba' 46 -x '$mating.proba'
45 #end if 47 #end if
46 -r '$seed' 48 -r '$seed'
49 && echo $log_test
47 ]]></command> 50 ]]></command>
48 <inputs> 51 <inputs>
49 <param name="input" type="data" format="fastq,fasta" label="Input sequences" help="FastQ format is recommended for kmer algorithm and Fasta for the alignment" argument="-s"/> 52 <param name="input" type="data" format="fastq,fasta" label="Input sequences" help="FastQ format is recommended for kmer algorithm and Fasta for the alignment" argument="-s"/>
50 <param name="algo" type="select" label="Nonpareil algorithm?" argument="-T"> 53 <param name="algo" type="select" label="Nonpareil algorithm?" argument="-T">
51 <option value="kmer">Kmer</option> 54 <option value="kmer">Kmer</option>
86 <filter>log_test</filter> 89 <filter>log_test</filter>
87 </data> 90 </data>
88 <data format="tabular" name="mating_vector_output" label="${tool.name} on ${on_string}: Mates distribution"/> 91 <data format="tabular" name="mating_vector_output" label="${tool.name} on ${on_string}: Mates distribution"/>
89 </outputs> 92 </outputs>
90 <tests> 93 <tests>
91 <test> 94 <test expect_num_outputs="4">
92 <param name="input" value="test.fasta"/> 95 <param name="input" value="test.fasta"/>
93 <param name="algo" value="alignment"/> 96 <param name="algo" value="alignment"/>
94 <param name="subsampling" value="0.7"/> 97 <param name="subsampling" value="0.7"/>
95 <param name="subsample_per_point" value="1024"/> 98 <param name="subsample_per_point" value="1024"/>
96 <param name="min_overlapping" value="50"/> 99 <param name="min_overlapping" value="50"/>
117 </assert_contents> 120 </assert_contents>
118 </output> 121 </output>
119 <output name="summary" value="test1-summary" compare="sim_size" delta="0"/> 122 <output name="summary" value="test1-summary" compare="sim_size" delta="0"/>
120 <output name="mating_vector_output" value="test1-mating_vector_output" compare="sim_size" delta="0"/> 123 <output name="mating_vector_output" value="test1-mating_vector_output" compare="sim_size" delta="0"/>
121 </test> 124 </test>
122 <test> 125 <test expect_num_outputs="3">
123 <param name="input" value="test.fastq"/> 126 <param name="input" value="test.fastq"/>
124 <param name="algo" value="kmer"/> 127 <param name="algo" value="kmer"/>
125 <param name="subsampling" value="0.7"/> 128 <param name="subsampling" value="0.7"/>
126 <param name="subsample_per_point" value="1024"/> 129 <param name="subsample_per_point" value="1024"/>
127 <param name="min_overlapping" value="50"/> 130 <param name="min_overlapping" value="50"/>