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comparison mashtree.xml @ 0:419ea5baf5b7 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
author dfornika
date Tue, 28 Jan 2020 01:18:59 +0000
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-1:000000000000 0:419ea5baf5b7
1 <?xml version="1.0"?>
2 <tool id="mashtree" name="mashtree" version="@VERSION@+galaxy0">
3 <description>Create a tree using Mash distances.</description>
4 <requirements>
5 <requirement type="package" version="@VERSION@">mashtree</requirement>
6 </requirements>
7 <command><![CDATA[
8 mashtree
9 --numcpus "\${GALAXY_SLOTS:-1}"
10 --genomesize '${genomesize}'
11 --mindepth '${mindepth}'
12 --outmatrix '${matrix}'
13 --outtree '${tree}'
14
15 ]]></command>
16
17 <inputs>
18 <conditional name="fastq_input">
19 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
20 <option value="paired">Paired</option>
21 <option value="single">Single</option>
22 <option value="paired_collection">Paired Collection</option>
23 <option value="paired_iv">Paired Interleaved</option>
24 </param>
25 <when value="paired">
26 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
27 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
28 </when>
29 <when value="single">
30 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
31 </when>
32 <when value="paired_collection">
33 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
34 </when>
35 </conditional>
36 <param name="genomesize" type="integer" min="1000" value="5000000" max="50000000" />
37 <param name="mindepth" type="integer" min="0" value="5" max="100" />
38 <param name="kmerlength" type="integer" min="4" value="21" max="31" />
39 <param name="sketch-size" type="integer" min="100" value="10000" max="100000" />
40 </inputs>
41
42 <outputs>
43 <data name="tree" format="" label="${tool.name} on ${on_string}: Tree" />
44 <data name="matrix" format="tabular" label="${tool.name} on ${on_string}: Distance matrix" />
45 </outputs>
46
47 <tests>
48
49 </tests>
50 <help><![CDATA[
51
52 ]]></help>
53 <citations>
54 </citations>
55 </tool>