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comparison mash_sketch.xml @ 0:68084b06ae83 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
author iuc
date Sun, 16 Feb 2020 17:03:04 -0500
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children 91ee99b4f05a
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-1:000000000000 0:68084b06ae83
1 <tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy0" profile="19.01">
2 <description>
3 Create a reduced representation of a sequence or set of sequences, based on min-hashes
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="version_command" />
10 <command detect_errors="exit_code"><![CDATA[
11 mash sketch
12 -s '${sketch_size}'
13 -k '${kmer_size}'
14 #if str ( $reads_assembly.reads_assembly_selector ) == "reads"
15 -m '${reads_assembly.minimum_kmer_copies}'
16 -r
17 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"
18 '$reads_assembly.reads_input.reads_1' '$reads_assembly.reads_input.reads_2'
19 #end if
20 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection"
21 '$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse'
22 #end if
23 #if str( $reads_assembly.reads_input.reads_input_selector ) == "single"
24 '$reads_assembly.reads_input.reads'
25 #end if
26 #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly"
27 -p \${GALAXY_SLOTS:-1}
28 '${assembly}'
29 ${reads_assembly.individual_sequences}
30 #end if
31 -o 'sketch'
32 ]]></command>
33 <inputs>
34 <conditional name="reads_assembly">
35 <param name="reads_assembly_selector" type="select" label="Input: Reads or Assemblies">
36 <option selected="True" value="reads">Reads</option>
37 <option value="assembly">Assembly</option>
38 </param>
39 <when value="reads">
40 <conditional name="reads_input">
41 <param name="reads_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
42 <option value="paired">Paired</option>
43 <option value="single">Single</option>
44 <option value="paired_collection">Paired Collection</option>
45 </param>
46 <when value="paired">
47 <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
48 <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
49 </when>
50 <when value="single">
51 <param name="reads" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
52 </when>
53 <when value="paired_collection">
54 <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
55 </when>
56 </conditional>
57 <param type="integer" name="minimum_kmer_copies" argument="-m" value="1" min="1" max="1000" label="Minimum copies of each k-mer required to pass noise filter"/>
58 </when>
59 <when value="assembly">
60 <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/>
61 <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences"/>
62 </when>
63 </conditional>
64 <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" label="Sketch size" />
65 <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32" label="kmer size" />
66 </inputs>
67 <outputs>
68 <data name="sketch" format="msh" from_work_dir="sketch.msh"/>
69 </outputs>
70 <tests>
71 <test>
72 <param name="reads_assembly_selector" value="reads" />
73 <param name="reads_input_selector" value="single"/>
74 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
75 <output name="sketch" file="ERR024951_seqtk_sample_1000_1.sketch.msh" compare="sim_size" />
76 </test>
77 <test>
78 <param name="reads_assembly_selector" value="assembly" />
79 <param name="assembly" value="test_assembly.fasta"/>
80 <output name="sketch" file="test_assembly.sketch.msh" compare="sim_size" />
81 </test>
82 </tests>
83 <help><![CDATA[
84
85 **What it does**
86
87 Create a sketch file, which is a reduced representation of a sequence or set
88 of sequences (based on min-hashes) that can be used for fast distance
89 estimations. Inputs can be fasta or fastq files (gzipped or not), and "-" can
90 be given to read from standard input. Input files can also be files of file
91 names (see -l). For output, one sketch file will be generated, but it can have
92 multiple sketches within it, divided by sequences or files (see -i). By
93 default, the output file name will be the first input file with a '.msh'
94 extension, or 'stdin.msh' if standard input is used (see -o).
95 ]]></help>
96 <expand macro="citations"/>
97 </tool>