Mercurial > repos > iuc > mash_sketch
comparison mash_sketch.xml @ 0:68084b06ae83 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
author | iuc |
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date | Sun, 16 Feb 2020 17:03:04 -0500 |
parents | |
children | 91ee99b4f05a |
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-1:000000000000 | 0:68084b06ae83 |
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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> |