Mercurial > repos > dfornika > mash_sketch

annotate mash_sketch.xml @ 7:c4182a046647 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit ca38c4ee1f8c7f71f31f3bee62781799c7608910-dirty"
author dfornika
date Fri, 14 Feb 2020 21:24:09 +0000
parents 1c6df46cddfd
children 56c1b5f9f8bf
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1 <tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy0" profile="19.01">
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2 <description>
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3 Create a reduced representation of a sequence or set of sequences, based on min-hashes.
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">mash</requirement>
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10 </requirements>
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11 <version_command>mash --version</version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 mash sketch
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14 -s '${sketch_size}'
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15 -k '${kmer_size}'
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16 #if str ( $reads_assembly.reads_assembly_selector ) == "reads"
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17 -m '${reads_assembly.minimum_kmer_copies}'
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18 -r
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19 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"
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20 '$reads_assembly.reads_input.reads_1' '$reads_assembly.reads_input.reads_2'
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21 #end if
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22 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection"
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23 '$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse'
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24 #end if
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25 #if str( $reads_assembly.reads_input.reads_input_selector ) == "single"
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26 '$reads_assembly.reads_input.reads'
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27 #end if
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28 #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly"
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29 -p \${GALAXY_SLOTS:-1}
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30 '${assembly}'
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31 ${reads_assembly.individual_sequences}
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32 #end if
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33 -o 'sketch'
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34 ]]></command>
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35 <inputs>
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36 <conditional name="reads_assembly">
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37 <param name="reads_assembly_selector" type="select" label="Input: Reads or Assemblies">
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38 <option selected="True" value="reads">Reads</option>
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39 <option value="assembly">Assembly</option>
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40 </param>
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41 <when value="reads">
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42 <conditional name="reads_input">
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43 <param name="reads_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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44 <option value="paired">Paired</option>
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45 <option value="single">Single</option>
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46 <option value="paired_collection">Paired Collection</option>
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47 </param>
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48 <when value="paired">
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49 <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
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50 <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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51 </when>
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52 <when value="single">
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53 <param name="reads" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
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54 </when>
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55 <when value="paired_collection">
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56 <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"/>
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57 </when>
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58 </conditional>
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59 <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"/>
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60 </when>
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61 <when value="assembly">
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62 <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/>
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63 <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences"/>
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64 </when>
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65 </conditional>
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66 <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" />
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67 <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32"/>
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68 </inputs>
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69 <outputs>
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70 <data name="sketch" format="msh" from_work_dir="sketch.msh"/>
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71 </outputs>
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72 <tests>
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73 <test>
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74 <param name="reads_assembly_selector" value="reads" />
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75 <param name="reads_input_selector" value="single"/>
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76 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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77 <output name="sketch" file="ERR024951_seqtk_sample_1000_1.sketch.msh" compare="sim_size" />
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78 </test>
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79 <test>
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80 <param name="reads_assembly_selector" value="assembly" />
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81 <param name="assembly" value="test_assembly.fasta"/>
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82 <output name="sketch" file="test_assembly.sketch.msh" compare="sim_size" />
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83 </test>
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84 </tests>
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85 <help><![CDATA[
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86 Description:
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87
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88 Create a sketch file, which is a reduced representation of a sequence or set
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89 of sequences (based on min-hashes) that can be used for fast distance
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90 estimations. Inputs can be fasta or fastq files (gzipped or not), and "-" can
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91 be given to read from standard input. Input files can also be files of file
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92 names (see -l). For output, one sketch file will be generated, but it can have
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93 multiple sketches within it, divided by sequences or files (see -i). By
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94 default, the output file name will be the first input file with a '.msh'
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95 extension, or 'stdin.msh' if standard input is used (see -o).
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96 ]]></help>
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97 <citations>
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98 <citation type="bibtex">
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99 @article{ondov2016mash,
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100 title={Mash: fast genome and metagenome distance estimation using MinHash},
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101 author={Ondov, Brian D and Treangen, Todd J and Melsted, P{\'a}ll and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M},
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102 journal={Genome biology},
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103 volume={17},
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104 number={1},
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105 pages={132},
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106 year={2016},
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107 publisher={BioMed Central}
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108 }
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109 </citation>
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110 </citations>
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111 </tool>