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annotate mash_sketch.xml @ 0:1aab9cf41bd0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
author iuc
date Wed, 24 Sep 2025 13:46:33 +0000
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1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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1 <tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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2 <description>Create a reduced sequence representation based on min-hashes</description>
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xref"/>
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code"><![CDATA[
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10
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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11 #if str ( $reads_assembly.reads_assembly_selector ) == "reads":
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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12 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired":
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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13 ln -s '$reads_assembly.reads_input.reads_1' "${reads_assembly.reads_input.reads_1.element_identifier}" &&
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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14 ln -s '$reads_assembly.reads_input.reads_2' "${reads_assembly.reads_input.reads_1.element_identifier}" &&
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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15 #end if
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16 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection":
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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17 ln -s '$reads_assembly.reads_input.reads.forward' "${reads_assembly.reads_input.reads.forward.element_identifier}" &&
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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18 ln -s '$reads_assembly.reads_input.reads.reverse' "${reads_assembly.reads_input.reads.reverse.element_identifier}" &&
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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19 #end if
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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20 #if str( $reads_assembly.reads_input.reads_input_selector ) == "single":
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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21 ln -s '$reads_assembly.reads_input.reads' "${reads_assembly.reads_input.reads.element_identifier}" &&
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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22 #end if
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23 #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly":
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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24 ln -s '${reads_assembly.assembly}' "${reads_assembly.assembly.element_identifier}" &&
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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25 #end if
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26
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27 mash sketch
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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28 -s '${sketch_size}'
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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29 -k '${kmer_size}'
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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30 -w '${prob_threshold}'
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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31 #if str( $reads_assembly.reads_assembly_selector ) == "reads":
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32 -m '${reads_assembly.minimum_kmer_copies}'
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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33 -r
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34 #if $reads_assembly.target_coverage :
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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35 -c '${reads_assembly.target_coverage}'
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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36 #end if
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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37 #if $reads_assembly.genome_size :
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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38 -g '${reads_assembly.genome_size}'
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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39 #end if
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40 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired" :
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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41 "${reads_assembly.reads_input.reads_1.element_identifier}" "${reads_assembly.reads_input.reads_1.element_identifier}}"
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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42 #end if
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43 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection":
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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44 "${reads_assembly.reads_input.reads.forward.element_identifier}" "${reads_assembly.reads_input.reads.reverse.element_identifier}"
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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45 #end if
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46 #if str( $reads_assembly.reads_input.reads_input_selector ) == "single":
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47 "${reads_assembly.reads_input.reads.element_identifier}"
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48 #end if
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49 #elif str( $reads_assembly.reads_assembly_selector ) == "assembly":
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50 -p \${GALAXY_SLOTS:-1}
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51 ${reads_assembly.individual_sequences}
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52 "${reads_assembly.assembly.element_identifier}"
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53 #end if
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54 -o 'sketch'
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55 ]]></command>
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56 <inputs>
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57 <conditional name="reads_assembly">
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58 <param name="reads_assembly_selector" type="select" label="Input: Reads or Assemblies">
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59 <option selected="True" value="reads">Reads</option>
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60 <option value="assembly">Assembly</option>
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61 </param>
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62 <when value="reads">
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63 <conditional name="reads_input">
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64 <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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65 <option value="paired">Paired</option>
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66 <option value="single">Single</option>
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67 <option value="paired_collection">Paired Collection</option>
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68 </param>
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69 <when value="paired">
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70 <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
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71 <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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72 </when>
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73 <when value="single">
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74 <param name="reads" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
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75 </when>
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76 <when value="paired_collection">
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77 <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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78 </when>
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79 </conditional>
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80 <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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81 <param type="integer" name="target_coverage" argument="-c" value="" min="0" max="500" optional="true" label="Target coverage" help="If specified, sketching will conclude if this coverage is reached before the end of the input file (estimated by average k-mer multiplicity)"/>
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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82 <param type="integer" name="genome_size" argument="-g" value="" min="1000" max="100000000000" optional="true" label="Genome size" help="If specified, will be used for p-value calculation instead of an estimated size from k-mer content"/>
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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83 </when>
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84 <when value="assembly">
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85 <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/>
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86 <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences" help="Sketch individual sequences, rather than whole files, e.g. for multi-fastas of single-chromosome genomes or pair-wise gene comparisons"/>
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87 </when>
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88 </conditional>
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89 <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" label="Sketch size" help="Each sketch will have at most this many non-redundant min-hashes"/>
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90 <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32" label="kmer size" />
1aab9cf41bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit f4e45447b1a8f2d99f3feda11a7c7d2bc7f84a57
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91 <param type="float" name="prob_threshold" argument="-w" value="0.01" min="0" max="1" label="Probability threshold for warning about low k-mer size" />
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92 </inputs>
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93 <outputs>
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94 <data name="sketch" format="msh" from_work_dir="sketch.msh"/>
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95 </outputs>
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96 <tests>
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97 <test expect_num_outputs="1">
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98 <conditional name="reads_assembly">
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99 <param name="reads_assembly_selector" value="reads"/>
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100 <conditional name="reads_input">
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101 <param name="reads_input_selector" value="single"/>
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102 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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103 </conditional>
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104 </conditional>
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105 <output name="sketch" file="test_01_mash_sketch.msh" compare="sim_size" />
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106 </test>
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107 <test expect_num_outputs="1">
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108 <conditional name="reads_assembly">
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109 <param name="reads_assembly_selector" value="reads"/>
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110 <conditional name="reads_input">
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111 <param name="reads_input_selector" value="single"/>
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112 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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113 </conditional>
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114 <param name="minimum_kmer_copies" value="10"/>
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115 </conditional>
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116 <output name="sketch" file="test_02_mash_sketch.msh" compare="sim_size" />
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117 </test>
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118 <test expect_num_outputs="1">
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119 <conditional name="reads_assembly">
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120 <param name="reads_assembly_selector" value="reads"/>
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121 <conditional name="reads_input">
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122 <param name="reads_input_selector" value="single"/>
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123 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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124 </conditional>
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125 <param name="target_coverage" value="1"/>
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126 </conditional>
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127 <output name="sketch" file="test_03_mash_sketch.msh" compare="sim_size" />
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128 </test>
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129 <test expect_num_outputs="1">
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130 <conditional name="reads_assembly">
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131 <param name="reads_assembly_selector" value="reads"/>
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132 <conditional name="reads_input">
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133 <param name="reads_input_selector" value="single"/>
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134 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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135 </conditional>
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136 <param name="genome_size" value="1000"/>
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137 </conditional>
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138 <output name="sketch" file="test_04_mash_sketch.msh" compare="sim_size" />
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139 </test>
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140 <test expect_num_outputs="1">
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141 <conditional name="reads_assembly">
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142 <param name="reads_assembly_selector" value="reads"/>
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143 <conditional name="reads_input">
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144 <param name="reads_input_selector" value="single"/>
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145 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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146 </conditional>
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147 </conditional>
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148 <param name="sketch_size" value="500"/>
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149 <output name="sketch" file="test_05_mash_sketch.msh" compare="sim_size" />
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150 </test>
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151 <test expect_num_outputs="1">
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152 <conditional name="reads_assembly">
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153 <param name="reads_assembly_selector" value="reads"/>
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154 <conditional name="reads_input">
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155 <param name="reads_input_selector" value="single"/>
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156 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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157 </conditional>
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158 </conditional>
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159 <param name="kmer_size" value="17"/>
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160 <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" />
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161 </test>
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162 <test expect_num_outputs="1">
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163 <conditional name="reads_assembly">
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164 <param name="reads_assembly_selector" value="reads"/>
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165 <conditional name="reads_input">
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166 <param name="reads_input_selector" value="single"/>
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167 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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168 </conditional>
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169 </conditional>
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170 <param name="prob_threshold" value="0.1"/>
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171 <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" />
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172 </test>
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173 <test expect_num_outputs="1">
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174 <conditional name="reads_assembly">
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175 <param name="reads_assembly_selector" value="assembly"/>
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176 <param name="assembly" value="test_assembly.fasta"/>
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177 </conditional>
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178 <output name="sketch" file="test_07_mash_sketch.msh" compare="sim_size" />
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179 </test>
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180 </tests>
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181 <help><![CDATA[
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182
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183 **What it does**
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184
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185 Create a sketch file, which is a reduced representation of a sequence or set
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186 of sequences (based on min-hashes) that can be used for fast distance
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187 estimations. Inputs can be fasta or fastq files (gzipped or not), and "-" can
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188 be given to read from standard input. Input files can also be files of file
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189 names (see -l). For output, one sketch file will be generated, but it can have
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190 multiple sketches within it, divided by sequences or files (see -i). By
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191 default, the output file name will be the first input file with a '.msh'
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192 extension, or 'stdin.msh' if standard input is used (see -o).
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193 ]]></help>
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194 <expand macro="citations"/>
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195 </tool>