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annotate mash_screen.xml @ 11:d85f64b694ca draft

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planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/mash commit 423cf96266f6ac433052ff72edb1397502313010-dirty
author dfornika
date Thu, 25 Jul 2019 15:50:37 -0400
parents 5918212ec576
children 8f70b0652cff
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1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy0">
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2 <description>determines how well query sequences are contained within a pool of sequences.</description>
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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 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">mash</requirement>
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8 </requirements>
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9 <version_command>mash --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ln -s '${queries.fields.path}/sketch.msh' queries.msh &&
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12 mash screen
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13 -p \${GALAXY_SLOTS:-4}
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14 $winner_takes_all
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15 -i $minimum_identity_to_report
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16 -v $maximum_p_value_to_report
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17 queries.msh
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18 #if str( $pool_input.pool_input_selector ) == "paired"
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19 '$pool_input.pool_1' '$pool_input.pool_2'
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20 #end if
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21 #if str( $pool_input.pool_input_selector ) == "paired_collection"
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22 '$pool_input.pool.forward' '$pool_input.pool.reverse'
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23 #end if
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24 #if str( $pool_input.pool_input_selector ) == "single"
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25 '$pool_input.pool'
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26 #end if
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27 > '$output'
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28 ]]></command>
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29 <inputs>
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30 <conditional name="pool_input">
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31 <param name="pool_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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32 <option value="paired">Paired</option>
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33 <option value="single">Single</option>
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34 <option value="paired_collection">Paired Collection</option>
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35 </param>
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36 <when value="paired">
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37 <param name="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
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38 <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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39 </when>
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40 <when value="single">
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41 <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
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42 </when>
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43 <when value="paired_collection">
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44 <param name="pool" 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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45 </when>
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46 </conditional>
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47 <param name="queries" type="select">
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48 <options from_data_table="mash_sketches">
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49 <validator type="no_options" message="No mash sketches are available." />
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50 </options>
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51 </param>
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52 <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/>
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53 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." />
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54 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/>
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55 </inputs>
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56 <outputs>
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57 <data name="output" format="tabular" />
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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62 <param name="pool_input_selector" value="single"/>
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63 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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64 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
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65 </test>
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66 <test>
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67 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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68 <param name="pool_input_selector" value="single"/>
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69 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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70 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
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71 </test>
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72 <test>
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73 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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74 <param name="pool_input_selector" value="paired"/>
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75 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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76 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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77 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
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78 </test>
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79 <test>
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80 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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81 <param name="pool_input_selector" value="paired_collection"/>
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82 <param name="pool">
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83 <collection type="paired">
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84 <element name="forward" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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85 <element name="reverse" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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86 </collection>
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87 </param>
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88 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
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89 </test>
0
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90 </tests>
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91 <help><![CDATA[
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92 Description:
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93
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94 Determine how well query sequences are contained within a pool of sequences.
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95 The queries must be formatted as a single Mash sketch file (.msh), created
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96 with the `mash sketch` command. The <pool> files can be contigs or reads, in
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97 fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from
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98 standard input. The <pool> sequences are assumed to be nucleotides, and will
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99 be 6-frame translated if the <queries> are amino acids. The output fields are
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100 [identity, shared-hashes, median-multiplicity, p-value, query-ID,
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101 query-comment], where median-multiplicity is computed for shared hashes, based
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102 on the number of observations of those hashes within the pool.
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103 ]]></help>
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104 <citations>
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105 <citation type="bibtex">
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106 @article{ondov2016mash,
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107 title={Mash: fast genome and metagenome distance estimation using MinHash},
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108 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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109 journal={Genome biology},
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110 volume={17},
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111 number={1},
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112 pages={132},
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113 year={2016},
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114 publisher={BioMed Central}
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115 }
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116 </citation>
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117 </citations>
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118 </tool>