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annotate mash_screen.xml @ 2:7eed09e9dabe draft

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author dfornika
date Mon, 24 Feb 2020 20:55:48 +0000
parents f27853effdd6
children 561dc2d84650
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1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy1" profile="19.01">
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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' queries.msh &&
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12 mash screen
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13 $winner_takes_all
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14 -i $minimum_identity_to_report
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15 -v $maximum_p_value_to_report
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16 queries.msh
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17 #if str( $pool_input.pool_input_selector ) == "paired"
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18 '$pool_input.pool_1' '$pool_input.pool_2'
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19 #end if
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20 #if str( $pool_input.pool_input_selector ) == "paired_collection"
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21 '$pool_input.pool.forward' '$pool_input.pool.reverse'
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22 #end if
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23 #if str( $pool_input.pool_input_selector ) == "single"
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24 '$pool_input.pool'
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25 #end if
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26 > '$output'
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27 ]]></command>
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28 <inputs>
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29 <conditional name="pool_input">
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30 <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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31 <option value="paired">Paired</option>
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32 <option value="single">Single</option>
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33 <option value="paired_collection">Paired Collection</option>
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34 </param>
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35 <when value="paired">
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36 <param name="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
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37 <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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38 </when>
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39 <when value="single">
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40 <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
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41 </when>
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42 <when value="paired_collection">
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43 <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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44 </when>
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45 </conditional>
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46 <param name="queries" type="data" format="msh" />
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47 <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/>
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48 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." />
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49 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/>
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50 </inputs>
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51 <outputs>
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52 <data name="output" format="tabular" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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57 <param name="pool_input_selector" value="single"/>
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58 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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59 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
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60 </test>
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61 <test>
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62 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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63 <param name="pool_input_selector" value="single"/>
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64 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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65 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
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66 </test>
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67 <test>
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68 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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69 <param name="pool_input_selector" value="paired"/>
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70 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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71 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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72 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
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73 </test>
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74 </tests>
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75 <help><![CDATA[
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76 Description:
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77
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78 Determine how well query sequences are contained within a pool of sequences.
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79 The queries must be formatted as a single Mash sketch file (.msh), created
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80 with the `mash sketch` command. The <pool> files can be contigs or reads, in
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81 fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from
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82 standard input. The <pool> sequences are assumed to be nucleotides, and will
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83 be 6-frame translated if the <queries> are amino acids. The output fields are
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84 [identity, shared-hashes, median-multiplicity, p-value, query-ID,
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85 query-comment], where median-multiplicity is computed for shared hashes, based
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86 on the number of observations of those hashes within the pool.
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87 ]]></help>
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88 <citations>
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89 <citation type="bibtex">
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90 @article{ondov2016mash,
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91 title={Mash: fast genome and metagenome distance estimation using MinHash},
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92 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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93 journal={Genome biology},
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94 volume={17},
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95 number={1},
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96 pages={132},
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97 year={2016},
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98 publisher={BioMed Central}
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99 }
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100 </citation>
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101 </citations>
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102 </tool>