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author dfornika
date Mon, 24 Feb 2020 21:06:13 +0000
parents 34869670b2d0
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1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy2" 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 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table":
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10 ln -s '$queries_input_source.queries.fields.path' queries.msh &&
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11 #elif str( $queries_input_source.queries_input_source_selector ) == 'history':
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12 ln -s '$queries_input_source.queries' queries.msh &&
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13 #end if
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14 mash screen
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15 $winner_takes_all
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16 -i $minimum_identity_to_report
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17 -v $maximum_p_value_to_report
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18 queries.msh
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19 #if str( $pool_input.pool_input_selector ) == "paired"
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20 '$pool_input.pool_1' '$pool_input.pool_2'
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21 #end if
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22 #if str( $pool_input.pool_input_selector ) == "paired_collection"
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23 '$pool_input.pool.forward' '$pool_input.pool.reverse'
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24 #end if
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25 #if str( $pool_input.pool_input_selector ) == "single"
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26 '$pool_input.pool'
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27 #end if
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28 > '$output'
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29 ]]></command>
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30 <inputs>
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31 <conditional name="pool_input">
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32 <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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33 <option value="paired">Paired</option>
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34 <option value="single">Single</option>
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35 <option value="paired_collection">Paired Collection</option>
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36 </param>
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37 <when value="paired">
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38 <param name="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
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39 <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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40 </when>
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41 <when value="single">
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42 <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
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43 </when>
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44 <when value="paired_collection">
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45 <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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46 </when>
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47 </conditional>
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48 <conditional name="queries_input_source">
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49 <param name="queries_input_source_selector" type="select" label="Select queries from your history or use one from a tool data table?" help="">
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50 <option value="tool_data_table">Queries from tool data table</option>
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51 <option selected="True" value="history">Queries from history</option>
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52 </param>
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53 <when value="tool_data_table">
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54 <param name="queries" type="select" label="Queries (Mash Sketch)">
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55 <options from_data_table="mash_sketches"/>
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56 </param>
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57 </when>
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58 <when value="history">
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59 <param name="queries" type="data" format="msh" />
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60 </when>
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61 </conditional>
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62 <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result"
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63 help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/>
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64 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report" />
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65 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report" />
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66 </inputs>
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67 <outputs>
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68 <data name="output" format="tabular" />
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="queries_input_source_selector" value="history"/>
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73 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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74 <param name="pool_input_selector" value="single"/>
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75 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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76 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
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77 </test>
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78 <test>
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79 <param name="queries_input_source_selector" value="history"/>
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80 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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81 <param name="pool_input_selector" value="single"/>
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82 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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83 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
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84 </test>
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85 <test>
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86 <param name="queries_input_source_selector" value="history"/>
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87 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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88 <param name="pool_input_selector" value="paired"/>
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89 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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90 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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91 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
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92 </test>
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93 </tests>
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94 <help><![CDATA[
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95
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96 **What it does**
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97
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98 Determine how well query sequences are contained within a pool of sequences.
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99 The queries must be formatted as a single Mash sketch file (.msh), created
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100 with the `mash sketch` command. The <pool> files can be contigs or reads, in
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101 fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from
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102 standard input. The <pool> sequences are assumed to be nucleotides, and will
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103 be 6-frame translated if the <queries> are amino acids. The output fields are
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104 [identity, shared-hashes, median-multiplicity, p-value, query-ID,
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105 query-comment], where median-multiplicity is computed for shared hashes, based
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106 on the number of observations of those hashes within the pool.
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107 ]]></help>
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108 <expand macro="citations"/>
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109 </tool>