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annotate mash_screen.xml @ 11:2aa387022b1f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash commit ff9564c2e6924fab084b6e02a3a196650041636a
author iuc
date Thu, 16 Oct 2025 16:42:12 +0000
parents a33df3111153
children
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9
a33df3111153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
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2 <description>Determine sequence conservation</description>
0
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
9
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6 <expand macro="xref"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
0
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9 <command detect_errors="exit_code"><![CDATA[
4
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10 #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table":
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11 ln -s '$queries_input_source.queries.fields.path' queries.msh &&
d9fb7a9bce28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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12 #elif str( $queries_input_source.queries_input_source_selector ) == 'history':
d9fb7a9bce28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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13 ln -s '$queries_input_source.queries' queries.msh &&
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14 #end if
0
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15 mash screen
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16 $winner_takes_all
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17 -i $minimum_identity_to_report
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18 -v $maximum_p_value_to_report
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19 queries.msh
1
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20 #if str( $pool_input.pool_input_selector ) == "paired"
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21 '$pool_input.pool_1' '$pool_input.pool_2'
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22 #end if
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23 #if str( $pool_input.pool_input_selector ) == "paired_collection"
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24 '$pool_input.pool.forward' '$pool_input.pool.reverse'
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25 #end if
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26 #if str( $pool_input.pool_input_selector ) == "single"
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27 '$pool_input.pool'
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28 #end if
0
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29 > '$output'
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30 ]]></command>
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31 <inputs>
1
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32 <conditional name="pool_input">
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33 <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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34 <option value="paired">Paired</option>
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35 <option value="single">Single</option>
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36 <option value="paired_collection">Paired Collection</option>
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37 </param>
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38 <when value="paired">
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39 <param name="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
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40 <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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41 </when>
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42 <when value="single">
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43 <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
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44 </when>
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45 <when value="paired_collection">
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46 <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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47 </when>
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48 </conditional>
4
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49 <conditional name="queries_input_source">
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50 <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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51 <option value="tool_data_table">Queries from tool data table</option>
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52 <option selected="True" value="history">Queries from history</option>
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53 </param>
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54 <when value="tool_data_table">
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55 <param name="queries" type="select" label="Queries (Mash Sketch)">
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56 <options from_data_table="mash_sketches"/>
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57 </param>
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58 </when>
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59 <when value="history">
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60 <param name="queries" type="data" format="msh"/>
4
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61 </when>
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62 </conditional>
9
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63 <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result" 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"/>
0
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66 </inputs>
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67 <outputs>
9
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68 <data name="output" format="tabular"/>
0
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69 </outputs>
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70 <tests>
9
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71 <test expect_num_outputs="1">
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72 <conditional name="pool_input">
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73 <param name="pool_input_selector" value="single"/>
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74 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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75 </conditional>
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76 <conditional name="queries_input_source">
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77 <param name="queries_input_source_selector" value="history"/>
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78 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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79 </conditional>
0
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80 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
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81 </test>
9
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82 <test expect_num_outputs="1">
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83 <conditional name="pool_input">
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84 <param name="pool_input_selector" value="single"/>
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85 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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86 </conditional>
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87 <conditional name="queries_input_source">
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88 <param name="queries_input_source_selector" value="tool_data_table"/>
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89 <param name="queries" value="test_sketch"/>
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90 </conditional>
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91 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
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92 </test>
9
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93 <test expect_num_outputs="1">
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94 <conditional name="pool_input">
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95 <param name="pool_input_selector" value="paired"/>
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96 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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97 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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98 </conditional>
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99 <conditional name="queries_input_source">
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100 <param name="queries_input_source_selector" value="history"/>
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101 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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102 </conditional>
0
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103 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
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104 </test>
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105 </tests>
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106 <help><![CDATA[
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107
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108 **What it does**
0
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109
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110 Determine how well query sequences are contained within a pool of sequences.
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111 The queries must be formatted as a single Mash sketch file (.msh), created
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112 with the `mash sketch` command. The <pool> files can be contigs or reads, in
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113 fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from
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114 standard input. The <pool> sequences are assumed to be nucleotides, and will
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115 be 6-frame translated if the <queries> are amino acids. The output fields are
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116 [identity, shared-hashes, median-multiplicity, p-value, query-ID,
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117 query-comment], where median-multiplicity is computed for shared hashes, based
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118 on the number of observations of those hashes within the pool.
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119 ]]></help>
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120 <expand macro="citations"/>
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121 </tool>