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annotate mash_screen.xml @ 8:d608e90fb3f0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 09:21:03 +0000
parents d9fb7a9bce28
children a33df3111153
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1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy3" 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 <xrefs>
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4 <xref type="bio.tools">mash</xref>
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5 </xrefs>
0
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
3
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9 <expand macro="requirements" />
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10 <expand macro="version_command" />
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11 <command detect_errors="exit_code"><![CDATA[
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12 #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table":
d9fb7a9bce28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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13 ln -s '$queries_input_source.queries.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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14 #elif str( $queries_input_source.queries_input_source_selector ) == 'history':
d9fb7a9bce28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 419003af9d5cdf7466b3bbc229256da4fb5852e6"
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15 ln -s '$queries_input_source.queries' queries.msh &&
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16 #end if
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17 mash screen
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18 $winner_takes_all
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19 -i $minimum_identity_to_report
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20 -v $maximum_p_value_to_report
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21 queries.msh
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22 #if str( $pool_input.pool_input_selector ) == "paired"
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23 '$pool_input.pool_1' '$pool_input.pool_2'
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24 #end if
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25 #if str( $pool_input.pool_input_selector ) == "paired_collection"
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26 '$pool_input.pool.forward' '$pool_input.pool.reverse'
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27 #end if
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28 #if str( $pool_input.pool_input_selector ) == "single"
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29 '$pool_input.pool'
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30 #end if
0
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31 > '$output'
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32 ]]></command>
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33 <inputs>
1
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34 <conditional name="pool_input">
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35 <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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36 <option value="paired">Paired</option>
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37 <option value="single">Single</option>
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38 <option value="paired_collection">Paired Collection</option>
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39 </param>
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40 <when value="paired">
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41 <param name="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
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42 <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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43 </when>
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44 <when value="single">
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45 <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
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46 </when>
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47 <when value="paired_collection">
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48 <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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49 </when>
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50 </conditional>
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51 <conditional name="queries_input_source">
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52 <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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53 <option value="tool_data_table">Queries from tool data table</option>
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54 <option selected="True" value="history">Queries from history</option>
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55 </param>
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56 <when value="tool_data_table">
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57 <param name="queries" type="select" label="Queries (Mash Sketch)">
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58 <options from_data_table="mash_sketches"/>
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59 </param>
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60 </when>
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61 <when value="history">
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62 <param name="queries" type="data" format="msh" />
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63 </when>
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64 </conditional>
3
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65 <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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66 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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67 <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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68 <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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69 </inputs>
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70 <outputs>
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71 <data name="output" format="tabular" />
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72 </outputs>
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73 <tests>
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74 <test>
4
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75 <param name="queries_input_source_selector" value="history"/>
0
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76 <param name="queries" value="NZ_MYON01000010.1.msh"/>
1
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77 <param name="pool_input_selector" value="single"/>
0
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78 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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79 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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80 </test>
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81 <test>
4
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82 <param name="queries_input_source_selector" value="tool_data_table"/>
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83 <param name="queries" value="test_sketch"/>
1
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84 <param name="pool_input_selector" value="single"/>
0
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85 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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86 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
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87 </test>
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88 <test>
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89 <param name="queries_input_source_selector" value="history"/>
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90 <param name="queries" value="NZ_MYON01000010.1.msh"/>
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91 <param name="pool_input_selector" value="paired"/>
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92 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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93 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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94 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
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95 </test>
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96 </tests>
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97 <help><![CDATA[
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98
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99 **What it does**
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100
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101 Determine how well query sequences are contained within a pool of sequences.
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102 The queries must be formatted as a single Mash sketch file (.msh), created
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103 with the `mash sketch` command. The <pool> files can be contigs or reads, in
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104 fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from
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105 standard input. The <pool> sequences are assumed to be nucleotides, and will
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106 be 6-frame translated if the <queries> are amino acids. The output fields are
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107 [identity, shared-hashes, median-multiplicity, p-value, query-ID,
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108 query-comment], where median-multiplicity is computed for shared hashes, based
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109 on the number of observations of those hashes within the pool.
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110 ]]></help>
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111 <expand macro="citations"/>
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112 </tool>