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annotate mlst.xml @ 1:8e8dc9a1e3e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
author iuc
date Mon, 30 Oct 2017 05:40:10 -0400
parents 735872ff8222
children 253b7a1cf87e
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8e8dc9a1e3e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 47ad236b09eaf7541fbd7dd5b95e970800d545a5
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1 <tool id="mlst" name="MLST" version="2.9">
0
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2 <requirements>
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3 <requirement type="package" version="2.9">mlst</requirement>
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4 </requirements>
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6 <version_command>mlst --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 mlst "$input_file" --nopath
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10 #if $settings.advanced == "advanced"
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11 #if $settings.min_dna_id
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12 --minid=$settings.min_dna_id
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13 #end if
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14 #if $settings.min_dna_cov
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15 --mincov=$settings.min_dna_cov
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16 #end if
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17 #if $settings.scheme
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18 --scheme=$settings.scheme
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19 #end if
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20 #end if
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21 > "$report"
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22 ]]></command>
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23
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24 <inputs>
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25 <param type="data" name="input_file" format="fasta,genbank" />
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26 <conditional name="settings">
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27 <param name="advanced" type="select" label="Specify advanced parameters">
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28 <option value="simple" selected="true">No, use program defaults.</option>
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29 <option value="advanced">Yes, see full parameter list.</option>
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30 </param>
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31 <when value="simple">
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32 </when>
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33 <when value="advanced">
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34 <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
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35 <param name="min_dna_cov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" />
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36 <param name="scheme" type="text" area="false" label="PubMLST Scheme" help="Turn off auto-detection and only use this scheme" optional="true" />
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37 </when>
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38 </conditional>
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39 </inputs>
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40
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41 <outputs>
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42 <data name="report" format="tabular" />
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43 </outputs>
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44
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45 <tests>
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46 <!-- Basic test - will produce no results. -->
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47 <test>
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48 <param name="input_file" value="Acetobacter.fna"/>
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49 <param name="advanced" value="simple"/>
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50 <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/>
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51 </test>
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52
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53 <!-- Basic test - will produce results. -->
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54 <test>
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55 <param name="input_file" value="MRSA0252_trimmed.fna"/>
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56 <param name="advanced" value="simple"/>
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57 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
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58 </test>
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59
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60 <!-- Advanced test - Min DNA Coverage 100 -->
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61 <test>
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62 <param name="input_file" value="MRSA0252_trimmed.fna"/>
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63 <param name="advanced" value="advanced"/>
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64 <param name="min_dna_cov" value="100"/>
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65 <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
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66 </test>
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67
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68 <!-- Advanced test - Min DNA ID 100 -->
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69 <test>
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70 <param name="input_file" value="MRSA0252_trimmed.fna"/>
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71 <param name="advanced" value="advanced"/>
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72 <param name="min_dna_id" value="100"/>
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73 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
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74 </test>
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75 </tests>
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76
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77 <help><![CDATA[
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78 **What it does**
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79
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80 Given a genome file in FASTA or Genbank format, MLST will scan the file against PubMLST typing schemes.
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81
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82 **Output**
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83
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84 MLST will produce a tab-seperated output file which contains:
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85 - the filename
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86 - the closest PubMLST scheme name
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87 - the ST (sequence type)
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88 - the allele IDs
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89
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90 **Example Output**
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91
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92 ::
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93
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94 genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3)
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95
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96 **Without auto-detection**
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97
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98 If you provide the 'scheme' parameter, it will print a fixed tabular output with a heading containing allele names specific to that scheme. To view a list of schemes, use the MLST List tool.
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99
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100 ::
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101
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102 FILE SCHEME ST abcZ adk aroE fumC gdh pdhC pgm
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103 NM003.fa neisseria 11 2 3 4 3 8 4 6
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104
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105 **Missing data**
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106 MLST does not just look for exact matches to full length alleles. It attempts to tell you as much as possible about what it found using the notation below:
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107
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108 +--------+---------------------------+
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109 | Symbol | Meaning |
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110 +========+===========================+
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111 | n | Exact intact allele |
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112 +--------+---------------------------+
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113 | ~n | Novel allele similar to n |
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114 +--------+---------------------------+
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115 | n,m | Multiple alleles |
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116 +--------+---------------------------+
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117 | *-* | Allele missing |
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118 +--------+---------------------------+
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119
1
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120 Galaxy wrapper maintained by Simon Gladman.
0
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121 ]]></help>
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122
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123 <citations>
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124 <citation type="bibtex">
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125 @UNPUBLISHED{Seemann2016,
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126 author = "Seemann T",
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127 title = "MLST: Scan contig files against PubMLST typing schemes",
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128 year = "2016",
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129 note = "https://github.com/tseemann/mlst"}
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130 </citation>
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131 </citations>
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132 </tool>