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annotate wgmlst_add.xml @ 0:a3cc35af3635 draft

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planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
author bvalot
date Thu, 16 Jun 2022 12:32:28 +0000
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children 5b2c48fa0175
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a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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1 <tool id="wgmlst_add_wrapper" name="Add strain to cg/wgMLST database" version="2.1.3">
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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2 <description></description>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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3 <requirements>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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4 <requirement type="package" version="2.1.3">pymlst</requirement>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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5 </requirements>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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6 <stdio>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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7 <exit_code range="1:" level="fatal" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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8 </stdio>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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9 <version_command>wgMLST -v</version_command>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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10 <command><![CDATA[
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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11 cp '${database}' '${databaseout}' &&
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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12 wgMLST
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13 #if $data.input == "fasta"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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14 add
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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15 #else
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16 add2
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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17 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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18 #if str($coverage)
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19 -c $coverage
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20 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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21 #if str($identity)
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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22 -i $identity
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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23 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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24 #if $data.input == "fasta"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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25 #if $strain
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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26 -s '$strain'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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27 #else
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28 -s '$data.fastain.name.replace(" ", "_").replace("-", "_")'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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29 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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30 '${databaseout}' '${data.fastain}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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31 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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32 #if $data.input == "fastqsingle"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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33 #if str($data.reads)
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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34 -r $data.reads
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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35 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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36 #if $strain
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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37 -s '$strain'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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38 #else
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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39 -s '$data.single.name.replace(" ", "_").replace("-", "_")'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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40 #end if
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41 '${databaseout}' '${data.single}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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42 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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43 #if $data.input == "fastqpaired"
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44 #if str($data.reads)
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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45 -r $data.reads
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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46 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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47 #if $strain
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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48 -s '$strain'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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49 #else
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50 -s '$data.forward.name.replace(" ", "_").replace("-", "_")'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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51 #end if
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52 '${databaseout}' '${data.forward}' '${data.reverse}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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53 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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54 #if $data.input == "fastqpaired2"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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55 #if str($data.reads)
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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56 -r $data.reads
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57 #end if
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58 #if $strain
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59 -s '$strain'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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60 #else
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61 -s '$data.pairedfile.name.replace(" ", "_").replace("-", "_")'
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62 #end if
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63 '${databaseout}' '${data.pairedfile.forward}'
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64 '${data.pairedfile.reverse}'
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65 #end if
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66 #if $log
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67 2> '${logfile}'
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68 #end if
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69 ]]>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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70 </command>
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71 <inputs>
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72 <param name="database" type="data"
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73 format="sqlite"
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74 label="cg/wgMLST database"
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75 help="Sqlite format from cg/wgMLST database" />
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76 <conditional name="data">
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77 <param name="input" type="select" label="Select type of data">
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78 <option value="fasta" selected="true">Assembly (fasta)</option>
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79 <option value="fastqsingle">Raw data (single)</option>
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80 <option value="fastqpaired">Raw data (paired separated)</option>
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81 <option value="fastqpaired2">Raw data (paired)</option>
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82 </param>
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83 <when value="fasta">
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84 <param name="fastain" type="data" format="fasta"
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85 label="Assembly Genome" help="Fasta format" />
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86 </when>
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87 <when value="fastqsingle">
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88 <param name="single" type="data" format="fastq,fastq.gz"
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89 label="Single read file" help="Fastq(gz) format" />
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90 <param name="reads" type="integer" value="10" optional="true"
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91 label="Minimum reads coverage to search gene" />
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92 </when>
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93 <when value="fastqpaired">
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94 <param name="forward" type="data" format="fastq,fastq.gz"
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95 label="Forward read file" help="Fastq(gz) format" />
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96 <param name="reverse" type="data" format="fastq,fastq.gz"
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97 label="Reverse read file" help="Fastq(gz) format" />
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98 <param name="reads" type="integer" value="10" optional="true"
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99 label="Minimum reads coverage to search gene" />
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100 </when>
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101 <when value="fastqpaired2">
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102 <param name="pairedfile" type="data_collection" format="fastq,fastq.gz"
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103 label="Paired of read files" help="Fastq(gz) format"
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104 collection_type="paired" />
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105 <param name="reads" type="integer" value="10" optional="true"
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106 label="Minimum reads coverage to search gene" />
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107 </when>
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108 </conditional>
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109 <param name="strain" type="text" value="" size="50"
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110 optional="false"
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111 label="Strain"
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112 help="Name of the strain">
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113 <sanitizer invalid_char="_" >
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114 <valid initial="string.ascii_letters,string.digits">
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115 <add value="_" />
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116 <add value="." />
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117 </valid>
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118 </sanitizer>
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119 </param>
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120 <param name="identity" type="float" value="0.9" optional="false"
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121 label="Identity"
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122 help="Minimum identity to search gene" />
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123 <param name="coverage" type="float" value="0.9" optional="false"
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124 label="Coverage"
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125 help="Minimum coverage to search gene" />
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126 <param name="log" type="boolean" checked="true"
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127 label="Write log file" />
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128 </inputs>
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129 <outputs>
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130 <data name="databaseout" format="sqlite" label="${database.name}">
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131 </data>
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132 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log">
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133 <filter>log</filter>
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134 </data>
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135 </outputs>
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136 <tests>
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137 <test expect_num_outputs="2">
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138 <param name="database" value="wgmlst_ecoli.db" />
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139 <conditional name="data">
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140 <param name="input" value="fasta" />
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141 <param name="fastain" ftype="fasta" value="EHSB-021.fasta" />
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142 </conditional>
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143 <param name="identity" value="0.8" />
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144 <output name="logfile" ftype="txt">
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145 <assert_contents>
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146 <has_text text="Added 2497 new MLST genes to the database" />
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147 <has_text text="Found 32 partial genes, filled 30" />
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148 <has_text text="Removed 4 genes" />
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149 </assert_contents>
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150 </output>
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151 </test>
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152 <!-- <test expect_num_outputs="2"> -->
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153 <!-- <param name="database" value="wgmlst_ecoli.db" /> -->
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154 <!-- <param name="strain" value="EHSB-021" /> -->
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155 <!-- <conditional name="data"> -->
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156 <!-- <param name="input" value="fastqpaired" /> -->
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157 <!-- <param name="forward" ftype="fastq.gz" value="EHSB-021_R1.fastq.gz" /> -->
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158 <!-- <param name="reverse" ftype="fastq.gz" value="EHSB-021_R2.fastq.gz" /> -->
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159 <!-- <param name="reads" value="5" /> -->
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160 <!-- </conditional> -->
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161 <!-- <output name="logfile" ftype="txt"> -->
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162 <!-- <assert_contents> -->
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163 <!-- <has_text_matching expression="Add 24\d\d new MLST genes to database" /> -->
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164 <!-- <has_text_matching expression="Remove \d genes with uncertain bases" /> -->
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165 <!-- <has_text_matching expression="Remove \d\d genes with bad CDS" /> -->
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166 <!-- </assert_contents> -->
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167 <!-- </output> -->
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168 <!-- </test> -->
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169 </tests>
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170 <help>
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171 **What it does**
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172
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173 Add a Strain to the cg/wgMLST database
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174
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175 You can use
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176 - Genome assembly (blat search)
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177 - Raw data (kma search)
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178
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179 **Options:**
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180 -s, --strain TEXT Name of the strain (default:genome name).
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181 -i, --identity FLOAT Minimum identity to search gene (default=0.9).
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182 -c, --coverage FLOAT Minimum coverage to search gene (default=0.95).
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183 -r, --reads INTEGER Minimum reads coverage to search gene (default=10).
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184 -f, --fasta FILENAME Write fasta file with gene allele.
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185
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186 **License and citation**
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187
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188 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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189 </help>
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190 <citations>
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191 </citations>
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192 </tool>