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annotate clamlst_search.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="clamlst_search_wrapper" name="Search MLST 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 <requirement type="package" version="4.8">sed</requirement>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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6 </requirements>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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7 <stdio>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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8 <exit_code range="1:" level="fatal" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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9 </stdio>
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10 <version_command>claMLST -v</version_command>
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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11 <command><![CDATA[
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12 ln -s $database.file_name \$_GALAXY_JOB_TMP_DIR/ &&
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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13 claMLST
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14 #if $data.input == "fasta"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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15 search
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16 #else
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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17 search2
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18 #end if
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19 #if str($coverage)
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20 -c $coverage
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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21 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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22 #if str($identity)
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23 -i $identity
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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24 #end if
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25 #if $fasta
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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26 -f '${fastaout}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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27 #end if
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28 #if $data.input == "fasta"
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29 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.fastain}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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30 | sed -e "~s/`echo $data.fastain.file_name | sed -e '~s/.*\///' |
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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31 sed -e '~s/.dat$//'`/$data.fastain.name/"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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32 #end if
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33 #if $data.input == "fastqsingle"
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34 #if str($data.reads)
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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35 -r $data.reads
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36 #end if
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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37 --single
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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38 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.single}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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39 | sed -e "~s/`echo $data.single.file_name | sed -e '~s/.*\///'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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40 | sed -e '~s/.dat$//'`/$data.single.name/"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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41 #end if
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42 #if $data.input == "fastqpaired"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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43 #if str($data.reads)
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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44 -r $data.reads
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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45 #end if
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46 --paired
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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47 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.forward}' '${data.reverse}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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48 | sed -e "~s/`echo $data.forward.file_name | sed -e '~s/.*\///'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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49 | sed -e '~s/.dat$//'`/$data.forward.name/"
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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50 #end if
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51 #if $data.input == "fastqpaired2"
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52 #if str($data.reads)
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53 -r $data.reads
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54 #end if
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55 --paired
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56 \$_GALAXY_JOB_TMP_DIR/`echo $database.file_name | sed -e '~s/.*\///'` '${data.pairedfile.forward}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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57 '${data.pairedfile.reverse}'
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58 | sed -e "~s/`echo $data.pairedfile.forward.file_name | sed -e '~s/.*\///'
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59 | sed -e '~s/.dat$//'`/$data.pairedfile.name/"
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60 #end if
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61 > '${mlst}'
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62 #if $log
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63 2> '${logfile}'
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64 #end if
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65 ]]>
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66 </command>
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67 <inputs>
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68 <param name="database" type="data"
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69 format="sqlite"
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70 label="Classical MLST database"
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71 help="Sqlite format from claMLST import" />
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72 <conditional name="data">
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73 <param name="input" type="select" label="Select type of data">
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74 <option value="fasta" selected="true">Assembly (fasta)</option>
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75 <option value="fastqsingle">Raw data (single)</option>
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76 <option value="fastqpaired">Raw data (paired separated)</option>
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77 <option value="fastqpaired2">Raw data (paired)</option>
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78 </param>
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79 <when value="fasta">
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80 <param name="fastain" type="data" format="fasta"
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81 label="Assembly Genome" help="Fasta format" />
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82 </when>
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83 <when value="fastqsingle">
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84 <param name="single" type="data" format="fastq,fastq.gz"
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85 label="Single read file" help="Fastq(gz) format" />
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86 <param name="reads" type="integer" value="10" optional="true"
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87 label="Minimum reads coverage to search gene" />
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88 </when>
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89 <when value="fastqpaired">
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90 <param name="forward" type="data" format="fastq,fastq.gz"
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91 label="Forward read file" help="Fastq(gz) format" />
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92 <param name="reverse" type="data" format="fastq,fastq.gz"
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93 label="Reverse read file" help="Fastq(gz) format" />
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94 <param name="reads" type="integer" value="10" optional="true"
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95 label="Minimum reads coverage to search gene" />
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96 </when>
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97 <when value="fastqpaired2">
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98 <param name="pairedfile" type="data_collection" format="fastq,fastq.gz"
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99 label="Paired of read files" help="Fastq(gz) format"
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100 collection_type="paired" />
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101 <param name="reads" type="integer" value="10" optional="true"
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102 label="Minimum reads coverage to search gene" />
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103 </when>
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104 </conditional>
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105 <param name="fasta" type="boolean" checked="false"
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106 label="Write fasta file with MLST genes allele" />
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107 <param name="identity" type="float" value="0.9" optional="false"
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108 label="Identity"
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109 help="Minimum identity to search gene" />
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110 <param name="coverage" type="float" value="0.9" optional="false"
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111 label="Coverage"
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112 help="Minimum coverage to search gene" />
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113 <param name="log" type="boolean" checked="false"
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114 label="Write log file" />
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115 </inputs>
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116 <outputs>
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117 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log">
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118 <filter>log</filter>
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119 </data>
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120 <data name="mlst" format="txt" label="${tool.name} on ${on_string}: mlst" />
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121 <data name="fastaout" format="fasta" label="${tool.name} on {on_string}: fasta">
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122 <filter>fasta</filter>
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123 </data>
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124 </outputs>
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125 <tests>
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126 <test expect_num_outputs="1">
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127 <param name="database" value="clamlst_ecoli.db" />
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128 <conditional name="data">
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129 <param name="input" value="fasta" />
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130 <param name="fastain" ftype="fasta" value="EHSB-021.fasta" />
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131 </conditional>
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132 <param name="identity" value="0.8" />
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133 <output name="mlst" ftype="txt">
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134 <assert_contents>
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135 <has_text_matching expression="155\t6\t4\t14\t16\t24\t8\t14" />
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136 </assert_contents>
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137 </output>
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138 </test>
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139 <!-- <test expect_num_outputs="3"> -->
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140 <!-- <param name="database" value="clamlst_ecoli.db" /> -->
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141 <!-- <conditional name="data"> -->
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142 <!-- <param name="input" value="fastqpaired" /> -->
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143 <!-- <param name="forward" ftype="fastq.gz" value="EHSB-021_R1.fastq.gz" /> -->
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144 <!-- <param name="reverse" ftype="fastq.gz" value="EHSB-021_R2.fastq.gz" /> -->
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145 <!-- <param name="reads" value="5" /> -->
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146 <!-- </conditional> -->
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147 <!-- <param name="fasta" value="true" /> -->
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148 <!-- <param name="log" value="true" /> -->
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149 <!-- <output name="fastaout" ftype="fasta"> -->
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150 <!-- <assert_contents> -->
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151 <!-- <has_n_lines n="14" /> -->
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152 <!-- </assert_contents> -->
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153 <!-- </output> -->
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154 <!-- <output name="mlst" ftype="txt"> -->
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155 <!-- <assert_contents> -->
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156 <!-- <has_text_matching expression="4\t14\t16\t24\t8\t14" /> -->
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157 <!-- </assert_contents> -->
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158 <!-- </output> -->
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159 <!-- </test> -->
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160 </tests>
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161 <help>
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162 **What it does**
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163
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164 Search ST number from pubMLST database
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165
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166 You can use
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167 - Genome assembly (blat search)
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168 - Raw data (kma search)
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169
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170 **Options:**
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171
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172 -i, --identity FLOAT Minimum identity to search gene (default=0.9).
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173 -c, --coverage FLOAT Minimum coverage to search gene (default=0.95).
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174 -r, --reads INTEGER Minimum reads coverage to search gene (default=10).
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175 -f, --fasta FILENAME Write fasta file with gene allele.
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176
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177 **License and citation**
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178
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179 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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180 </help>
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181 <citations>
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182 </citations>
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183 </tool>