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planemo upload for repository https://github.com/bvalot/pyMLST commit 142042a3856f8886031cacaa4fb28743a1bcd540
author bvalot
date Wed, 15 Nov 2023 12:22:07 +0000
parents 5b2c48fa0175
children
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1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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1 <tool id="clamlst_search_wrapper" name="Search MLST database"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
0
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3 <description></description>
1
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4 <macros>
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5 <import>macro.xml</import>
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6 </macros>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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7 <expand macro="requirements">
0
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8 <requirement type="package" version="4.8">sed</requirement>
1
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9 </expand>
0
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10 <stdio>
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11 <exit_code range="1:" level="fatal" />
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12 </stdio>
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13 <version_command>claMLST -v</version_command>
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14 <command><![CDATA[
1
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15 #set $databaselink = $database.file_name.split("/")[-1]
0
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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16 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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17 claMLST
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18 #if $data.input == "fasta"
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19 search
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20 #else
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21 search2
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22 #end if
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23 #if str($coverage)
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24 -c $coverage
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25 #end if
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26 #if str($identity)
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27 -i $identity
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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28 #end if
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29 #if $fasta
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30 -f '${fastaout}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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31 #end if
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32 #if $data.input == "fasta"
1
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33 \$_GALAXY_JOB_TMP_DIR/'${databaselink}'
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34 #for $datain in $data.fastain:
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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35 '${datain}'
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36 #end for
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37 #for $datain in $data.fastain:
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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38 #set $name = $datain.file_name.split("/")[-1].rstrip(".dat")
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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39 | sed -e "~s/$name/$datain.name/"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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40 #end for
0
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41 #end if
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42 #if $data.input == "fastqsingle"
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43 #if str($data.reads)
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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44 -r $data.reads
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45 #end if
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46 --single
1
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47 \$_GALAXY_JOB_TMP_DIR/'${databaselink}'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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48 #for $datain in $data.single:
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49 '${datain}'
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50 #end for
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51 #for $datain in $data.single:
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52 #set $name = $datain.file_name.split("/")[-1].rstrip(".dat")
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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53 | sed -e "~s/$name/$datain.name/"
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54 #end for
0
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55 #end if
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56 #if $data.input == "fastqpaired"
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57 #if str($data.reads)
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58 -r $data.reads
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59 #end if
1
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60 --paired
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61 \$_GALAXY_JOB_TMP_DIR/'${databaselink}'
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62 '${data.pairedfile.forward}' '${data.pairedfile.reverse}'
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63 #set $name = $data.pairedfile.forward.file_name.split("/")[-1].rstrip(".dat")
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64 | sed -e "~s/$name/$data.pairedfile.name/"
0
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65 #end if
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66 #if $data.input == "fastqpaired2"
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67 #if str($data.reads)
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68 -r $data.reads
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69 #end if
1
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70 --paired
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71 \$_GALAXY_JOB_TMP_DIR/'${databaselink}'
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72 #for $datain in $data.pairedfilelist:
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73 '${datain.forward}' '${datain.reverse}'
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74 #end for
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75 #for $datain in $data.pairedfilelist:
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76 #set $name = $datain.forward.file_name.split("/")[-1].rstrip(".dat")
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77 | sed -e "~s/$name/$datain.name/"
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78 #end for
0
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79 #end if
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80 > '${mlst}'
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81 #if $log
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82 2> '${logfile}'
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83 #end if
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84 ]]>
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85 </command>
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86 <inputs>
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87 <param name="database" type="data"
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88 format="sqlite"
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89 label="Classical MLST database"
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90 help="Sqlite format from claMLST import" />
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91 <conditional name="data">
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92 <param name="input" type="select" label="Select type of data">
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93 <option value="fasta" selected="true">Assembly (fasta)</option>
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94 <option value="fastqsingle">Raw data (single)</option>
1
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95 <option value="fastqpaired">Raw data (paired)</option>
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96 <option value="fastqpaired2">Raw data (List of paired)</option>
0
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97 </param>
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98 <when value="fasta">
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99 <param name="fastain" type="data" format="fasta"
1
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100 label="Assembly Genome" help="Fasta format"
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101 multiple="true" />
0
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102 </when>
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103 <when value="fastqsingle">
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104 <param name="single" type="data" format="fastq,fastq.gz"
1
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105 label="Single read file" help="Fastq(gz) format"
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106 multiple="true" />
0
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107 <param name="reads" type="integer" value="10" optional="true"
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108 label="Minimum reads coverage to search gene" />
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109 </when>
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110 <when value="fastqpaired">
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111 <param name="pairedfile" type="data_collection" format="fastq,fastq.gz"
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112 label="Paired of read files" help="Fastq(gz) format"
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113 collection_type="paired" />
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114 <param name="reads" type="integer" value="10" optional="true"
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115 label="Minimum reads coverage to search gene" />
1
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116 </when>
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117 <when value="fastqpaired2">
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118 <param name="pairedfilelist" type="data_collection" format="fastq,fastq.gz"
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119 label="Paired of read files" help="Fastq(gz) format"
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120 collection_type="list:paired" />
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121 <param name="reads" type="integer" value="10" optional="true"
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122 label="Minimum reads coverage to search gene" />
0
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123 </when>
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124 </conditional>
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125 <param name="fasta" type="boolean" checked="false"
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126 label="Write fasta file with MLST genes allele" />
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127 <param name="identity" type="float" value="0.9" optional="false"
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128 label="Identity"
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129 help="Minimum identity to search gene" />
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130 <param name="coverage" type="float" value="0.9" optional="false"
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131 label="Coverage"
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132 help="Minimum coverage to search gene" />
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133 <param name="log" type="boolean" checked="false"
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134 label="Write log file" />
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135 </inputs>
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136 <outputs>
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137 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log">
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138 <filter>log</filter>
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139 </data>
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140 <data name="mlst" format="txt" label="${tool.name} on ${on_string}: mlst" />
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141 <data name="fastaout" format="fasta" label="${tool.name} on {on_string}: fasta">
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142 <filter>fasta</filter>
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143 </data>
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144 </outputs>
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145 <tests>
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146 <test expect_num_outputs="1">
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147 <param name="database" value="clamlst_ecoli.db" />
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148 <conditional name="data">
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149 <param name="input" value="fasta" />
1
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150 <param name="fastain" ftype="fasta" value="EHSB-021.fasta,EHSB-092.fasta" />
0
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151 </conditional>
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152 <param name="identity" value="0.8" />
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153 <output name="mlst" ftype="txt">
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154 <assert_contents>
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155 <has_text_matching expression="155\t6\t4\t14\t16\t24\t8\t14" />
1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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156 <has_text_matching expression="3018\t12\t58\t54\t344\t1\t2\t47" />
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157 </assert_contents>
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158 </output>
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159 </test>
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160 <test expect_num_outputs="1">
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161 <param name="database" value="clamlst_ecoli.db" />
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162 <conditional name="data">
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163 <param name="input" value="fastqsingle" />
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164 <param name="single" ftype="fastqsanger" value="EHSB-021_R1.fastq.gz,EHSB-021_R2.fastq.gz" />
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165 </conditional>
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166 <param name="identity" value="0.8" />
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167 <param name="reads" value="5" />
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168 <output name="mlst" ftype="txt">
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169 <assert_contents>
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170 <has_text_matching expression="14\t16\t24\t8" />
0
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171 </assert_contents>
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172 </output>
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173 </test>
1
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174 <test expect_num_outputs="1">
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175 <param name="database" value="clamlst_ecoli.db" />
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176 <conditional name="data">
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177 <param name="input" value="fastqpaired" />
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178 <param name="pairedfile">
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179 <collection type="paired">
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180 <element name="forward" value="EHSB-021_R1.fastq.gz" />
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181 <element name="reverse" value="EHSB-021_R2.fastq.gz" />
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182 </collection>
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diff changeset
183 </param>
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184 <param name="reads" value="5" />
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185 </conditional>
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diff changeset
186 <output name="mlst" ftype="txt">
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187 <assert_contents>
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188 <has_text_matching expression="4\t14\t16\t24\t8\t14" />
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189 </assert_contents>
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190 </output>
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191 </test>
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192 <test expect_num_outputs="3">
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193 <param name="database" value="clamlst_ecoli.db" />
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194 <conditional name="data">
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195 <param name="input" value="fastqpaired2" />
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196 <param name="pairedfilelist">
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197 <collection type="list:paired">
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diff changeset
198 <element name="EHSB-021">
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199 <collection type="paired">
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200 <element name="forward" value="EHSB-021_R1.fastq.gz" />
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201 <element name="reverse" value="EHSB-021_R2.fastq.gz" />
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202 </collection>
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203 </element>
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204 </collection>
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205 </param>
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206 <param name="reads" value="5" />
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207 </conditional>
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208 <param name="fasta" value="true" />
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209 <param name="log" value="true" />
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210 <output name="fastaout" ftype="fasta">
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211 <assert_contents>
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212 <has_n_lines n="14" />
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213 </assert_contents>
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214 </output>
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215 <output name="mlst" ftype="txt">
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216 <assert_contents>
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217 <has_text_matching expression="4\t14\t16\t24\t8\t14" />
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218 </assert_contents>
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219 </output>
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220 </test>
0
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221 </tests>
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222 <help>
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223 **What it does**
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224
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225 Search ST number from pubMLST database
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226
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227 You can use
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228 - Genome assembly (blat search)
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229 - Raw data (kma search)
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230
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231 **Options:**
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232
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233 -i, --identity FLOAT Minimum identity to search gene (default=0.9).
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234 -c, --coverage FLOAT Minimum coverage to search gene (default=0.95).
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235 -r, --reads INTEGER Minimum reads coverage to search gene (default=10).
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236 -f, --fasta FILENAME Write fasta file with gene allele.
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237
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238 **License and citation**
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239
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240 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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241 </help>
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242 <citations>
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243 </citations>
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244 </tool>