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2
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1 <tool id="config_builder" name="PathOGiST - Config Builder" version="1.0.0">
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2 <description>: Creates and populates the config file to run PathOGiST</description>
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3 <requirements>
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6
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4 <requirement type="package" version="0.3">pathogist</requirement>
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2
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5 </requirements>
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6
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7 <command><![CDATA[
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8 $__tool_directory__/config_builder
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9
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5
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10 #if $snippy.snippy_checkbox
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2
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11 --snippy
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12 --reference $snippy.reference
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5
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13 #if $snippy.snippy_adv.snippy_adv_checkbox
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14 --mapqual $snippy.snippy_adv.mapqual
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15 --basequal $snippy.snippy_adv.basequal
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16 --mincov $snippy.snippy_adv.mincov
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17 --minfrac $snippy.snippy_adv.minfrac
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4
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18 #end if
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2
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19 $snippy.snp_fine
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20 --snp_thresh $snippy.snp_threshold
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4
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21 #end if
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2
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22
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5
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23 #if $mentalist.mentalist_checkbox
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2
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24 --mentalist
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5
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25 #if $mentalist.db_loc.db_selector == "local_file"
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2
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26 --local_file
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5
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27 --local_db $mentalist.db_loc.mlst_database
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4
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28 #end if
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5
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29 #if $mentalist.db_loc.db_selector == "build_db"
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2
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30 --build_db
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5
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31 --kmer $mentalist.db_loc.k
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32 --fasta_files $mentalist.db_loc.fasta_files
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33 --profile $mentalist.db_loc.profile
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4
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34 #end if
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5
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35 #if $mentalist.db_loc.db_selector == "download_pubmlst"
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2
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36 --download_pubmlst
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5
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37 --kmer $mentalist.db_loc.k
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38 --scheme $mentalist.db_loc.scheme
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4
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39 #end if
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5
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40 #if $mentalist.db_loc.db_selector == "download_cgmlst"
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2
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41 --download_cgmlst
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5
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42 --kmer $mentalist.db_loc.k
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43 --scheme $mentalist.db_loc.scheme
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4
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44 #end if
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5
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45 #if $mentalist.db_loc.db_selector == "download_enterobase"
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46 --download_enterobase $mentalist.db_loc.k
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47 --entero_scheme $mentalist.db_loc.scheme
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48 --entero_type $mentalist.db_loc.type
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4
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49 #end if
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5
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50 #if $mentalist.mentalist_adv.mentalist_adv_checkbox
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51 --mutation_threshold $mentalist.mentalist_adv.mutation_thresh
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52 --kt $mentalist.mentalist_adv.kt
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4
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53 #end if
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2
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54 $mentalist.mlst_fine
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55 --mlst_thresh $mentalist.mlst_threshold
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4
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56 #end if
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2
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57
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5
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58 #if $prince.prince_checkbox
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2
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59 --prince
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60 $prince.cnv_fine
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61 --cnv_thresh $prince.cnv_threshold
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4
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62 #end if
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2
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63
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5
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64 #if $kwip.kwip_checkbox
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2
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65 --kwip
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5
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66 #if $kwip.kwip_adv.kwip_adv_checkbox
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67 --N $kwip.kwip_adv.N
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68 --x $kwip.kwip_adv.x
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69 --ksize $kwip.kwip_adv.ksize
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70 --unique_kmers $kwip.kwip_adv.unique_kmers
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4
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71 #end if
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2
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72 $kwip.kwip_fine
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73 --kwip_thresh $kwip.kwip_threshold
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4
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74 #end if
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2
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75
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5
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76 #if $spotyping.spotyping_checkbox
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2
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77 --spotyping
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78 $spotyping.spoligo_fine
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79 --spoligo_thresh $spotyping.spoligo_threshold
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4
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80 #end if
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2
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81
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5
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82 #if $adv_clustering.adv_clustering_checkbox
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2
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83 $adv_clustering.all_constraints
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84 --method $adv_clustering.method
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85 $adv_clustering.presolve
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86 $adv_clustering.visualize
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4
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87 #end if
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3
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88
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89 $forward
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90 $reverse
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8
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91 cc
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2
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92 ]]></command>
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93
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94
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95 <inputs>
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3
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96 <param name="forward" type="data" format="txt,tabular" label="List of forward reads"/>
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97 <param name="reverse" type="data" format="txt,tabular" label="List of reverse reads"/>
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2
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98
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99 <conditional name="snippy">
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100 <param name="snippy_checkbox" type="boolean" label="Run Snippy"/>
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101 <when value="true">
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102 <param name="reference" type="data" format="fasta,fa,fasta.gz,fa.gz" label="Reference Genome"/>
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103 <conditional name="snippy_adv">
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104 <param name="snippy_adv_checkbox" type="boolean" label="Advanced Snippy Parameters"/>
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105 <when value="true">
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106 <param name="mapqual" type="integer" value="60" min="0" label="Minimum read mapping
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107 quality to consider"/>
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108 <param name="basequal" type="integer" value="20" min="0" label="Minimum base quality
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109 to consider"/>
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110 <param name="mincov" type="integer" value="10" min="0" label="Minimum coverage of
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111 variant site"/>
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112 <param name="minfrac" type="float" value="0.9" min="0" label="Minimum proportion of
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113 variant evidence"/>
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114 </when>
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115 </conditional>
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7
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116 <param name="snp_fine" type="boolean" checked="true" falsevalue="" truevalue="--fine_snp"
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117 label="Consider SNP as a fine datatype"/>
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2
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118 <param name="snp_threshold" type="integer" value="2500" min="0"
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119 label="Correlation clustering threshold for MLST"/>
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120 </when>
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121 </conditional>
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122
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123 <conditional name="mentalist">
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124 <param name="mentalist_checkbox" type="boolean" label="Run MentaLiST"/>
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125 <when value="true">
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126 <conditional name="db_loc">
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127 <param name="db_selector" type="select" label="Option for obtaining MLST database">
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128 <option value="local_file">Local File</option>
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129 <option value="build_db">Build DB</option>
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130 <option value="download_pubmlst">Download PubMLST Scheme</option>
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131 <option value="download_cgmlst">Download cgMLST Scheme</option>
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132 <option value="download_enterobase">Download Enterobase Scheme</option>
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133 </param>
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134 <when value="local_file">
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135 <param name="mlst_database" format="db" type="data" label="MLST database file"/>
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136 </when>
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137 <when value="build_db">
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138 <param name="k" type="integer" value="31" min="1" label="kmer size"/>
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139 <param name="fasta_files" type="data" format="txt,tabular" label="List of FASTA files"/>
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140 <param name="profile" type="data" format="txt" label="Profile file for known
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141 genotypes"/>
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142 </when>
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143 <when value="download_pubmlst">
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144 <param name="k" type="integer" value="31" min="1" label="kmer size"/>
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145 <param name="scheme" type="text" label="Species name or scheme ID"/>
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146 </when>
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147 <when value="download_cgmlst">
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148 <param name="k" type="integer" value="31" min="1" label="kmer size"/>
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149 <param name="scheme" type="text" label="Species name or scheme ID"/>
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150 </when>
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151 <when value="download_enterobase">
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152 <param name="k" type="integer" value="31" min="1" label="kmer size"/>
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153 <param name="scheme" type="text" label="(S)almonella, (Y)ersinia, or
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154 (E)scherichia/Shigella"/>
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155 <param name="type" type="text" label="'cg' or 'wg' for cgMLST or wgMLST, respectively"/>
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156 </when>
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157 </conditional>
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158
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159 <conditional name="mentalist_adv">
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160 <param name="mentalist_adv_checkbox" type="boolean" label="Advanced MentaLiST Parameters"/>
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161 <when value="true">
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162 <param name="mutation_thresh" type="integer" min="1" value="6" label="Maximum number of
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163 mutations when looking for novel alleles"/>
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164 <param name="kt" type="integer" value="10" min="1" label="Minimum number of times a
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165 kmer is seen to be considered present in the sample"/>
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166 </when>
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167 </conditional>
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7
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168 <param name="mlst_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_mlst"
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169 label="Consider MLST as a fine datatype"/>
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2
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170 <param name="mlst_threshold" type="integer" value="300" min="0"
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171 label="Correlation clustering threshold for MLST"/>
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172 </when>
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173 </conditional>
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174
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175 <conditional name="prince">
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176 <param name="prince_checkbox" type="boolean" label="Run PRINCE"/>
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177 <when value="true">
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7
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178 <param name="cnv_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_cnv"
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179 label="Consider CNV as a fine datatype"/>
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2
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180 <param name="cnv_threshold" type="integer" value="100" min="0"
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181 label="Correlation clustering threshold for CNV"/>
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182 </when>
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183 </conditional>
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184
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185 <conditional name="kwip">
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186 <param name="kwip_checkbox" type="boolean" label="Run kWIP"/>
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187 <when value="true">
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188 <conditional name="kwip_adv">
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3
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189 <param name="kwip_adv_checkbox" type="boolean" label="Advanced kWIP Parameters"/>
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2
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190 <when value="true">
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191 <param name="N" type="integer" value="1" min="1" label="Number of tables"/>
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192 <param name="x" type="float" value="1e9" min="1" label="Maximum table size"/>
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193 <param name="ksize" type="integer" value="31" min="1" label="kmer size"/>
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194 <param name="unique_kmers" type="integer" value="0" min="0" label="Approximate number
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195 of unique kmers in the input set"/>
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196 </when>
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197 </conditional>
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7
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198 <param name="kwip_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_kwip"
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199 label="Consider kWIP as a fine datatype"/>
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2
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200 <param name="kwip_threshold" type="float" value="0.4" min="0"
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201 label="Correlation clustering threshold for kWIP"/>
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202 </when>
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203 </conditional>
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204
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205 <conditional name="spotyping">
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206 <param name="spotyping_checkbox" type="boolean" label="Run SpoTyping"/>
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207 <when value="true">
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7
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208 <param name="spoligo_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_spoligo"
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209 label="Consider spoligotype as a fine datatype"/>
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2
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210 <param name="spoligo_threshold" type="integer" value="8" min="0"
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211 label="Correlation clustering threshold for Spoligotyping"/>
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212 </when>
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213 </conditional>
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214
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215 <conditional name="adv_clustering">
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216 <param name="adv_clustering_checkbox" type="boolean"
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217 label="Advanced settings for correlation and consensus clustering"/>
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218 <when value="true">
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219 <param name="all_constraints" type="boolean" checked="true" falsevalue="--less_constraints"
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220 truevalue="" label="Use all constraints when performing clustering"/>
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221 <param name="method" type="text" value="C4" size="3"
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222 label="`C4` or `ILP` method for clustering algorithm"/>
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223 <param name="presolve" type="boolean" checked="true" falsevalue="--no_presolve" truevalue=""
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224 label="Perform presolving for clustering"/>
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225 <param name="visualize" type="boolean" checked="false" falsevalue="" truevalue="--visualize"
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226 label="Visualize clusters"/>
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227 </when>
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228 </conditional>
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229 </inputs>
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230
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231 <outputs>
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232 <data name="output" label="PathOGiST Config File" format="yaml" from_work_dir="config.yaml"/>
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233 </outputs>
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234
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235 <help>
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236
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237 </help>
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238
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239 <citations>
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240
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241 </citations>
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242 </tool>
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