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1 <tool id="SsuisSerotyping_pipeline" name="Use SsuisSerotyping_pipeline." version="0.1.1">
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2 <requirements>
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3 <requirement type="package">perl-bioperl</requirement>
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4 <requirement type="package">scipy</requirement>
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5 <requirement type="package" version="2.7">python</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11 python $__tool_directory__/Prepare_Ssuis_serotypingPipeline.py
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12 --fastq_file $input1
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13 --scoreName '$output1'
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14 --output2 '$output2'
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15 --output3 '$output3'
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16 --output4 '$output4'
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17 --output5 '$output5'
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18 --output6 '$output6'
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19 --output7 '$output7'
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20 --output8 '$output8'
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21 #if $optionalfiles.analysis_selector == "specific":
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22 --serotype_db '$options.serotype_db'
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23 --serotype_definitions '$options.serotype_definitions'
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24 --cps2K '$options.cps2K'
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25 --Virulence_db '$options.Virulence_db'
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26 --recN_db '$options.recN_db'
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27 --MLST_definitions '$options.MLST_definitions'
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28 --MLST_db '$options.MLST_db'
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29 #end if
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30 #if $typeofdata.pors == "paired":
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31 --ends pe
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32 --forward '$typeofdata.forward'
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33 --reverse '$typeofdata.reverse'
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34 #else:
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35 --ends se
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36 #end if
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37
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38 ]]></command>
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39 <inputs>
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40 <param type="data" name="input1" format="fastq" />
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41 <conditional name="optionalfiles">
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42 <param name="analysis_selector" type="select" label="Use specific or default configuration?">
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43 <option value="default" selected="True">Use default configuration.</option>
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44 <option value="specific">Use specific file</option>
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45 </param>
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46 <when value="default" />
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47 <when value="specific">
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48 <param type="data" name="serotype_db" format="fasta" label="Serotype database in fasta format." />
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49 <param type="data" name="serotype_definitions" format="txt" label="Definition of the serotype database" />
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50 <param type="data" name="cps2K" format="fasta" label="Multifasta with cpsH confirmation database" />
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51 <param type="data" name="Virulence_db" format="fasta" label="Virulence genes" />
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52 <param type="data" name="recN_db" format="fasta" label="recN species specfic gene" />
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53 <param type="data" name="MLST_definitions" format="txt" label="Definitions of MLST database file" />
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54 <param type="data" name="MLST_db" format="fasta" label="MLST database" />
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55 </when>
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56 </conditional>
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57 <conditional name="typeofdata">
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58 <param name="pors" type="select" label="Read option">
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59 <option value="single" selected="True">Single-end</option>
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60 <option value="paired">Paired-end</option>
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61 </param>
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62 <when value="single" />
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63 <when value="paired">
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64 <param type="text" name="reverse" value="_R1" />
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65 <param type="text" name="forward" value="_R2" />
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66 </when>
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67 </conditional>
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68 </inputs>
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69 <outputs>
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70 <data name="output1" format="txt" label="${tool.name} on ${on_string}: Results_FinalResults.txt" />
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71 <data name="output2" format="txt" label="${tool.name} on ${on_string}: Results_MLSTResults.txt" />
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72 <data name="output3" format="txt" label="${tool.name} on ${on_string}: Results_recN__fullgenes__recN_full__results.txt" />
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73 <data name="output4" format="txt" label="${tool.name} on ${on_string}: Results_speciesConfirmation.txt" />
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74 <data name="output5" format="txt" label="${tool.name} on ${on_string}: Results_FinalSerotypingResults.txt" />
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75 <data name="output6" format="txt" label="${tool.name} on ${on_string}: Results_InitialCapsuleResults.txt" />
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76 <data name="output7" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactors__fullgenes__Virulence__results.txt" />
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77 <data name="output8" format="txt" label="${tool.name} on ${on_string}: Results_VirulenceFactorResults.txt" />
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="input1" value="/home/plucas/TEST/SsuisSerotyping_pipeline/input_fastq/SS1218_IonXpress_008_R_2016_02_23.soft_clean.trimmomatic_trimmed.fastq"/>
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82 <output name="output1" file="/home/plucas/TEST/SsuisSerotyping_pipeline/results/Results_FinalResults.txt"/>
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83 </test>
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84 </tests>
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85 <help><![CDATA[
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86 Implementation of the S. suis serotyping pipeline:
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87
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88 perl Ssuis_serotypingPipeline.pl --fastq_directory /path/to/fastq/directory --scoreName Scores_output_name --serotype_db serotype.fasta --serotype_definitions serotype_definitions.txt --cps2K cps2K.fasta
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89
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90 --fastq_directory Path to directory containing paired-end fastq files.
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91 Must be full path to directory, please do not use '.'
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92 or '..' to declare path
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93 If no path is given, the current working
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94 directory is used
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95 --scoreName Name of SRST2 results file
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96 [optional: default name 'Results']
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97 --serotype_db Multifasta file containing the serotype database
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98 (Ssuis_Serotyping.fasta)
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99 [If none is provided, Ssuis_Serotyping.fasta is looked
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100 for in the directory containing the script]
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101 --serotype_definitions Text file containing the definitions for the
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102 serotype database file
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103 (Ssuis_Serotyping_Definitions.txt)
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104 [If none is provided, Ssuis_Serotyping_Definitions.txt is looked
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105 for in the directory containing the script]
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106 --cps2K Multifasta file containing the cpsH confirmation database
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107 (Ssuis_cps2K.fasta)
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108 [If none is provided, Ssuis_cps2K.fasta is looked
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109 for in the directory containing the script]
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110 --MLST_db Multifasta file containing the MLST database
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111 (Streptococcus_suis.fasta)
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112 [If none is provided, Streptococcus_suis.fasta is looked
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113 for in the directory containing the script]
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114 --MLST_definitions Text file containing the definitions for the
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115 MLST database file
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116 (ssuis.txt)
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117 [If none is provided, ssuis.txt is looked
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118 for in the directory containing the script]
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119 --recN_db Fasta file containing the recN species specfic gene
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120 (recN_Full.fasta)
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121 [If none is provided, recN_full.fasta is looked
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122 for in the directory containing the script]
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123 --Virulence_db Multifasta file containing the Virulence genes
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124 (Virulence.fasta)
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125 [If none is provided, Virulence.fasta is looked
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126 for in the directory containing the script]
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127 --forward Indicator delimiting the forward reads file for
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128 paired read fastq files
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129
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130 This option is ignored if single-end reads is selected
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131 [optional: default '_R1']
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132
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133 --reverse Indicator delimiting the reverse reads file for
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134 paired read fastq files
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135
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136 This option is ignored if single-end reads is selected
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137 [optional: default '_R2']
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138
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139 --ends Indicates whether the reads are paired-end (pe) or single-end (se)
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140 [optional: default 'pe']
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141
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142 Note: We recommend using paired end reads of at least 100nt in length
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143 and at least 30X coverage.
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144 We have not tested the efficiency of the pipeline with reads shorter than 80nt.
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145 ]]></help>
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146 <citations>
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147 <citation type="bibtex">
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148 @misc{githubSsuisSerotyping_pipeline,
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149 author = {LastTODO, FirstTODO},
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150 year = {TODO},
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151 title = {SsuisSerotyping_pipeline},
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152 publisher = {GitHub},
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153 journal = {GitHub repository},
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154 url = {https://github.com/streplab/SsuisSerotyping_pipeline},
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155 }</citation>
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156 </citations>
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157 </tool>
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