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1 <tool id="VAP" name="VAPPER" version="1.1.0">
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2 <description>is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.10">velvet</requirement>
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5 <requirement type="package" version="3.1b2">HMMER</requirement>
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6 <requirement type="package" version="2.2.6">bowtie2</requirement>
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7 <requirement type="package" version="1.6">samtools</requirement>
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8 <requirement type="package" version="2.2.1">cufflinks</requirement>
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9 <requirement type="package" version="2.7.1">blast</requirement>
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10 <requirement type="package" version="6.6.0.0">EMBOSS</requirement>
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11 <requirement type="package" version="0.8.0">seaborn</requirement>
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12 </requirements>
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10
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13
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14
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15 <command interpreter="python" detect_errors="exit_code">
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16 #if $TrypType.species == "Trypanosoma congolense":
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17 #if $TrypType.GT.analysis == "Genomic":
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18 #if $TrypType.GT.contigs.preassem == "Contig available":
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19 <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 -->
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20 Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path
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21 #else
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22 <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 -->
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23 Vap.py g_assemble $xname $P $TrypType.GT.contigs.kmers $TrypType.GT.contigs.inslen $TrypType.GT.contigs.covcut $TrypType.GT.contigs.forward $TrypType.GT.contigs.reverse $html_file $html_file.extra_files_path
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24 #end if
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25 #else
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26 <!-- name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 -->
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27 Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path
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28 #end if
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29 #else
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30 #if $TrypType.GT.analysis == "Transcriptomic":
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31 Vap.py v_transcript $xname $P $TrypType.GT.vtreference $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path
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32 #else
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33 #if $TrypType.contigs.preassem == "Contig available":
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34 <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 -->
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35 Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path
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36 #else
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37 <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 -->
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38 Vap.py v_assemble $xname $P $TrypType.contigs.kmers $TrypType.contigs.inslen 0 $TrypType.contigs.forward $TrypType.contigs.reverse $html_file $html_file.extra_files_path
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39 #end if
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40 #end if
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41 #end if
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42
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43 </command>
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44
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45 <inputs>
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46 <param name="xname" size = "30" type="text" value = "Test" label="Prefix Name" />
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47 <conditional name = "TrypType">
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48 <param name = "species" type = 'select' label="Select Species">
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49 <option value = "Trypanosoma congolense" selected="true"></option>
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50 <option value = "Trypanosoma vivax"></option>
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51 </param>
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52 <when value = "Trypanosoma congolense">
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53 <conditional name = "GT">
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54 <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?">
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55 <option value = "Genomic" selected = "true"></option>
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56 <option value = "Transcriptomic"></option>
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57 </param>
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58 <when value = "Genomic">
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59 <conditional name = "contigs">
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60 <param name = "preassem" type = "select" label = "Contig file available?">
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61 <option value = "Full assembly" selected = "true"></option>
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62 <option value = "Contig available"></option>
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63 </param>
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64 <when value = "Full assembly">
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65 <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param>
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66 <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param>
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67 <param name = "covcut" type="integer" value="5" min="1" max="999" label = "Coverage cut off"></param>
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68 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
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69 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
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70 </when>
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71 <when value = "Contig available">
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72 <param name="contig" type="data" format="fasta" label="Contig file"/>
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73 </when>
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74 </conditional>
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75 </when>
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76 <when value = "Transcriptomic">
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77 <param name = "strain" type="select" label = "Select Reference Strain">
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78 <option value = "Tc148"></option>
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79 <option value = "IL3000"></option>
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80 </param>
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81 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
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82 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
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83 </when>
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84 </conditional>
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85 </when>
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86 <when value="Trypanosoma vivax">
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87 <conditional name = "GT">
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88 <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?">
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89 <option value = "Genomic" selected = "true"></option>
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90 <option value = "Transcriptomic"></option>
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91 </param>
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92 <when value = "Genomic">
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93 <conditional name = "contigs">
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94 <param name = "preassem" type = "select" label = "Contig file available?">
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95 <option value = "Full assembly" selected = "true"></option>
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96 <option value = "Contig available"></option>
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97 </param>
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98 <when value = "Full assembly">
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99 <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param>
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100 <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param>
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101 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
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102 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
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103 </when>
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104 <when value = "Contig available">
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105 <param name="contig" type="data" format="fasta" label="Contig file"/>
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106 </when>
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107 </conditional>
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108 </when>
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109 <when value = "Transcriptomic">
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110 <param name = "vtreference" type="data" format="fasta" label = "Reference File"/>
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111 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/>
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112 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/>
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113 </when>
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114 </conditional>
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115 </when>
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116 </conditional>
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117
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118 <param name="P" type="boolean" truevalue='PDF_Yes' falsevalue='PDF_No' label="Export PDF of figures" />
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119 </inputs>
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120
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121 <outputs>
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122 <data format="html" name = "html_file" label = "${xname.value}_html"/>
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123 </outputs>
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124 <tests>
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125 <test>
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126 <param name = "xname" value = "Test"/>
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127 <conditional name = "TrypType">
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128 <param name = "species" value = "Trypanosoma congolense"/>
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129 </conditional>
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130 <conditional name = "GT">
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131 <param name = "analysis" value = "Genomic"/>
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132 </conditional>
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133 <conditional name = "contigs">
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134 <param name = "preassem" value = "Contig available"/>
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135 <param name="contig" value = "Test.fa"/>
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136 </conditional>
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137 <param name = "P" value = 'PDF_No'/>
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138 <output name = "html_file" file = 'Test_html' ftype = 'html'/>
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139 </test>
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140 </tests>
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141 </tool>
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