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1 <tool id="ngsFilt" name="IMGT Report Filtering" version="0.9" profile="15.10">
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2 <description>Filter IMGT Summary Data</description>
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3 <command interpreter="python">ngs_filtering.py $input $TCR_or_BCR $Vfun $spChar $prod $delCF $threshold $Vg.Vgid $clen.cdr3len1 $cdp.cdr3part $filtin $filtout $summ $Jg.Jgid $Dg.Dgid $clen.cdr3len2 $process_id
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4
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5 </command>
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6 <inputs>
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7 <param format="txt" name="input" type="data" label="IMGT Summary Output"/>
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8 <param format="txt" name="process_id" type="text" label="Process ID"/>
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9 <param name="TCR_or_BCR" type="select" label="T-cell or B-cell option">
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10 <option value="TCR">T-cell</option>
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11 <option value="BCR">B-cell</option>
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12 </param>
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13 <param name="Vfun" type="select" label="Only Take Into Account Fuctional V-GENE? ">
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14 <option value="y">yes</option>
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15 <option value="n">no</option>
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16 </param>
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17
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18 <param name="spChar" type="select" label="Only Take Into Account CDR3 with no Special Characters (X,*,#)? ">
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19 <option value="y">yes</option>
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20 <option value="n">no</option>
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21 </param>
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22
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23 <param name="prod" type="select" label="Only Take Into Account Productive Sequences? ">
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24 <option value="y">yes</option>
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25 <option value="n">no</option>
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26 </param>
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27
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28 <param name="delCF" type="select" label="Only Take Into Account CDR3 with valid start/end landmarks? ">
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29 <option value="y">yes</option>
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30 <option value="n">no</option>
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31 </param>
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32
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33 <param name="threshold" type="float" size="3" value="0" min="0" max="100" label="V-REGION identity %" />
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34
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35 <conditional name="Vg">
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36
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37 <param name="Vg_select" type="select" label="Select Specific V gene?">
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38 <option value="y">Yes</option>
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39 <option value="n" selected="true">No</option>
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40 </param>
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41
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42 <when value="y">
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43 <param format="txt" name="Vgid" type="text" label="Type V gene"/>
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44 </when>
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45
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46 <when value="n">
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47 <param name="Vgid" type="hidden" value="null" />
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48 </when>
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49
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50 </conditional>
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51
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52 <conditional name="Jg">
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53
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54 <param name="Jg_select" type="select" label="Select Specific J gene?">
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55 <option value="y">Yes</option>
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56 <option value="n" selected="true">No</option>
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57 </param>
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58
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59 <when value="y">
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60 <param format="txt" name="Jgid" type="text" label="Type J gene"/>
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61 </when>
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62
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63 <when value="n">
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64 <param name="Jgid" type="hidden" value="null" />
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65 </when>
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66
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67 </conditional>
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68
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69 <conditional name="Dg">
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70
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71 <param name="Dg_select" type="select" label="Select Specific D gene?">
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72 <option value="y">Yes</option>
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73 <option value="n" selected="true">No</option>
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74 </param>
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75
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76 <when value="y">
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77 <param format="txt" name="Dgid" type="text" label="Type D gene"/>
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78 </when>
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79
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80 <when value="n">
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81 <param name="Dgid" type="hidden" value="null" />
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82 </when>
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83
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84 </conditional>
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85
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86
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87
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88 <conditional name="clen">
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89
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90 <param name="clen_select" type="select" label="Select CDR3 length range?">
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91 <option value="y">Yes</option>
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92 <option value="n" selected="true">No</option>
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93 </param>
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94
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95 <when value="y">
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96 <param name="cdr3len1" type="integer" size="3" value="0" min="0" max="100" label="CDR3 Length Lower Threshold" />
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97 <param name="cdr3len2" type="integer" size="3" value="0" min="0" max="100" label="CDR3 Length Upper Threshold" />
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98 </when>
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99
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100 <when value="n">
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101 <param name="cdr3len1" type="hidden" value="null" />
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102 <param name="cdr3len2" type="hidden" value="null" />
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103 </when>
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104
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105 </conditional>
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106
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107 <conditional name="cdp">
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108
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109 <param name="cdp_select" type="select" label="Only select CDR3 containing specific amino-acid sequence?">
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110 <option value="y">Yes</option>
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111 <option value="n" selected="true">No</option>
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112 </param>
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113
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114 <when value="y">
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115 <param format="txt" name="cdr3part" type="text" label="Type specific amino-acid sequence"/>
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116 </when>
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117
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118 <when value="n">
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119 <param name="cdr3part" type="hidden" value="null" />
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120 </when>
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121 </conditional>
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122
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123 </inputs>
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124
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125
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126 <outputs>
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127 <data name="filtin" format="tabular" label="${process_id}_filterin"/>
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128 <data name="filtout" format="tabular" label="${process_id}_filterout"/>
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129 <data name="summ" format="tabular" label="${process_id}_Summary"/>
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130
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131
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132 </outputs>
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133
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134
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135 <help>
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136 This tool filters IMGT Summary Data based on a combination of criteria.
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137 </help>
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138
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139 </tool>
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