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1 <tool id="SelectByTag" name="select by tag">
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2 <description>Keep the genomic coordinates such that a value of a given tag.</description>
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3 <command interpreter="python">
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4 ../Java/Python/SelectByTag.py -i $formatType.inputFileName
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5 #elif $formatType.FormatInputFileName == 'gff':
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6 -f gff
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7 #elif $formatType.FormatInputFileName == 'gff2':
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8 -f gff2
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9 #elif $formatType.FormatInputFileName == 'gff3':
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10 -f gff3
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11 #elif $formatType.FormatInputFileName == 'gtf':
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12 -f gtf
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13 #end if
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14
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15 -g $Tag
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16 #if $OptionValue.Value == "Yes":
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17 -a $OptionValue.valeur
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18 #end if
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19 #if $OptionMax.maximum == "Yes":
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20 -M $OptionMax.max
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21 #end if
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22 #if $OptionMin.minimum == "Yes":
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23 -m $OptionMin.min
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24 #end if
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25
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26 #if $OptionDefault.default == "Yes":
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27 -d $OptionDefault.defaultValue
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28 #end if
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29
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30 -o $outputFileGff
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31 </command>
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32
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33 <inputs>
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34 <conditional name="formatType">
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35 <param name="FormatInputFileName" type="select" label="Input File Format">
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36 <option value="gff">gff</option>
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37 <option value="gff2">gff2</option>
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38 <option value="gff3">gff3</option>
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39 <option value="gtf">gtf</option>
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40 </param>
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41 <when value="gff">
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42 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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43 </when>
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44 <when value="gff2">
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45 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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46 </when>
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47 <when value="gff3">
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48 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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49 </when>
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50 <when value="gtf">
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51 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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52 </when>
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53 </conditional>
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54
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55 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/>
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56
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57 <conditional name="OptionValue">
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58 <param name="Value" type="select" label="given value for the tag">
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59 <option value="Yes">Yes</option>
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60 <option value="No" selected="true">No</option>
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61 </param>
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62 <when value="Yes">
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63 <param name="valeur" type="integer" value="1"/>
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64 </when>
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65 <when value="No">
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66 </when>
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67 </conditional>
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68
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69 <conditional name="OptionMax">
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70 <param name="maximum" type="select" label="maximum value of tag">
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71 <option value="Yes">Yes</option>
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72 <option value="No" selected="true">No</option>
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73 </param>
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74 <when value="Yes">
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75 <param name="max" type="integer" value="1"/>
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76 </when>
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77 <when value="No">
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78 </when>
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79 </conditional>
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80
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81 <conditional name="OptionMin">
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82 <param name="minimum" type="select" label="minimum value of tag">
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83 <option value="Yes">Yes</option>
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84 <option value="No" selected="true">No</option>
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85 </param>
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86 <when value="Yes">
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87 <param name="min" type="integer" value="1"/>
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88 </when>
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89 <when value="No">
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90 </when>
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91 </conditional>
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92
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93 <conditional name="OptionDefault">
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94 <param name="default" type="select" label="give this value if tag is not present">
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95 <option value="Yes">Yes</option>
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96 <option value="No" selected="true">No</option>
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97 </param>
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98 <when value="Yes">
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99 <param name="defaultValue" type="float" value="0" />
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100 </when>
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101 <when value="No">
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102 </when>
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103 </conditional>
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104 </inputs>
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105
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106 <outputs>
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107 <data name="outputFileGff" format="gff3" label="[SelectByTag] Output File"/>
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108 </outputs>
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109
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110 <help>
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111 The script reads a list of genomic coordinates and output all the features with specific tag values. If you want to know more about tags, please consult the GFF format page: http://www.sequenceontology.org/gff3.shtml
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112
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113 The tools reads the input file, and more specifically the tag that you specified. You can mention a lower and a upper bound for its value, or a specific value, and the tool will print all the features such that the tags are between the specified bounds or matches the string.
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114
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115 A tag has to be present for each feature. If not, you can specify a default value which will be used if the tag is absent.
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116
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117 This tool can be used to select the clusters with a minimum number of elements (the tag **nbElements** counts the number of elements per clusters) or to select the reads which have mapped less than *n* times (the tag **nbOccurrences** counts the number of mappings per read).
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118 </help>
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119 </tool>
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