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1 <tool id="restrictFromSize" name="restrict from size">
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2 <description>Select the elements of a list of sequences or transcripts with a given size.</description>
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 ../Java/Python/restrictFromSize.py -i $formatType.inputFileName
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8 #if $formatType.FormatInputFileName == 'fasta':
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9 -f fasta
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10 #elif $formatType.FormatInputFileName == 'bed':
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11 -f bed
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12 #elif $formatType.FormatInputFileName == 'gff':
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13 -f gff
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14 #elif $formatType.FormatInputFileName == 'gff2':
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15 -f gff2
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16 #elif $formatType.FormatInputFileName == 'gff3':
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17 -f gff3
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18 #elif $formatType.FormatInputFileName == 'sam':
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19 -f sam
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20 #elif $formatType.FormatInputFileName == 'gtf':
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21 -f gtf
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22 #end if
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23
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24 #if $OptionMax.maximum == "Yes":
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25 -M $OptionMax.max
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26 #end if
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27 #if $OptionMin.minimum == "Yes":
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28 -m $OptionMin.min
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29 #end if
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30
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31 -o $outputFileGff
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32 </command>
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33
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34 <inputs>
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35 <conditional name="formatType">
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36 <param name="FormatInputFileName" type="select" label="Input File Format">
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37 <option value="fasta">fasta</option>
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38 <option value="bed">bed</option>
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39 <option value="gff">gff</option>
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40 <option value="gff2">gff2</option>
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41 <option value="gff3">gff3</option>
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42 <option value="sam">sam</option>
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43 <option value="gtf">gtf</option>
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44 </param>
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45 <when value="fasta">
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46 <param name="inputFileName" format="fasta" type="data" label="Input File"/>
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47 </when>
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48 <when value="bed">
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49 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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50 </when>
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51 <when value="gff">
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52 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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53 </when>
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54 <when value="gff2">
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55 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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56 </when>
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57 <when value="gff3">
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58 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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59 </when>
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60 <when value="sam">
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61 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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62 </when>
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63 <when value="gtf">
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64 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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65 </when>
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66 </conditional>
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67
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68 <conditional name="OptionMax">
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69 <param name="maximum" type="select" label="maximum number of np">
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70 <option value="Yes">Yes</option>
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71 <option value="No" selected="true">No</option>
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72 </param>
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73 <when value="Yes">
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74 <param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
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75 </when>
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76 <when value="No">
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77 </when>
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78 </conditional>
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79
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80 <conditional name="OptionMin">
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81 <param name="minimum" type="select" label="minimum number of np">
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82 <option value="Yes">Yes</option>
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83 <option value="No" selected="true">No</option>
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84 </param>
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85 <when value="Yes">
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86 <param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
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87 </when>
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88 <when value="No">
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89 </when>
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90 </conditional>
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91
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92 </inputs>
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93
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94 <outputs>
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95 <data name="outputFileGff" format="gff3" label="[restrict from size] output file"/>
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96 </outputs>
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97
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98 <help>
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99 Reads a list of sequences or genomic coordinates and outputs those which are longer and / or shorter than a given size ---which you provide.
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100 </help>
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101
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102 </tool>
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