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1 <tool id="ClosestToStartSite" name="ClosestToStartSite" version="1.0">
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2 <description>ClosestToStartSite parses a bed file and create a bed file to create a report about positions of features A to features B.</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">TEiso_Tools</requirement>
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5 </requirements>
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6 <version_command>
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7 ClosestToStartSite.py --version
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8 </version_command>
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9 <command interpreter="python">
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10 ClosestToStartSite_Wrapper.py -i $inputFile -o $outputFile
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11 </command>
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12 <inputs>
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13 <param name="inputFile" type="data" format="bed" label="indicate a bed file."/>
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14 </inputs>
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15 <outputs>
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16 <data name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
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17 </outputs>
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18 <help><![CDATA[
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19
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20 **ClosestToStartSite_wrapper parses a bed file and create a bed file to create a report about positions of features A to features B.**
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21
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22
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23 **what it does :**
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24
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25 parses a bed file and create a bed file to create a report about positions of features A to features B
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26
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27 -----
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28
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29 **input format :**
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30
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31 .. class:: infomark
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32
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33 **output format :**
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34
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35 fake 140 532 CUFF.1.1 CUFF.1 + 26875.607
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36
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37 -----
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38
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39
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40
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41 ****** "B_close_TSS"
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42 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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43
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44 F[1] gene F[2]
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45 =========================>
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46 ------------
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47 F[8] F[9]
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48
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49
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50 F[1] F[2]
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51 <=========================
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52 ---------------
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53
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54
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55 ****** "B_overlap_TSS"
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56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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57
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58 F[1] gene F[2]
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59 =========================>
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60 -------------
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61 F[8] F[9]
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62
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63 gene
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64 F[1]=========================>F[2]
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65
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66 F[8]---------------F[9]
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67
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68
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69
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70 F[1]=============================>F[2]
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71 F[8]---------------F[9]
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72
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73
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74 F[1]<=============================F[2]
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75 ---------------------------
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76 F[8] F[9]
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77
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78
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79 F[1]<=============================F[2]
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80 F[8]---------------F[9]
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81
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82
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83 F[1]<=============================F[2]
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84 F[8]---------------F[9]
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85
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86 ****** "B-inclus-A"
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87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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88
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89
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90
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91 F[1] gene F[2]
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92 ==============================
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93 -------------
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94 F[8] F[9]
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95
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96 ****** "A-inclus-B"
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97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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98
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99
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100 F[1]======================F[2]
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101 F[8]----------------------------------------------------F[9]
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102
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103
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104
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105
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106 F[1]==================================>F[2]
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107 F[8]----------------------------------------------------------F[9]
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108
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109
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110
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111 F[1]<==================================F[2]
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112 F[8]----------------------------------------------------------F[9]
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113
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114
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115
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116 ****** "A-inclus-B-inTSS"
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117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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118
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119 F[1]<==================================F[2]
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120 [8]----------------------------------------------------------F[9]
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121
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122
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123 F[1]==================================>F[2]
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124 F[8]----------------------------------------------------------F[9]
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125
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126
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127 -----
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128
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129 **reference :**
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130
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131 ]]>
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132 </help>
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133 </tool>
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