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1 <tool id="plotTranscriptList" name="plot transcript list">
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2 <description>Plot some information from a list of transcripts. </description>
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3 <command interpreter="python">
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4 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName
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5 #if $formatType.FormatInputFileName == 'bed':
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6 -f bed
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7 #elif $formatType.FormatInputFileName == 'gff':
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8 -f gff
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9 #elif $formatType.FormatInputFileName == 'gff2':
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10 -f gff2
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11 #elif $formatType.FormatInputFileName == 'gff3':
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12 -f gff3
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13 #elif $formatType.FormatInputFileName == 'sam':
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14 -f sam
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15 #elif $formatType.FormatInputFileName == 'gtf':
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16 -f gtf
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17 #end if
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18
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19 -x $xVal
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20 -y $yVal
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21 #if $optionz.z == 'Yes':
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22 -z $optionz.zVal
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23 #end if
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24
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25 -X $XVal
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26 -Y $YVal
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27 -Z $ZVal
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28
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29 #if $optionxLab.xLab == 'Yes':
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30 -n $optionxLab.labVal
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31 #end if
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32 #if $optionyLab.yLab == 'Yes':
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33 -m $optionyLab.labVal
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34 #end if
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35
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36 #if $optionyLog.log == 'Yes':
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37 -l $optionyLog.logVal
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38 #end if
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39
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40 -s $shape
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41 -b $bucket
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42
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43 -o $outputFilePNG
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44 </command>
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45
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46 <inputs>
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47 <conditional name="formatType">
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48 <param name="FormatInputFileName" type="select" label="Input File Format">
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49 <option value="bed">bed</option>
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50 <option value="gff">gff</option>
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51 <option value="gff2">gff2</option>
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52 <option value="gff3">gff3</option>
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53 <option value="sam">sam</option>
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54 <option value="gtf">gtf</option>
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55 </param>
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56 <when value="bed">
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57 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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58 </when>
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59 <when value="gff">
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60 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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61 </when>
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62 <when value="gff2">
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63 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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64 </when>
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65 <when value="gff3">
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66 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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67 </when>
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68 <when value="sam">
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69 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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70 </when>
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71 <when value="gtf">
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72 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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73 </when>
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74 </conditional>
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75
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76 <param name="xVal" type="text" value="None" label="tag for the x value [compulsory option]"/>
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77 <param name="yVal" type="text" value="None" label="tag for the y value [compulsory option]"/>
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78
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79 <conditional name="optionz">
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80 <param name="z" type="select" label="tag for the z value ">
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81 <option value="Yes">Yes</option>
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82 <option value="No" selected="true">No</option>
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83 </param>
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84 <when value="Yes">
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85 <param name="zVal" type="text" value="None"/>
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86 </when>
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87 <when value="No">
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88 </when>
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89 </conditional>
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90
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91 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/>
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92
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93 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/>
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94
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95 <param name="ZVal" type="float" value="0.0" label="value for z when tag is not present"/>
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96
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97 <conditional name="optionxLab">
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98 <param name="xLab" type="select" label="label on the x-axis ">
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99 <option value="Yes">Yes</option>
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100 <option value="No" selected="true">No</option>
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101 </param>
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102 <when value="Yes">
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103 <param name="labVal" type="text" value=" "/>
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104 </when>
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105 <when value="No">
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106 </when>
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107 </conditional>
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108 <conditional name="optionyLab">
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109 <param name="yLab" type="select" label="label on the y-axis ">
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110 <option value="Yes">Yes</option>
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111 <option value="No" selected="true">No</option>
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112 </param>
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113 <when value="Yes">
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114 <param name="labVal" type="text" value=" "/>
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115 </when>
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116 <when value="No">
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117 </when>
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118 </conditional>
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119
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120 <conditional name="optionyLog">
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121 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
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122 <option value="Yes">Yes</option>
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123 <option value="No" selected="true">No</option>
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124 </param>
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125 <when value="Yes">
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126 <param name="logVal" type="text" value=" "/>
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127 </when>
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128 <when value="No">
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129 </when>
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130 </conditional>
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131
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132 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/>
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133 <param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/>
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134
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135 </inputs>
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136
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137 <outputs>
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138 <data name="outputFilePNG" format="png" label="[plotTranscriptList]out file"/>
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139 </outputs>
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140
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141 </tool>
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