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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 == '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 -x $xVal
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16 -y $yVal
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17 #if $optionz.z == 'Yes':
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18 -z $optionz.zVal
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19 #end if
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20
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21 -X $XVal
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22 -Y $YVal
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23 -Z $ZVal
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24
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25 #if $optionxLab.xLab == 'Yes':
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26 -n $optionxLab.labVal
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27 #end if
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28 #if $optionyLab.yLab == 'Yes':
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29 -m $optionyLab.labVal
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30 #end if
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31
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32 $log
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33 -s $shape
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34 -b $bucket
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35
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36 -o $outputFilePNG
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37 </command>
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38
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39 <inputs>
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40 <conditional name="formatType">
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41 <param name="FormatInputFileName" type="select" label="Input File Format">
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42 <option value="gff">gff</option>
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43 <option value="gff2">gff2</option>
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44 <option value="gff3">gff3</option>
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45 <option value="gtf">gtf</option>
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46 </param>
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47 <when value="gff">
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48 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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49 </when>
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50 <when value="gff2">
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51 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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52 </when>
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53 <when value="gff3">
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54 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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55 </when>
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56 <when value="gtf">
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57 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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58 </when>
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59 </conditional>
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60
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61 <param name="xVal" type="text" value="None" label="tag for the x value"/>
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62 <param name="yVal" type="text" value="None" label="tag for the y value"/>
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63
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64 <conditional name="optionz">
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65 <param name="z" type="select" label="tag for the z value ">
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66 <option value="Yes">Yes</option>
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67 <option value="No" selected="true">No</option>
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68 </param>
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69 <when value="Yes">
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70 <param name="zVal" type="text" value="None"/>
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71 </when>
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72 <when value="No">
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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="float" value="0.0" label="value for x when tag is not present "/>
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77
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78 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/>
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79
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80 <param name="ZVal" type="float" value="0.0" label="value for z when tag is not present (if applicable)"/>
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81
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82 <conditional name="optionxLab">
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83 <param name="xLab" type="select" label="label on the x-axis ">
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84 <option value="Yes">Yes</option>
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85 <option value="No" selected="true">No</option>
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86 </param>
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87 <when value="Yes">
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88 <param name="labVal" type="text" value=" "/>
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89 </when>
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90 <when value="No">
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91 </when>
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92 </conditional>
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93 <conditional name="optionyLab">
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94 <param name="yLab" type="select" label="label on the y-axis ">
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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="labVal" type="text" value=" "/>
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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
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105 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
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106 <option value="" selected="true">No</option>
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107 <option value="-l x">log on the x-axis</option>
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108 <option value="-l y">log on the y-axis</option>
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109 <option value="-l xy">log on the x- and y-axis</option>
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110 </param>
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111
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112 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/>
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113 <param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/>
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114
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115 </inputs>
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116
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117 <outputs>
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118 <data name="outputFilePNG" format="png" label="[plot transcript list] output file"/>
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119 </outputs>
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120
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121 <help>
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122 Plot the data attached as tags in a transcript list. This can be used for displaying the comparison of different sets of sliding windows, for instance.
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123
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124 The tool reads the tags of a transcript file (actually, a GFF3 file). It considers more specifically the tag names that you specify as parameter. If you use only one tag name, you can display a line plot. In this case, you have to specify a bucket size *s* (which is by defaut 1) and a point (*x*, *y*) tells you that there are *y* transcripts with tag values *x* to *x + s*.
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125
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126 You can display could plots if you use two tag names. Each point represents the values of the two tags of a transcript. If you use three variables, the third variable will be the color of the point. You can also use a log scale and name the axes of the plot.
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127
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128 Each transcript must contain the tags which are specified. If not, you should provide a default value, which is used when the tag is not present.
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129
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130 If you use a cloud plot, you can compute the Spearman's rho to quantify a correlation between your two tag values.
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131 </help>
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132 </tool>
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