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