Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/plotTranscriptList.xml @ 36:44d5973c188c
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 15:02:29 -0400 |
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| 35:d94018ca4ada | 36:44d5973c188c |
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| 1 <tool id="plotTranscriptList" name="plot transcript list"> | |
| 2 <description>Plot some information from a list of transcripts. </description> | |
| 3 <command interpreter="python"> | |
| 4 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName | |
| 5 #if $formatType.FormatInputFileName == 'gff': | |
| 6 -f gff | |
| 7 #elif $formatType.FormatInputFileName == 'gff2': | |
| 8 -f gff2 | |
| 9 #elif $formatType.FormatInputFileName == 'gff3': | |
| 10 -f gff3 | |
| 11 #elif $formatType.FormatInputFileName == 'gtf': | |
| 12 -f gtf | |
| 13 #end if | |
| 14 | |
| 15 -x $xVal | |
| 16 -y $yVal | |
| 17 #if $optionz.z == 'Yes': | |
| 18 -z $optionz.zVal | |
| 19 #end if | |
| 20 | |
| 21 -X $XVal | |
| 22 -Y $YVal | |
| 23 -Z $ZVal | |
| 24 | |
| 25 #if $optionxLab.xLab == 'Yes': | |
| 26 -n $optionxLab.labVal | |
| 27 #end if | |
| 28 #if $optionyLab.yLab == 'Yes': | |
| 29 -m $optionyLab.labVal | |
| 30 #end if | |
| 31 | |
| 32 $log | |
| 33 -s $shape | |
| 34 -b $bucket | |
| 35 | |
| 36 -o $outputFilePNG | |
| 37 </command> | |
| 38 | |
| 39 <inputs> | |
| 40 <conditional name="formatType"> | |
| 41 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 42 <option value="gff">gff</option> | |
| 43 <option value="gff2">gff2</option> | |
| 44 <option value="gff3">gff3</option> | |
| 45 <option value="gtf">gtf</option> | |
| 46 </param> | |
| 47 <when value="gff"> | |
| 48 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 49 </when> | |
| 50 <when value="gff2"> | |
| 51 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
| 52 </when> | |
| 53 <when value="gff3"> | |
| 54 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 55 </when> | |
| 56 <when value="gtf"> | |
| 57 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
| 58 </when> | |
| 59 </conditional> | |
| 60 | |
| 61 <param name="xVal" type="text" value="None" label="tag for the x value"/> | |
| 62 <param name="yVal" type="text" value="None" label="tag for the y value"/> | |
| 63 | |
| 64 <conditional name="optionz"> | |
| 65 <param name="z" type="select" label="tag for the z value "> | |
| 66 <option value="Yes">Yes</option> | |
| 67 <option value="No" selected="true">No</option> | |
| 68 </param> | |
| 69 <when value="Yes"> | |
| 70 <param name="zVal" type="text" value="None"/> | |
| 71 </when> | |
| 72 <when value="No"> | |
| 73 </when> | |
| 74 </conditional> | |
| 75 | |
| 76 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/> | |
| 77 | |
| 78 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/> | |
| 79 | |
| 80 <param name="ZVal" type="float" value="0.0" label="value for z when tag is not present (if applicable)"/> | |
| 81 | |
| 82 <conditional name="optionxLab"> | |
| 83 <param name="xLab" type="select" label="label on the x-axis "> | |
| 84 <option value="Yes">Yes</option> | |
| 85 <option value="No" selected="true">No</option> | |
| 86 </param> | |
| 87 <when value="Yes"> | |
| 88 <param name="labVal" type="text" value=" "/> | |
| 89 </when> | |
| 90 <when value="No"> | |
| 91 </when> | |
| 92 </conditional> | |
| 93 <conditional name="optionyLab"> | |
| 94 <param name="yLab" type="select" label="label on the y-axis "> | |
| 95 <option value="Yes">Yes</option> | |
| 96 <option value="No" selected="true">No</option> | |
| 97 </param> | |
| 98 <when value="Yes"> | |
| 99 <param name="labVal" type="text" value=" "/> | |
| 100 </when> | |
| 101 <when value="No"> | |
| 102 </when> | |
| 103 </conditional> | |
| 104 | |
| 105 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"> | |
| 106 <option value="" selected="true">No</option> | |
| 107 <option value="-l x">log on the x-axis</option> | |
| 108 <option value="-l y">log on the y-axis</option> | |
| 109 <option value="-l xy">log on the x- and y-axis</option> | |
| 110 </param> | |
| 111 | |
| 112 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/> | |
| 113 <param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/> | |
| 114 | |
| 115 </inputs> | |
| 116 | |
| 117 <outputs> | |
| 118 <data name="outputFilePNG" format="png" label="[plot transcript list] output file"/> | |
| 119 </outputs> | |
| 120 | |
| 121 <help> | |
| 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. | |
| 123 | |
| 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*. | |
| 125 | |
| 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. | |
| 127 | |
| 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. | |
| 129 | |
| 130 If you use a cloud plot, you can compute the Spearman's rho to quantify a correlation between your two tag values. | |
| 131 </help> | |
| 132 </tool> |