Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/galaxy/plotRepartition.xml @ 4:1fc014126d55

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Uploaded
author yufei-luo
date Fri, 18 Jan 2013 04:45:50 -0500
parents e0f8dcca02ed
children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 <tool id="plotRepartition" name="plot repartition">
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2 <description>Plot the repartition of different data on a whole genome. (This tool uses only 1 input file, the different values are stored in the tags. )</description>
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3 <command interpreter="python">
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4 ../Java/Python/WrappPlotRepartition.py -i $inputFileName
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 -n $names
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6 $normalize
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7 #if $optionColor.Color == 'Yes':
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8 -c $optionColor.colValue
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9 #end if
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10 -f $format
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11
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12 #if $optionLog.log == 'Yes':
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13 -l $optionLog.logVal
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14 #end if
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15
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 -o $outputFilePNG
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17 </command>
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18
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19 <inputs>
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20 <param name="inputFileName" type="data" label="Input Gff3 File" format="gff3"/>
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21 <param name="names" type="text" value="None" label="name for the tags (separated by commas and no space) [compulsory option]"/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 <param name="normalize" type="boolean" truevalue="-r" falsevalue="" checked="false" label="normalize data (when panels are different)"/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 <param name="format" type="text" value="png" label="format of the output file[default: png]"/>
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24
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 <conditional name="optionColor">
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26 <param name="Color" type="select" label="scolor of the lines (separated by commas and no space) ">
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27 <option value="Yes">Yes</option>
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28 <option value="No" selected="true">No</option>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 </param>
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30 <when value="Yes">
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31 <param name="colValue" type="text" value="None"/>
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32 </when>
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33 <when value="No">
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34 </when>
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35 </conditional>
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36
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37 <conditional name="optionLog">
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38 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
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39 <option value="Yes">Yes</option>
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40 <option value="No" selected="true">No</option>
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41 </param>
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42 <when value="Yes">
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43 <param name="logVal" type="text" value=" "/>
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44 </when>
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45 <when value="No">
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46 </when>
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47 </conditional>
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48
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49 </inputs>
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50
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51 <outputs>
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52 <data name="outputFilePNG" format="tar" label="[plotRepartition]out file"/>
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53 </outputs>
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54
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55 <help>
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56 This script gives a .tar out file, if you want to take look at the results, you have to download it.
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57 </help>
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58
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59 </tool>