Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
author yufei-luo
date Fri, 18 Jan 2013 04:45:50 -0500
parents e0f8dcca02ed
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 <tool id="getExons" name="get exons">
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2 <description>Get the exons of a set of transcripts.</description>
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3 <command interpreter="python">
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4 ../Java/Python/getExons.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':
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 -f gff2
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11 #elif $formatType.FormatInputFileName == 'gff3':
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 -f gff3
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13 #elif $formatType.FormatInputFileName == 'sam':
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 -f sam
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 #elif $formatType.FormatInputFileName == 'gtf':
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 -f gtf
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17 #end if
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18
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19 #if $optionSelect.Value == "Yes":
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20 -s $optionSelect.selectValue
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21 #end if
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22
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 -o $outputFileGff
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24 </command>
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25
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26 <inputs>
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27 <conditional name="formatType">
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28 <param name="FormatInputFileName" type="select" label="Input File Format">
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29 <option value="bed">bed</option>
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30 <option value="gff">gff</option>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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31 <option value="gff2">gff2</option>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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32 <option value="gff3">gff3</option>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 <option value="sam">sam</option>
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34 <option value="gtf">gtf</option>
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35 </param>
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36 <when value="bed">
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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37 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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38 </when>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 <when value="gff">
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40 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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41 </when>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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42 <when value="gff2">
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43 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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44 </when>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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45 <when value="gff3">
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 </when>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 <when value="sam">
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49 <param name="inputFileName" format="sam" type="data" label="Input File"/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 </when>
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51 <when value="gtf">
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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52 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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53 </when>
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54 </conditional>
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55
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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56 <conditional name="optionSelect">
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57 <param name="Value" type="select" label="select some of the exons (like '1,2,5..-3,-1')">
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58 <option value="Yes">Yes</option>
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59 <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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60 </param>
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61 <when value="Yes">
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62 <param name="selectValue" type="text" value="None" label="select option" help="like '1,2,5..-3,-1'"/>
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63 </when>
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64 <when value="No">
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65 </when>
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66 </conditional>
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67 </inputs>
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68
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69 <outputs>
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70 <data format="gff3" name="outputFileGff" label="[getExons -> gff3] Output File"/>
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71 </outputs>
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72 </tool>