Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/galaxy/changeTagName.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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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="changeTagName" name="change tag name"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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2 <description>Changes the name of tag of a list of transcripts.</description> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 <command interpreter="python"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 ../Java/Python/changeTagName.py -i $formatType.inputFileName |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 #if $formatType.FormatInputFileName == 'bed': |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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6 -f bed |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 #elif $formatType.FormatInputFileName == 'gff': |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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8 -f gff |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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9 #elif $formatType.FormatInputFileName == 'gff2': |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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10 -f gff2 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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11 #elif $formatType.FormatInputFileName == 'gff3': |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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12 -f gff3 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 #end if |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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14 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 -t $Tag |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 -n $name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 -o $outputFileGff |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 </command> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 <inputs> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 <conditional name="formatType"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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23 <param name="FormatInputFileName" type="select" label="Input File Format"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 <option value="bed">bed</option> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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25 <option value="gff">gff</option> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 <option value="gff2">gff2</option> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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27 <option value="gff3">gff3</option> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 </param> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 <when value="bed"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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30 <param name="inputFileName" format="bed" type="data" label="Input File"/> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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31 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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32 <when value="gff"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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33 <param name="inputFileName" format="gff" type="data" label="Input File"/> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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34 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 <when value="gff2"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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36 <param name="inputFileName" format="gff2" type="data" label="Input File"/> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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37 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 <when value="gff3"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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39 <param name="inputFileName" format="gff3" type="data" label="Input File"/> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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40 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 </conditional> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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42 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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43 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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44 <param name="name" type="text" value="None" label="name option" help="new name for the tag, you must choose a new name."/> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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45 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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47 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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48 </inputs> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 <outputs> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 <data name="outputFileGff" format="gff3" label="[changeTagName] Output File"/> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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52 </outputs> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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53 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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54 </tool> |