Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/galaxy/getReadDistribution.xml @ 4:1fc014126d55
Uploaded
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:45:50 -0500 |
parents | e0f8dcca02ed |
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rev | line source |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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1 <tool id="getReadDistribution" name="get read distribution"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 <description>Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented.</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/WrappGetReadDistribution.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 == 'fasta': |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 -f fasta |
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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 == 'fastq': |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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8 -f fastq |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 #end if |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 #if $optionnumber.number == 'Yes': |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 -n $optionnumber.bestNumber |
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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.
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14 #if $optionpercent.percent == 'Yes': |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 -p $optionpercent.percentage |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 #end if |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 -o $outputFile |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 </command> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 <inputs> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 <conditional name="formatType"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 <param name="FormatInputFileName" type="select" label="Sequence input File Format "> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 <option value="fasta">fasta</option> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 <option value="fastq">fastq</option> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 </param> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 <when value="fasta"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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27 <param name="inputFileName" format="fasta" type="data" label="Sequence input File"/> |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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28 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 <when value="fastq"> |
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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="fastq" type="data" label="Sequence input File"/> |
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31 </when> |
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32 </conditional> |
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33 |
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34 <conditional name="optionnumber"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 <param name="number" type="select" label="keep the best n"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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36 <option value="Yes">Yes</option> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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37 <option value="No" selected="true">No</option> |
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38 </param> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 <when value="Yes"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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40 <param name="bestNumber" type="integer" value="0" /> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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42 <when value="No"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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43 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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44 </conditional> |
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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 <conditional name="optionpercent"> |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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47 <param name="percent" type="select" label="keep the best n percentage"> |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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48 <option value="Yes">Yes</option> |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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49 <option value="No" selected="true">No</option> |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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50 </param> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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51 <when value="Yes"> |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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52 <param name="percentage" type="integer" value="0" /> |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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53 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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54 <when value="No"> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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55 </when> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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56 </conditional> |
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57 |
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58 </inputs> |
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59 |
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60 <outputs> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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61 <data name="outputFile" format="tar" label="[getReadDistribution] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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62 </outputs> |
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63 |
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64 <help> |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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65 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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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66 </help> |
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67 </tool> |