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comparison blockbuster.xml @ 1:bfaa2f0d9515 draft

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author rnateam
date Thu, 23 Jan 2014 06:10:10 -0500
parents 2f9d4b518b03
children f141f485e0e2
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0:2f9d4b518b03 1:bfaa2f0d9515
15 $input 15 $input
16 16
17 > $output 17 > $output
18 </command> 18 </command>
19 <inputs> 19 <inputs>
20 <param name="input" type="data" format="fasta" label="Fasta file of sequeces" help="-input" /> 20 <param name="input" type="data" format="bed" label="BED file containing read expressions"/>
21 <param name="distance" type="integer" value="30" size="5" label="minimum distance between two clusters" help="-distance" /> 21 <param name="distance" type="integer" value="40" size="5" label="minimum distance between two clusters"/>
22 <param name="minClusterHeight" type="float" value="10" size="5" label="minimum height (readno) of a cluster" help="-minClusterHeight" /> 22 <param name="minClusterHeight" type="float" value="50" size="5" label="minimum height (readno) of a cluster"/>
23 <param name="minBlockHeight" type="float" value="2" size="5" label="minimum height (readno) of a block" help="-minBlockHeight" /> 23 <param name="minBlockHeight" type="float" value="1" size="5" label="minimum height (readno) of a block"/>
24 <param name="scale" type="float" value="0.4" size="5" label="scale stddev for a single read" help="-scale" /> 24 <param name="scale" type="float" value="0.5" size="5" label="scale stddev for a single read"/>
25 <param name="merge" type="integer" value="0" size="5" label="merge reads with almost similar means" help="-merge" /> 25 <param name="merge" type="integer" value="0" size="5" label="merge reads with almost similar means"/>
26 <param name="tagFilter" type="integer" value="0" size="5" label="skip tags with expression smaller than this value" help="-tagFilter" /> 26 <param name="tagFilter" type="integer" value="0" size="5" label="skip tags with expression smaller than this value"/>
27 <param name="print" type="select" label="Type of output" help="-print" > 27 <param name="print" type="select" label="Type of output" >
28 <option value="1" selected="True">blocks</option> 28 <option value="1">blocks</option>
29 <option value="2">reads</option> 29 <option value="2" selected="True">reads</option>
30 </param> 30 </param>
31 </inputs> 31 </inputs>
32 32
33 <outputs> 33 <outputs>
34 <data format="tabular" name="output" label="blockbuster on ${on_string}"/> 34 <data format="tabular" name="output" label="blockbuster on ${on_string}"/>
47 .. _Blockbuster: http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html 47 .. _Blockbuster: http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html
48 48
49 49
50 **References** 50 **References**
51 51
52 7. Reference
53 52
54 If you use this program in your work you might want to cite: 53 If you use this program in your work you might want to cite:
55 54
56 Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovitch P, Stadler PF: "Evidence for Human microRNA-Offset RNAs in Small RNA Sequencing Data", Bioinformatics (2009) vol. 25 (18) pp. 2298-301 55 Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovitch P, Stadler PF: "Evidence for Human microRNA-Offset RNAs in Small RNA Sequencing Data", Bioinformatics (2009) vol. 25 (18) pp. 2298-301
57 56