Mercurial > repos > tyty > structurefold
comparison reactivity_cal/reactivity_calculation.xml @ 5:7a8ddf1819b1 draft
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author | tyty |
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date | Mon, 15 Sep 2014 14:52:52 -0400 |
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4:a292aaf51735 | 5:7a8ddf1819b1 |
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1 <tool id="react_cal_pipeline" name="Reactivity calculation" version="1.0"> | |
2 <description></description> | |
3 <command interpreter="python">react_cal.py $dist_file1 $dist_file2 $seq_file $nt_spec $flag_in $threshold $output </command> | |
4 <requirements> | |
5 <requirement type="package" version="1.61">biopython</requirement> | |
6 <requirement type="package" version="1.7">numpy</requirement> | |
7 </requirements> | |
8 <inputs> | |
9 <param name="dist_file1" type="data" format="txt" label="RTSC file for (+) library"/> | |
10 <param name="dist_file2" type="data" format="txt" label="RTSC file for (-) library"/> | |
11 <param name="seq_file" type="data" format="fasta" label="Reference library"/> | |
12 <param name="nt_spec" type="select" label="Nucleotide specificity"> | |
13 <option value="AC">AC</option> | |
14 <option value="ATCG">AUCG</option> | |
15 </param> | |
16 <param name="flag_in" type="boolean" checked="true" truevalue = "1" falsevalue = "0" label="Normalization is performed if checked"/> | |
17 <param name="threshold" type="float" value = "7" optional = "true" label="Value to cap the reactivities"/> | |
18 </inputs> | |
19 <outputs> | |
20 <data name="output" format="txt"/> | |
21 </outputs> | |
22 | |
23 <help> | |
24 | |
25 | |
26 **TIPS**: | |
27 | |
28 ----- | |
29 | |
30 **Input**: | |
31 | |
32 * 1. RTSC files (Output of II) for (+) and (-) library | |
33 * 2. Reference file (fasta) used to map the reads | |
34 * 3. Nucleotide Specificity (Type of nucleotide to have reactivity, e.g. AC for DMS and ACTG for SHAPE) | |
35 * [Optional]: | |
36 * 1. A threshold to cap the structural reactivities. {Default: 7} | |
37 * 2. Flag that determines whether to perform 2%-8% normalization {Default: yes} | |
38 | |
39 ----- | |
40 | |
41 **Output**: | |
42 | |
43 A text file with structural reactivity for each nucleotide (Reactivity file) | |
44 | |
45 | |
46 | |
47 </help> | |
48 </tool> |