Mercurial > repos > tyty > structurefold
comparison reactivity_cal/reactivity_calculation.xml~ @ 26:8bf6c855353b draft
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author | tyty |
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date | Mon, 20 Oct 2014 14:41:56 -0400 |
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25:90bc1ead3abd | 26:8bf6c855353b |
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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 </requirements> | |
7 <inputs> | |
8 <param name="dist_file1" type="data" format="txt" label="RTSC file for (+) library"/> | |
9 <param name="dist_file2" type="data" format="txt" label="RTSC file for (-) library"/> | |
10 <param name="seq_file" type="data" format="fasta" label="Reference library"/> | |
11 <param name="nt_spec" type="text" value = "AC" label="Nucleotide specificity"/> | |
12 <param name="flag_in" type="boolean" checked="true" truevalue = "1" falsevalue = "0" label="Normalization is performed if checked"/> | |
13 <param name="threshold" type="float" value = "7" label="Value to cap the reactivities"/> | |
14 </inputs> | |
15 <outputs> | |
16 <data name="output" format="txt"/> | |
17 </outputs> | |
18 | |
19 <help> | |
20 | |
21 | |
22 **TIPS**: | |
23 | |
24 ----- | |
25 | |
26 **Input**: | |
27 | |
28 * 1. RTSC files (Output of II) for (+) and (-) library | |
29 * 2. Reference file (fasta) used to map the reads | |
30 * 3. Nucleotide Specificity (Type of nucleotide to have reactivity, e.g. AC for DMS and ACTG for SHAPE) | |
31 * [Optional]: | |
32 * 1. A threshold to cap the structural reactivities. {Default: 7} | |
33 * 2. Flag that determines whether to perform 2%-8% normalization {Default: yes} | |
34 | |
35 ----- | |
36 | |
37 **Output**: | |
38 | |
39 A text file with structural reactivity for each nucleotide (Reactivity file) | |
40 | |
41 | |
42 | |
43 </help> | |
44 </tool> |