comparison reactivity_cal/reactivity_calculation.xml @ 5:7a8ddf1819b1 draft

Uploaded
author tyty
date Mon, 15 Sep 2014 14:52:52 -0400
parents
children
comparison
equal deleted inserted replaced
4:a292aaf51735 5:7a8ddf1819b1
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>