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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children | 28664b289a69 |
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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 <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 <tests> | |
23 <test> | |
24 <param name="dist_file1" value="dis_f_N1Ap_rrna.txt" /> | |
25 <param name="dist_file2" value="dis_f_N1Am_rrna.txt" /> | |
26 <param name="seq_file" value="rRNA.txt" /> | |
27 <param name="nt_spec" value="AC" /> | |
28 <param name="flag_in" value="1" /> | |
29 <param name="threshold" value="7" /> | |
30 <output name="output" file="DMS_reactivities.out" /> | |
31 | |
32 </test> | |
33 </tests> | |
34 | |
35 <help> | |
36 | |
37 | |
38 **TIPS**: | |
39 | |
40 ----- | |
41 | |
42 **Input**: | |
43 | |
44 * 1. RTSC files (Output of II) for (+) and (-) library | |
45 * 2. Reference file (fasta) used to map the reads | |
46 * 3. Nucleotide Specificity (Type of nucleotide to have reactivity, e.g. AC for DMS and ACTG for SHAPE) | |
47 * [Optional]: | |
48 * 1. A threshold to cap the structural reactivities. {Default: 7} | |
49 * 2. Flag that determines whether to perform 2%-8% normalization {Default: yes} | |
50 | |
51 ----- | |
52 | |
53 **Output**: | |
54 | |
55 A text file with structural reactivity for each nucleotide (Reactivity file) | |
56 | |
57 | |
58 | |
59 </help> | |
60 </tool> |