27
|
1 <tool id="predict_pipeline" name="RNA structure prediction" version="1.0">
|
|
2 <description></description>
|
|
3 <command interpreter="python">predict_RNAs.py $rna_list $reference_file $reactivity_file $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="rna_list" type="data" format="txt" label="List of RNA ids to predict"/>
|
|
10 <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
|
|
11 <param name="reactivity_file" type="data" optional = "true" label="Reactivity"/>
|
|
12 <!---
|
|
13 <conditional name="reactivity">
|
|
14 <param name="choose" type="select" label="Reactivity files exists?">
|
|
15 <option value="N">No</option>
|
|
16 <option value="Y">Yes</option>
|
|
17 </param>
|
|
18 <when value="Y">
|
|
19 <param name="reactivity_file" type="data" optional = "true" label="Reactivity"/>
|
|
20 </when>
|
|
21 <when value="N"/>
|
|
22 </conditional>
|
|
23
|
|
24 -->
|
|
25 </inputs>
|
|
26 <outputs>
|
|
27 <data name="output" format=".tgz"/>
|
|
28 </outputs>
|
|
29
|
|
30 <help>
|
|
31
|
|
32
|
|
33 **TIPS**:
|
|
34
|
|
35 -----
|
|
36
|
|
37 **Input**:
|
|
38
|
|
39 * 1. A file with transcript Ids (Max num. 20), (each ID one line)
|
|
40 * 2. Reference file (fasta) used to map the reads
|
|
41 * [Optional]:
|
|
42 * 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided
|
|
43
|
|
44 -----
|
|
45
|
|
46 **Output**:
|
|
47
|
|
48 * 1. .ct files with predicted RNA structures [transciptID.ct]
|
|
49 * 2. .ps files which depict the predicted RNA structures [[transciptID.ps]
|
|
50 * [Optional]
|
|
51 * 3. .png files that shows the distribution of the reactivity of each nucleotide on the transcripts of interest. [transciptID.png]
|
|
52 * 4. A .txt file that includes the reactivities of all the nucleotides on the transcripts of interest. [transciptID.txt]
|
|
53
|
|
54 -----
|
|
55
|
|
56 **Attention**
|
|
57
|
|
58 Make sure any of the transcript Ids does not contain "|" or space!
|
|
59
|
|
60
|
|
61
|
|
62 </help>
|
|
63 </tool>
|