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comparison predict/predict_RNAs.xml @ 4:a292aaf51735 draft

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author tyty
date Mon, 15 Sep 2014 14:52:43 -0400
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3:f4cc06e92530 4:a292aaf51735
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>