Mercurial > repos > tyty > structurefold
comparison predict/predict_RNAs.xml @ 52:12551ae128be draft
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author | tyty |
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date | Mon, 27 Oct 2014 01:52:39 -0400 |
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51:765da0718336 | 52:12551ae128be |
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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="1.7.1">numpy</requirement> | |
7 <requirement type="package" version="1.2.1">matplotlib</requirement> | |
8 </requirements> | |
9 <inputs> | |
10 <param name="rna_list" type="data" format="txt" label="List of RNA ids to predict"/> | |
11 <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/> | |
12 <param name="reactivity_file" type="data" optional = "true" label="Reactivity file"/> | |
13 | |
14 </inputs> | |
15 <outputs> | |
16 <data name="output" format=".tgz"/> | |
17 </outputs> | |
18 <tests> | |
19 <test> | |
20 <param name="rna_list" value="id_list_test.txt" /> | |
21 <param name="reference_file" value="cdna.txt" /> | |
22 <param name="reactivity_file" value="mRNA_react_test2.txt" /> | |
23 <output name="output" file="structures.out" /> | |
24 </test> | |
25 </tests> | |
26 <help> | |
27 | |
28 | |
29 **TIPS**: | |
30 | |
31 ----- | |
32 | |
33 **Input**: | |
34 | |
35 * 1. A file with transcript Ids (Max num. 20), (each ID one line) | |
36 * 2. Reference file (fasta) used to map the reads to | |
37 * [Optional]: | |
38 * 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided | |
39 | |
40 ----- | |
41 | |
42 **Output**: | |
43 | |
44 * 1. .ct files with predicted RNA structures [transciptID.ct] | |
45 * 2. .ps files which depict the predicted RNA structures [[transciptID.ps] | |
46 * [Optional] | |
47 * 3. .png files that shows the distribution of the reactivity of each nucleotide on the transcripts of interest. [transciptID.png] | |
48 * 4. A .txt file that includes the reactivities of all the nucleotides on the transcripts of interest. [transciptID.txt] | |
49 | |
50 ----- | |
51 | |
52 **Attention** | |
53 | |
54 Make sure any of the transcript Ids does not contain "|" or space! | |
55 | |
56 | |
57 | |
58 </help> | |
59 </tool> |