Mercurial > repos > tyty > structurefold
comparison predict/predict_RNAs.xml @ 74:63c41304b221 draft
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| author | tyty |
|---|---|
| date | Tue, 09 Dec 2014 03:03:30 -0500 |
| parents | |
| children | f221931149a4 |
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| 73:1c325ff557d9 | 74:63c41304b221 |
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| 1 <tool id="predict_pipeline" name="RNA Structure Prediction" version="1.0"> | |
| 2 <description></description> | |
| 3 <command interpreter="python"> | |
| 4 #if $reactivity.type == "restraint" | |
| 5 predict_RNAs.py $rna_list $reference_file $reactivity.type $temperature $output $reactivity.reactivity_file $reactivity.slope $reactivity.intercept | |
| 6 #else | |
| 7 predict_RNAs.py $rna_list $reference_file $reactivity.type $temperature $output | |
| 8 #end if | |
| 9 </command> | |
| 10 <requirements> | |
| 11 <requirement type="package" version="1.61">biopython</requirement> | |
| 12 <requirement type="package" version="1.7.1">numpy</requirement> | |
| 13 <requirement type="package" version="1.2.1">matplotlib</requirement> | |
| 14 </requirements> | |
| 15 <inputs> | |
| 16 <param name="rna_list" type="data" format="txt" label="List of RNA ids to predict"/> | |
| 17 <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/> | |
| 18 <param name="temperature" type="float" value="310.15" label="Temperature (K)"/> | |
| 19 <conditional name="reactivity"> | |
| 20 <param name="type" type="select" label="RNA structure prediction type"> | |
| 21 <option value="silico">In silico</option> | |
| 22 <option value="restraint">With experimental restraints</option> | |
| 23 </param> | |
| 24 <when value="silico"/> | |
| 25 <when value="restraint"> | |
| 26 <param name="reactivity_file" type="data" label="Reactivity file"/> | |
| 27 <param name="slope" type="float" value="1.8" label="Slope used with structural restraints"/> | |
| 28 <param name="intercept" type="float" value="-0.6" label="Intercept used with structural restraints"/> | |
| 29 </when> | |
| 30 </conditional> | |
| 31 | |
| 32 </inputs> | |
| 33 <outputs> | |
| 34 <data name="output" format=".tgz"/> | |
| 35 </outputs> | |
| 36 | |
| 37 <help> | |
| 38 | |
| 39 | |
| 40 **TIPS**: | |
| 41 | |
| 42 ----- | |
| 43 | |
| 44 **Input**: | |
| 45 | |
| 46 * 1. A file with transcript Ids (Max num. 100), (each ID one line) | |
| 47 * 2. Reference file (fasta) used to map the reads to | |
| 48 * 3. Temperature for RNA structure prediction | |
| 49 * [Optional]: | |
| 50 * 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided | |
| 51 * 2. Slope used with structural restraints (default 1.8) | |
| 52 * 3. Intercept used with structural restraints (default -0.6) | |
| 53 | |
| 54 ----- | |
| 55 | |
| 56 **Output**: | |
| 57 | |
| 58 * 1. .ct files with predicted RNA structures [transciptID.ct] | |
| 59 * 2. .ps files which depict the predicted RNA structures [[transciptID.ps] | |
| 60 * [Optional] | |
| 61 * 3. .png files that shows the distribution of the reactivity of each nucleotide on the transcripts of interest. [transciptID.png] | |
| 62 | |
| 63 ----- | |
| 64 | |
| 65 **Attention** | |
| 66 | |
| 67 Make sure any of the transcript Ids does not contain "|" or space! | |
| 68 | |
| 69 ----- | |
| 70 | |
| 71 **Backend program**: | |
| 72 | |
| 73 * 1. This module is using RNAstructure (http://rna.urmc.rochester.edu/RNAstructure.html) as the backend program to predict RNA structures. | |
| 74 * 2. Default parameters are used for RNAstructure expect -T (Temperature), -sm (slope used with SHAPE restraints) and -si (intercept used with SHAPE restraints) which users can specify the value | |
| 75 | |
| 76 | |
| 77 | |
| 78 </help> | |
| 79 </tool> |