annotate predict/predict_RNAs.xml @ 117:75e3711e23c4 draft

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<tool id="predict_pipeline" name="RNA Structure Prediction" version="1.0">
	<description>predict RNA structures with or without experimental constraints from the Reactivity Calculation module</description>
	<command interpreter="python">
        #if $program.wh == "rs"
            #if $program.rs_reactivity.type == "restraint"
                predict_RNAs.py $rna_list $reference_file $program.rs_reactivity.type $temperature $program.wh $output $output.files_path $program.rs_reactivity.reactivity_file $program.rs_reactivity.slope $program.rs_reactivity.intercept
            #else
                predict_RNAs.py $rna_list $reference_file $program.rs_reactivity.type $temperature $program.wh $output $output.files_path
            #end if
        #else
            #if $program.vp_reactivity.type == "restraint"
                predict_RNAs.py $rna_list $reference_file $program.vp_reactivity.type $temperature $program.wh $output $output.files_path $program.vp_reactivity.reactivity_file $program.vp_reactivity.threshold_high $program.vp_reactivity.threshold_low $program.gqs
            #else
                predict_RNAs.py $rna_list $reference_file $program.vp_reactivity.type $temperature $program.wh $output $output.files_path $program.gqs
            #end if
        #end if
    </command>
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
        <requirements>
                <requirement type="package" version="5.7">rnastructure</requirement>
                <requirement type="package" version="1.61">biopython</requirement>
                <requirement type="package" version="1.7.1">numpy</requirement>
                <requirement type="package" version="1.1.7">imaging</requirement>
                <requirement type="package" version="1.2.1">matplotlib</requirement>
                <requirement type="package" version="2.1">vienna_rna</requirement>
        </requirements>
	<inputs>
        <param name="rna_list" type="data" format="txt" label="List of RNA ids to predict"/>
        <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
        <param name="temperature" type="float" value="310.15" label="Temperature (K)"/>
        <conditional name="program">
            <param name="wh" type="select" label="Program for RNA structure prediction">
                <option value="rs">RNAstructure</option>
                <option value="vp">ViennaRNA Package</option>
            </param>
            <when value="rs">
                <conditional name="rs_reactivity">
                    <param name="type" type="select" label="RNA structure prediction type">
                        <option value="silico">In silico</option>
                        <option value="restraint">With experimental restraints</option>
                    </param>
                    <when value="silico"/>
                    <when value="restraint">
                        <param name="reactivity_file" type="data" label="Reactivity file"/>
                        <param name="slope" type="float" value="1.8" label="Slope used with structural restraints"/>
                        <param name="intercept" type="float" value="-0.6" label="Intercept used with structural restraints"/>
                    </when>
                </conditional>
            </when>
            <when value="vp">
                <conditional name="vp_reactivity">
                    <param name="type" type="select" label="RNA structure prediction type">
                        <option value="silico">In silico</option>
                        <option value="restraint">With experimental restraints</option>
                    </param>
                    <when value="silico"/>
                    <when value="restraint">
                        <param name="reactivity_file" type="data" label="Reactivity file"/>
                        <param name="threshold_high" type="float" value="0.6" label="Threshold for high reactivities"/>
                        <param name="threshold_low" type="float" value="0.3" label="Threshold for low reactivities"/>
                    </when>
                </conditional>
                <param name="gqs" type="boolean" checked="false" truevalue = "1" falsevalue = "0" label="Incoorporate G-Quadruplex prediction if checked"/>
            </when>
         </conditional>
            
	
	</inputs>
	<outputs>
		<data name="output" format="html" />
	</outputs>

	<help>


**Function**

RNA Structure Prediction uses the RNAstructure program (V5.6) and ViennaRNA package (V2.1.9) to predict RNA structures without restraints (in silico) or with restraints from structural reactivities, as provided by the Reactivity Calculation module. Users can designate the temperature under which to predict the RNA structures.

-----

**Input**:

* 1. A file with transcript Ids (Max num. 100), (each ID one line)
* 2. Reference file (fasta) used to map the reads to
* 3. Temperature for RNA structure prediction
* [Optional]:
* 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided
* /RNAstructure prediction mode/
* 2. Slope used with structural restraints (default 1.8)
* 3. Intercept used with structural restraints (default -0.6)
* /ViennaRNA package prediction mode/
* 2. Flag that determines whether to incoorporate G-Quadruplex prediction
* 3. High reactivity threshold (Any nucleotide with structural reactivity that is higher than it will be constrainted as single stranded) (default 0.6)
* 4. Low reactivity threshold (Any nucleotide with structural reactivity that is lower than it will be constrainted as double stranded) (default 0.3)

-----

**Output**:

* 1. Dot bracket files with predicted RNA structures [transciptID.dbn]
* 2. .ps files which depict the predicted RNA structures [transciptID.ps]
* [Optional]
* 3. .tif files that shows the distribution of the reactivity of each nucleotide on the transcripts of interest. [transciptID.tif]

-----

**Attention**

Make sure that none of the transcript Ids contains a "|" or a space!

-----

**Backend program**:

* 1. This module uses RNAstructure (http://rna.urmc.rochester.edu/RNAstructure.html) or ViennaRNA package (http://www.tbi.univie.ac.at/RNA/) as the backend programs to predict RNA structures.
* 2. Default parameters are used for RNAstructure and ViennaRNA package except -T (Temperature), -sm (slope used with SHAPE restraints [RNAstructure prediction mode]), -si (intercept used with SHAPE restraints [RNAstructure prediction mode]) and thresholds for high and low reactivity [ViennaRNA package prediciton mode], for which users can specify the value



	</help>
</tool>