annotate predict/predict_RNAs.xml @ 82:8b25759cc83a draft

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<tool id="predict_pipeline" name="RNA Structure Prediction" version="1.0">
	<description></description>
	<command interpreter="python">
        #if $reactivity.type == "restraint"
            predict_RNAs.py $rna_list $reference_file $reactivity.type $temperature $output $reactivity.reactivity_file $reactivity.slope $reactivity.intercept
        #else
            predict_RNAs.py $rna_list $reference_file $reactivity.type $temperature $output
        #end if
    </command>
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
        <requirements>
                <requirement type="package" version="1.61">biopython</requirement>
                <requirement type="package" version="1.7.1">numpy</requirement>
                <requirement type="package" version="1.2.1">matplotlib</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="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>
	
	</inputs>
	<outputs>
		<data name="output" format=".tar"/>
	</outputs>

	<help>


**TIPS**:

-----

**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
* 2. Slope used with structural restraints (default 1.8)
* 3. Intercept used with structural restraints (default -0.6)

-----

**Output**:

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

-----

**Attention**

Make sure any of the transcript Ids does not contain "|" or space!

-----

**Backend program**:

* 1. This module is using RNAstructure (http://rna.urmc.rochester.edu/RNAstructure.html) as the backend program to predict RNA structures.
* 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



	</help>
</tool>