# HG changeset patch
# User tyty
# Date 1419013356 18000
# Node ID e581e89e331879fab71defaa17d4ce4e88d749be
# Parent  6b7429975fdefb7a41138456a3da2f541ee44951
Uploaded

diff -r 6b7429975fde -r e581e89e3318 predict/predict_RNAs.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/predict_RNAs.xml	Fri Dec 19 13:22:36 2014 -0500
@@ -0,0 +1,87 @@
+<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 $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>
+
+
+**Function**
+
+RNA Structure Prediction uses the RNAstructure algorithm (Version 5.6, http://rna.urmc.rochester.edu/RNAstructure.html) to predict RNA structures without restraints (in silico) or with restraints from structural reactivities, typically 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
+* 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 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) as the backend program to predict RNA structures.
+* 2. Default parameters are used for RNAstructure except -T (Temperature), -sm (slope used with SHAPE restraints) and -si (intercept used with SHAPE restraints), for which users can specify the value
+
+
+
+	</help>
+</tool>