diff predict/predict_RNAs.xml @ 74:63c41304b221 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/predict_RNAs.xml	Tue Dec 09 03:03:30 2014 -0500
@@ -0,0 +1,79 @@
+<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>
+        <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=".tgz"/>
+	</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>