diff predict/predict_RNAs.xml~ @ 27:564795252d1a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/predict/predict_RNAs.xml~	Mon Oct 20 14:42:09 2014 -0400
@@ -0,0 +1,63 @@
+<tool id="predict_pipeline" name="RNA structure prediction" version="1.0">
+	<description></description>
+	<command interpreter="python">predict_RNAs.py $rna_list $reference_file $reactivity_file $output </command>
+        <requirements>
+                <requirement type="package" version="1.61">biopython</requirement>
+                <requirement type="package" version="1.7">numpy</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="reactivity_file" type="data" optional = "true" label="Reactivity"/>
+<!---
+        <conditional name="reactivity">
+            <param name="choose" type="select" label="Reactivity files exists?">
+                <option value="N">No</option>
+                <option value="Y">Yes</option>
+            </param>
+            <when value="Y">
+                <param name="reactivity_file" type="data" optional = "true" label="Reactivity"/>
+            </when>
+            <when value="N"/>
+        </conditional>  
+
+-->		
+	</inputs>
+	<outputs>
+		<data name="output" format=".tgz"/>
+	</outputs>
+
+	<help>
+
+
+**TIPS**:
+
+-----
+
+**Input**:
+
+* 1. A file with transcript Ids (Max num. 20), (each ID one line)
+* 2. Reference file (fasta) used to map the reads
+* [Optional]:
+* 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided
+
+-----
+
+**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]
+* 4. A .txt file that includes the reactivities of all the nucleotides on the transcripts of interest. [transciptID.txt]
+
+-----
+
+**Attention**
+
+Make sure any of the transcript Ids does not contain "|" or space!	
+
+
+
+	</help>
+</tool>