diff reactivity_cal/reactivity_calculation.xml @ 78:332a0da1508d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/reactivity_calculation.xml	Tue Dec 09 03:05:57 2014 -0500
@@ -0,0 +1,60 @@
+<tool id="react_cal_pipeline" name="Reactivity Calculation" version="1.0">
+	<description></description>
+	<command interpreter="python">react_cal.py $dist_file1 $dist_file2 $seq_file $nt_spec $flag_in $threshold $output </command>
+        <requirements>
+                <requirement type="package" version="1.61">biopython</requirement>
+                <requirement type="package" version="1.7.1">numpy</requirement>
+        </requirements>
+	<inputs>
+                <param name="dist_file1" type="data" format="txt" label="RTSC file for (+) library"/>
+		        <param name="dist_file2" type="data" format="txt" label="RTSC file for (-) library"/>
+                <param name="seq_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
+                <param name="nt_spec" type="select" label="Nucleotide specificity">
+                    <option value="AC">AC</option>
+                    <option value="ATCG">AUCG</option>
+                </param>
+                <param name="flag_in" type="boolean" checked="true" truevalue = "1" falsevalue = "0" label="Normalization is performed if checked"/>
+                <param name="threshold" type="float" value = "7" optional = "true" label="Threshold to cap the reactivities"/>
+	</inputs>
+	<outputs>
+		<data name="output" format="txt"/>
+	</outputs>
+    <tests>
+        <test>
+            <param name="dist_file1" value="dis_f_N1Ap_rrna.txt" />
+	        <param name="dist_file2" value="dis_f_N1Am_rrna.txt" />
+            <param name="seq_file" value="rRNA.txt" />
+            <param name="nt_spec" value="AC" />
+            <param name="flag_in" value="1" />
+            <param name="threshold" value="7" />
+	        <output name="output" file="DMS_reactivities.out" />
+ 
+          </test>
+    </tests>
+
+	<help>
+
+
+**TIPS**:
+
+-----
+
+**Input**:
+
+* 1. RTSC files (Output of Get RT Stop Counts) for (+) and (-) library
+* 2. Reference file (fasta) used to map the reads to
+* 3. Nucleotide Specificity (Type of nucleotides to have reactivity, e.g. AC for DMS and ACTG for SHAPE)
+* [Optional]:
+* 1. A threshold to cap the structural reactivities. {Default: 7}
+* 2. Flag that determines whether to perform 2%-8% normalization {Default: Yes}
+
+-----
+
+**Output**:
+
+A text file with structural reactivity for each nucleotide (Reactivity file)
+
+
+
+	</help>
+</tool>