diff ngs_filtering.xml @ 12:cdf95051bc55 draft default tip

Uploaded 2 tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ngs_filtering.xml	Sun Mar 18 07:11:06 2018 -0400
@@ -0,0 +1,139 @@
+<tool id="ngsFilt" name="IMGT Report Filtering" version="0.9" profile="15.10">
+  <description>Filter IMGT Summary Data</description>
+  <command interpreter="python">ngs_filtering.py $input $TCR_or_BCR $Vfun $spChar $prod $delCF $threshold $Vg.Vgid $clen.cdr3len1 $cdp.cdr3part $filtin $filtout $summ $Jg.Jgid $Dg.Dgid $clen.cdr3len2 $process_id
+	
+  </command>
+  <inputs>
+    <param format="txt" name="input" type="data" label="IMGT Summary Output"/>
+	<param format="txt" name="process_id" type="text" label="Process ID"/>
+	<param name="TCR_or_BCR" type="select" label="T-cell or B-cell option">
+    <option value="TCR">T-cell</option>
+    <option value="BCR">B-cell</option>
+    </param>
+	<param name="Vfun" type="select" label="Only Take Into Account Fuctional V-GENE? ">
+	<option value="y">yes</option>
+      <option value="n">no</option>
+      </param>
+
+	<param name="spChar" type="select" label="Only Take Into Account CDR3 with no Special Characters (X,*,#)? ">
+     <option value="y">yes</option> 
+	<option value="n">no</option>
+      </param>
+
+  <param name="prod" type="select" label="Only Take Into Account Productive Sequences? ">
+     <option value="y">yes</option> 
+	<option value="n">no</option>
+      </param>
+
+  <param name="delCF" type="select" label="Only Take Into Account CDR3 with valid start/end landmarks? ">
+	<option value="y">yes</option>
+      <option value="n">no</option>
+      </param>
+
+    <param name="threshold" type="float" size="3" value="0" min="0" max="100" label="V-REGION identity %" />
+  
+  <conditional name="Vg">
+	
+	<param name="Vg_select" type="select" label="Select Specific V gene?">
+        <option value="y">Yes</option>
+		<option value="n" selected="true">No</option>
+    </param>
+	
+	<when value="y">
+          <param format="txt" name="Vgid" type="text" label="Type V gene"/>
+     </when>
+	
+	<when value="n">
+		<param name="Vgid" type="hidden" value="null" />
+     </when>
+
+	 </conditional>
+	 
+	  <conditional name="Jg">
+	
+	<param name="Jg_select" type="select" label="Select Specific J gene?">
+        <option value="y">Yes</option>
+		<option value="n" selected="true">No</option>
+    </param>
+	
+	<when value="y">
+          <param format="txt" name="Jgid" type="text" label="Type J gene"/>
+     </when>
+	
+	<when value="n">
+		<param name="Jgid" type="hidden" value="null" />
+     </when>
+
+	 </conditional>
+	 
+	 <conditional name="Dg">
+	
+	<param name="Dg_select" type="select" label="Select Specific D gene?">
+        <option value="y">Yes</option>
+		<option value="n" selected="true">No</option>
+    </param>
+	
+	<when value="y">
+          <param format="txt" name="Dgid" type="text" label="Type D gene"/>
+     </when>
+	
+	<when value="n">
+		<param name="Dgid" type="hidden" value="null" />
+     </when>
+
+	 </conditional>
+	 
+	 
+	
+	<conditional name="clen">
+
+	<param name="clen_select" type="select" label="Select CDR3 length range?">
+        <option value="y">Yes</option>
+		<option value="n" selected="true">No</option>
+    </param>
+
+	<when value="y">
+		<param name="cdr3len1" type="integer" size="3" value="0" min="0" max="100" label="CDR3 Length Lower Threshold" />
+		<param name="cdr3len2" type="integer" size="3" value="0" min="0" max="100" label="CDR3 Length Upper Threshold" />
+	</when>
+
+	<when value="n">
+		<param name="cdr3len1" type="hidden" value="null" />
+		<param name="cdr3len2" type="hidden" value="null" />
+	</when>
+
+	</conditional>
+	
+	<conditional name="cdp">
+	
+	<param name="cdp_select" type="select" label="Only select CDR3 containing specific amino-acid sequence?">
+        <option value="y">Yes</option>
+		<option value="n" selected="true">No</option>
+    </param>
+	
+	<when value="y">
+    <param format="txt" name="cdr3part" type="text" label="Type specific amino-acid sequence"/>
+	</when>
+	
+	<when value="n">
+		<param name="cdr3part" type="hidden" value="null" />
+	</when>
+	</conditional>
+  
+  </inputs>
+  
+  
+  <outputs>
+	<data name="filtin" format="tabular" 	label="${process_id}_filterin"/>
+	<data name="filtout" format="tabular" 	label="${process_id}_filterout"/>
+	<data name="summ" format="tabular" 	label="${process_id}_Summary"/>
+
+
+  </outputs>
+
+
+  <help>
+This tool filters IMGT Summary Data based on a combination of criteria.
+  </help>
+
+</tool>