diff rmapq_wrapper.xml @ 0:bccaba937482 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmapq_wrapper.xml	Mon May 19 10:59:58 2014 -0400
@@ -0,0 +1,94 @@
+<tool id="rmapq_wrapper" name="RMAPQ" version="1.0.0">
+    <description>for Solexa Short Reads Alignment with Quality Scores</description>
+    <requirements>
+      <requirement type="package" version="2.05">rmap</requirement>
+    </requirements>
+    <command interpreter="python">
+    #if $trim.choice=="No":
+        rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len 0 $align_len $mismatch $output1
+    #else:
+        rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len $trim.read_len $align_len $mismatch $output1
+    #end if
+    </command>
+    <inputs>
+        <param name="database" type="select" display="radio" label="Target database">
+			<options from_file="faseq.loc">
+			  <column name="name" index="0"/>
+			  <column name="value" index="0"/>
+			</options>
+        </param>
+        <param name="input_seq" type="data" format="fasta" label="Sequence file"/>
+        <param name="input_score" type="data" format="qualsolexa" label="Quality score file"/>
+        <param name="high_score" type="float" size="15" value="40" label="Minimum score for high-quality base (-q)"/>
+        <param name="high_len" type="integer" size="15" value="36" label="Minimal high-quality bases (-M)"/>
+        <param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed"/>
+        <param name="mismatch" type="select" label="Number of mismatches allowed (-m)">
+            <option value="0">0</option>
+            <option value="1">1</option>
+            <option value="3">3</option>
+            <option value="5">5</option>
+        </param>
+        <conditional name="trim">
+            <param name="choice" type="select" label="To trim the reads">
+                <option value="No">No</option>
+                <option value="Yes">Yes</option>
+            </param>
+            <when value="No">
+            </when>
+            <when value="Yes">
+                <param name="read_len" type="integer" size="15" value="36" label="Read length (-w)" /> 
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output1" format="bed"/>
+    </outputs>
+    <!-- 
+    <tests>
+        <test>
+            <param name="database" value="/galaxy/data/faseq/test" />
+            <param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/>
+            <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qualsolexa" />
+            <param name="high_score" value="40" />
+            <param name="high_len" value="36" />
+            <param name="read_len" value="36" />
+            <param name="align_len" value="36" />
+            <param name="mismatch" value="3" />
+            <output name="output1" file="rmapq_wrapper_test1.bed"/> 
+        </test>
+    </tests>
+    -->
+    <help>
+    
+.. class:: warningmark
+
+ RMAPQ was developed for **Solexa** reads. 
+
+.. class:: infomark
+
+**TIP**. The tool will guess the length of the reads, however, if you select to trim the reads, the *Maximal Length of the Reads* must be between 20 and 64. Reads with lengths longer than the specified value will be trimmed at the 3'end. 
+
+-----
+
+**What it does**
+
+This tool runs **rmapq** (for more information, please see the reference below), searching against a genome build with sequence qualities.   
+
+-----
+
+**Parameters**
+
+- *Minimal High-quality Bases* (**-M**): the minimal length of the high quality score bases
+- *Minimum Score for High-quality Base* (**-q**) : the minimal quality score 
+- *Minimal Length of a Hit* (**-h**) : the minimal length of an exact match or seed  
+- *Number of Mismatches Allowed* (**-m**) : the maximal number of mismatches allowed in an alignment
+- *Read Length* (**-w**) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end.
+
+-----
+
+**Reference**
+
+ **RMAP** is developed by Dr. Andrew D Smith and Dr. Zhenyu Xuan at the Cold Spring Harbor Laboratory. Please see http://rulai.cshl.edu/rmap/
+
+    </help>
+</tool>