diff compalignp.xml @ 0:7e55ac3bd458 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compalignp.xml	Tue Jun 09 05:36:03 2015 -0400
@@ -0,0 +1,48 @@
+<tool id="compalignp" name="Compalignp" version="1.0">
+    <description>Fractional identities between alignments</description>
+    <requirements>
+        <requirement type="package" version="1.0">compalignp</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+    <command>
+<![CDATA[
+    compalignp
+        -t $rna_alignment_target
+        -r $rna_alignment_reference
+    > $output
+]]>
+    </command>
+    <inputs>
+        <param format="clustalw,stockholm" name="rna_alignment_target" type="data" label="Target RNA Alignment" help="(-t)" />
+        <param format="clustalw,stockholm" name="rna_alignment_reference" type="data" label="Reference RNA Alignment" help="(-r)" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="rna_alignment_target" value="eukaryotic-trnas_2.1.clustal"/>
+            <param name="rna_alignment_reference" value="eukaryotic-trnas_2.1.clustal"/>
+            <output name="output" file="eukaryotic-trnas_2.1.out"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**compalignp**
+
+> Paranoia version of squids compalign. 
+
+Compute fractional "identity" between trusted alignment and test alignment
+Identity of the multiple sequence alignments is defined as
+the averaged identity over all N(N-1)/2 pairwise alignments.
+
+
+]]>
+    </help>
+<citations>
+  <citation type="doi">10.1186/1748-7188-1-19</citation>
+</citations>
+</tool>