diff BlastParser_and_hits.xml @ 1:1964514aabde draft

planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8

--- a/BlastParser_and_hits.xml	Sun Jun 21 14:31:29 2015 -0400
+++ b/BlastParser_and_hits.xml	Mon Sep 14 12:18:46 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.1.0">
+<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.0">
 <description>for virus discovery</description>
 <requirements></requirements>
 <command interpreter="python">
@@ -9,6 +9,15 @@
 	--fastaOutput $fastaOutput
 	--flanking $flanking
 	--mode $mode
+	## Additional parameters.
+    #if $additional_filters.use_filters == "yes":
+        --filter_relativeCov $additional_filters.filter_relativeCov
+        --filter_maxScore $additional_filters.filter_maxScore
+        --filter_meanScore $additional_filters.filter_meanScore
+    #end if
+    --al_sequences $al_sequences
+    --un_sequences $un_sequences
+
 </command>
 <inputs>
 	<param name="sequences" type="data" format="fasta"  label="fasta sequences that have been blasted" />
@@ -18,10 +27,25 @@
 	    <option value="verbose" default="true">verbose</option>
 	    <option value="short">do not report oases contigs</option>
 	</param>
+    <conditional name="additional_filters">
+            <param name="use_filters" type="select" label="Use Additional Filters?">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">            
+                <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
+                <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
+                <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
+            </when>
+    </conditional>
 </inputs>
 <outputs>
 	<data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
 	<data name="fastaOutput" format="fasta" label="hits"/>
+	<data name="al_sequences" format="fasta" label="Blast aligned sequences"/>
+	<data name="un_sequences" format="fasta" label="Blast unaligned sequences"/>
 </outputs>
 
   <tests>
@@ -29,9 +53,12 @@
         <param ftype="fasta" name="sequences" value="input.fa" />
         <param ftype="tabular" name="blast" value="blast.tab" />
         <param name="flanking" value="5" />
+        <param name="use_filters" value="no" />
         <param name="mode" value="verbose" />
         <output name="tabularOutput" ftype="tabular" file="output.tab" />
         <output name="fastaOutput" ftype="fasta" file="output.fa" />
+        <output name="al_sequences" ftype="fasta" file="al_sequences.fa" />
+        <output name="un_sequences" ftype="fasta" file="un_sequences.fa" />
     </test>
   </tests>
 
@@ -39,7 +66,7 @@
 
 **What it does**
 
-Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly
+Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly. Output also the contig sequences which have or not been blast aligned with the indicated cut-off
 
 </help>
 </tool>