diff BlastParser_and_hits.xml @ 0:69ea2a13947f draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BlastParser_and_hits.xml	Sun Jun 21 14:31:29 2015 -0400
@@ -0,0 +1,45 @@
+<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.1.0">
+<description>for virus discovery</description>
+<requirements></requirements>
+<command interpreter="python">
+BlastParser_and_hits.py
+	--sequences $sequences
+	--blast $blast
+	--tabularOutput $tabularOutput
+	--fastaOutput $fastaOutput
+	--flanking $flanking
+	--mode $mode
+</command>
+<inputs>
+	<param name="sequences" type="data" format="fasta"  label="fasta sequences that have been blasted" />
+	<param name="blast" type="data" format="tabular" label="The blast output you wish to parse" />
+	<param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
+	<param name="mode" type="select" label="Verbose or short reporting mode" help="display or not the oases contigs">
+	    <option value="verbose" default="true">verbose</option>
+	    <option value="short">do not report oases contigs</option>
+	</param>
+</inputs>
+<outputs>
+	<data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
+	<data name="fastaOutput" format="fasta" label="hits"/>
+</outputs>
+
+  <tests>
+    <test>
+        <param ftype="fasta" name="sequences" value="input.fa" />
+        <param ftype="tabular" name="blast" value="blast.tab" />
+        <param name="flanking" value="5" />
+        <param name="mode" value="verbose" />
+        <output name="tabularOutput" ftype="tabular" file="output.tab" />
+        <output name="fastaOutput" ftype="fasta" file="output.fa" />
+    </test>
+  </tests>
+
+<help>
+
+**What it does**
+
+Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly
+
+</help>
+</tool>