changeset 3:14894a8de3a7 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_tool.xml	Wed Oct 12 18:12:18 2016 -0400
@@ -0,0 +1,39 @@
+<tool id="blast_tool" name="BLAST caller for ORF" version="0.1.0">
+    <description>from given fasta polypeptide sequence</description>
+    <requirements>
+        <requirement type="package" version="1.64">biopython</requirement>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <version_command interpreter="python">blast_entry.py --version</version_command>
+    <command interpreter="python">
+blast_entry.py -i "$input_file" -o "$output_xml" -f "$ext" -p "$program" -d "database"
+    </command>
+    <inputs>
+      <param name="input_file" type="data" label="Input File" format="fasta,fastq,sam,bam" help="FASTA, FASTQ, or SFF format." />
+      <param name="ext" type="select" value="fasta" label="Input file type">
+	<option value="fasta">Fasta</option>
+	<option value="fastq">Fastq</option>
+	<option value="sam">Sam</option>
+	<option value="bam">Bam</option>
+      </param>
+      <param name="program" type="select" value="blastp" label="BLAST program">
+	<option value="blastn">BLASTN</option>
+	<option value="blastp">BLASTP</option>
+	<option value="blastx">BLASTX</option>
+	<option value="tblastn">TBLASTN</option>
+	<option value="tblastx">TBLASTX</option>
+      </param>
+      <param name="database" type="select" value="nr" label="BLAST database">
+	<option value="nr">Nucleotide collection</option>
+      </param>
+    </inputs>
+    <outputs>
+        <data name="output_xml" format="XML" label="$input_file.name BLAST result">
+        </data>
+    </outputs>
+</tool>