diff lipory.xml @ 0:f678e282b320 draft default tip

"planemo upload"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lipory.xml	Fri May 06 07:07:23 2022 +0000
@@ -0,0 +1,60 @@
+<?xml version="1.0"?>
+<tool id="edu.tamu.cpt.fasta.lipory" name="Identify Lipoboxes" version="19.1.0.0">
+  <description> in protein sequences</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements">
+    <requirement type="package" version="2019.06.08">regex</requirement>
+  </expand>
+  <command interpreter="python" detect_errors="aggressive"><![CDATA[lipory.py
+$positional_1
+$positional_2
+
+--lipobox_mindist $lipobox_mindist
+--lipobox_maxdist $lipobox_maxdist
+
+> $default]]></command>
+  <inputs>
+    <param label="Naive orf calls" name="positional_1" type="data" format="gff3"/>
+    <param label="Genome" name="positional_2" type="data" format="fasta"/>
+
+    <param label="Minimum distance in codons to start of lipobox" name="lipobox_mindist" type="integer" value="10"/>
+    <param label="Maximum distance in codons to start of lipobox" name="lipobox_maxdist" type="integer" value="40"/>
+  </inputs>
+  <outputs>
+      <data format="gff3" name="default" label="Lipoboxes from ${on_string}"/>
+  </outputs>
+  <tests>
+      <test>
+          <param name="positional_1" value="T7_LiporyIn.gff3" />
+          <param name="positional_2" value="T7_LiporyIn.fasta" />
+          <param name="lipobox_mindist" value="10" />
+          <param name="lipobox_maxdist" value="60" />
+          <output name="default" value="T7_LiporyOut.gff3" />
+      </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Identifies possible LipoBoxes from an input GFF3 and FASTA.
+
+**How it works**
+
+Searches in the first 10-40 amino acids of an input protein sequence using regular expressions 
+for a 4-amino acid motif based on the consensus sequences described in (**Babu** et al. 2006. *J 
+Bacteriol.* 188(8):2761-2773 and **Kongari** *et al.* 2018 *BMC Bioinformatics*. 19:326). The 
+amino acids allowed here are relaxed to allow for the diversity of amino acids known to occur in lipoboxes.
+
+Position 1: ILMFTV or only A
+
+Position 2: any residue except REKD or only W
+
+Position 3: GAS 
+
+Position 4: C
+
+      ]]></help>
+		<expand macro="citations-2020" />
+</tool>