diff lipory.xml @ 4:b79df4966ebb draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

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+++ b/lipory.xml	Mon Jun 05 02:45:43 2023 +0000
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+<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="2022.1.18">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>