diff disruptin_finder.xml @ 1:b973bc75693d draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

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+++ b/disruptin_finder.xml	Mon Jun 05 02:40:49 2023 +0000
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+<tool id="edu.tamu.cpt2.phage.disruptin_finder" name="Disruptin Finder" version="1.1">
+  <description>finds proteins with size and charge criteria</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+python '$__tool_directory__/disruptin_finder.py'
+'$fasta_file'
+--thresh_net_charge '$thresh_net_charge'
+--thresh_size '$thresh_size'
+--thresh_charge_ratio '$thresh_charge_ratio'
+--selection_criteria '$selection_criteria'
+
+> '$output']]></command>
+  <inputs>
+    <param label="Fasta" name="fasta_file" type="data" format="fasta"/>
+    <param label="Minimum Net Charge" name="thresh_net_charge" type="integer" value="4"/>
+    <param label="Maximum Length" name="thresh_size" type="integer" value="100"/>
+    <param label="Minimum Charge to Length Ratio" name="thresh_charge_ratio" type="float" value="0.25"/>
+    <param type="select" label="Type of selection criteria" name="selection_criteria">
+      <option value="net">Net charge</option>
+      <option value="ratio">Ratio of charged residues to sequence length</option>
+      <option value="both" selected="true">Both net charge and ratio</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="output"/>
+  </outputs>
+  <help><![CDATA[
+**What it does**
+This program finds proteins sequences based on given selection criteria: net charge, sequence length, 
+and/or number of charged residues per amino acid. Inputs include a multi fasta file of protein sequences,
+thresholds for size, charge, and charge-to-size ratio criteria.
+
+This tool returns the selected sequences in a fasta format.
+
+        ]]></help>
+  <citations>
+    <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+    <citation type="bibtex">
+      @unpublished{galaxyTools, 
+          author = {A. Holt},
+          title = {CPT Galaxy Tools},
+          year = {2020},
+          note = {https://github.com/tamu-cpt/galaxy-tools/}
+      }
+      </citation>
+  </citations>
+</tool>