diff PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.xml @ 0:0118cc553f3b draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.xml	Wed Oct 28 02:04:41 2020 +0000
@@ -0,0 +1,71 @@
+<tool id="pdaug_peptide_structure_builder" name="PDAUG Peptide Structure Builder" version="0.1.0">
+  <description>Builds 3D structures of peptide sequences up to 3 amino acid </description>
+
+  <requirements>
+    <requirement type="package" version="0.24.2">pandas</requirement>
+    <requirement type="package" version="1.0.1">fragbuilder</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1" level="fatal" />
+  </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/PDAUG_Peptide_Structure_Builder.py' -p '$input1'  
+
+    ]]></command>
+
+  <inputs>
+    <param name="input1" type="data" format="fasta" argument= "--pep" label="Input file" help="Input fasta file with peptides"/>
+  </inputs>
+
+  <outputs>
+    <collection name="output" type="list" label="${tool.name} on $on_string - (PDB)">
+        <discover_datasets pattern="__name_and_ext__" format='pdb' directory="DataFile" />
+    </collection>
+  </outputs>  
+
+  <tests>
+    <test>
+      <param name="input1" value="test.fasta"/>
+      <output_collection name="output" type="list"  >
+        <element name="GLF" file="DataFile/GLF.pdb" lines_diff="102" />
+      </output_collection>
+    </test>
+  </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+This tool generates 3D structures of peptide sequences up to three amino acids that can be utilized for peptide docking with macromolecules with tools such as Autodock Vina. 
+
+-----
+
+**Inputs**
+    * **--InFile** A fasta file witth the peptide sequences.
+
+-----
+
+**Outputs**
+    * Return collection of peptides with 3D structure.]]></help>
+<citations>
+  <citation type="bibtex">
+    @misc{PDAUGGITHUB, 
+      author = {Joshi, Jayadev  and Blankenberg, Daniel}, 
+      year = {2020}, 
+      title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, 
+      publisher = {GitHub}, 
+      journal = {GitHub repository}, 
+      url =
+      {https://github.com/jaidevjoshi83/pdaug.git}, 
+    }
+</citation>
+
+<citation type="bibtex">
+    @article{christensen_hamelryck_jensen_2013, 
+      title={FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models}, DOI={10.7287/peerj.preprints.169v2}, 
+      author={Christensen, Anders Steen and Hamelryck, Thomas and Jensen, Jan H}, 
+      year={2013}}
+        }
+  </citation>
+</citations>
+</tool>