diff ramachandran_plots.xml @ 0:d710c7f00ae6 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ramachandran_plots.xml	Wed Apr 03 15:46:32 2019 -0400
@@ -0,0 +1,193 @@
+<tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="0.1.3">
+    <description>Calculate and plot the distribution of two diheadrals in a trajectory</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.2.1">scipy</requirement>
+        <requirement type="package" version="0.9.0">seaborn</requirement>
+        <requirement type="package" version="1.0.5">nbdime</requirement>
+    </expand>
+    <command detect_errors="exit_code">
+<![CDATA[
+    python '$__tool_directory__/ramachandran_plots.py'
+        --idcd '$dcdin' 
+        --ipdb '$pdbin'
+        --isegid1  '$phi.segid1'
+        --iresid1  '$phi.resid1' 
+        --iname1   '$phi.name1'
+        --isegid2  '$phi.segid2'
+        --iresid2  '$phi.resid2' 
+        --iname2   '$phi.name2'
+        --isegid3  '$phi.segid3'
+        --iresid3  '$phi.resid3' 
+        --iname3   '$phi.name3'
+        --isegid4  '$phi.segid4'
+        --iresid4  '$phi.resid4' 
+        --iname4   '$phi.name4'
+        --isegid5  '$psi.segid1'
+        --iresid5  '$psi.resid1' 
+        --iname5   '$psi.name1'
+        --isegid6  '$psi.segid2'
+        --iresid6  '$psi.resid2' 
+        --iname6   '$psi.name2' 
+        --isegid7  '$psi.segid3' 
+        --iresid7  '$psi.resid3' 
+        --iname7   '$psi.name3' 
+        --isegid8  '$psi.segid4' 
+        --iresid8  '$psi.resid4' 
+        --iname8   '$psi.name4' 
+        --output   '$output'  
+        --oramachandran_plot '$ramachandran_plot'
+    2>&1
+]]></command>
+    <inputs>
+        <expand macro="analysis_inputs"/>
+        <section name="phi" title="Phi" expanded="False">
+          <param name="segid1"  type="text" value="HET" label="Segid of atom 1">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="resid1"  type="text" value="3" label="Resid of atom 1">
+            <expand macro="sanitizer_resids"/>
+          </param>
+          <param name="name1"  type="text" value="O5" label="Atom name of atom 1">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="segid2"  type="text" value="HET" label="Segid of atom 2">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="resid2"  type="text" value="3" label="Resid of atom 2">
+            <expand macro="sanitizer_resids"/>
+          </param>
+          <param name="name2"  type="text" value="C1" label="Atom name of atom 2">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="segid3"  type="text" value="HET" label="Segid of atom 3">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="resid3"  type="text" value="2" label="Resid of atom 3">
+            <expand macro="sanitizer_resids"/>
+          </param>
+          <param name="name3"  type="text" value="O4" label="Atom name of atom 3">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="segid4"  type="text" value="HET" label="Segid of atom 4">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="resid4"  type="text" value="2" label="Resid of atom 4">
+            <expand macro="sanitizer_resids"/>
+          </param>
+          <param name="name4"  type="text" value="C4" label="Atom name of atom 4">
+            <expand macro="sanitizer"/>
+          </param>
+        </section>
+        <section name="psi" title="Psi" expanded="False">
+          <param name="segid1"  type="text" value="HET" label="Segid of atom 1">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="resid1"  type="text" value="3" label="Resid of atom 1">
+            <expand macro="sanitizer_resids"/>
+          </param>
+          <param name="name1"  type="text" value="C1" label="Atom name of atom 1">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="segid2"  type="text" value="HET" label="Segid of atom 2">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="resid2"  type="text" value="2" label="Resid of atom 2">
+            <expand macro="sanitizer_resids"/>
+          </param>
+          <param name="name2"  type="text" value="O4" label="Atom name of atom 2">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="segid3"  type="text" value="HET" label="Segid of atom 3">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="resid3"  type="text" value="2" label="Resid of atom 3">
+            <expand macro="sanitizer_resids"/>
+          </param>
+          <param name="name3"  type="text" value="C4" label="Atom name of atom 3">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="segid4"  type="text" value="HET" label="Segid of atom 4">
+            <expand macro="sanitizer"/>
+          </param>
+          <param name="resid4"  type="text" value="2" label="Resid of atom 4">
+            <expand macro="sanitizer_resids"/>
+          </param>
+          <param name="name4"  type="text" value="C3" label="Atom name of atom 4">
+            <expand macro="sanitizer"/>
+          </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="Ramachandran Plot raw data"/>
+        <data format="png" name="ramachandran_plot" label="Ramachandran Plot"/>
+    </outputs>
+    <tests>
+        <test>
+            <expand macro="tests_inputs"/>
+            <param name="phi.segid1" value="HET"/>
+            <param name="phi.resid1" value="3"/>
+            <param name="phi.name1" value="O5"/>
+            <param name="phi.segid2" value="HET"/>
+            <param name="phi.resid2" value="3"/>
+            <param name="phi.name2" value="C1"/>
+            <param name="phi.segid3" value="HET"/>
+            <param name="phi.resid3" value="2"/>
+            <param name="phi.name3" value="O4"/>
+            <param name="phi.segid4" value="HET"/>
+            <param name="phi.resid4" value="2"/>
+            <param name="phi.name4" value="C4"/>
+            <param name="psi.segid1" value="HET"/>
+            <param name="psi.resid1" value="3"/>
+            <param name="psi.name1" value="C1"/>
+            <param name="psi.segid2" value="HET"/>
+            <param name="psi.resid2" value="2"/>
+            <param name="psi.name2" value="O4"/>
+            <param name="psi.segid3" value="HET"/>
+            <param name="psi.resid3" value="2"/>
+            <param name="psi.name3" value="C4"/>
+            <param name="psi.segid4" value="HET"/>
+            <param name="psi.resid4" value="2"/>
+            <param name="psi.name4" value="C3"/>
+            <output name="output" file="Ramachandran_Plot_raw_data.tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+        
+A Ramachandran plot ([φ,ψ] plot), originally developed as a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid.
+This can be also used to calculate glycosidic φ and ψ angles formed between carbohydrates. This tool can calculate and plot the histogram (ramachandran plot) of user define φ and ψ angles of a trajectory. 
+
+  - For protien φ and ψ diheadral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html.
+ 
+  - For glycan φ and ψ diheadral definitions see http://www.glycanstructure.org/
+
+_____
+
+
+.. class:: infomark
+
+**Input**
+
+       - Trajectory file  (DCD).
+       - PDB file.
+       - Segids, resids and names of the four atoms to calculate diheadrals.
+     
+_____
+
+        
+.. class:: infomark
+
+**Output**
+
+       - Tab-separated file of raw data of the φ,ψ angles time series.
+       - Image (as png) of the Ramachandran Plot.
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>