diff end-to-end.xml @ 0:78aa3659fcd1 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/end-to-end.xml	Mon Aug 24 16:47:23 2020 -0400
@@ -0,0 +1,91 @@
+<tool id="mdanalysis_endtoend" name="End-to-End Analysis" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>- End-to-End distance timeseries and histogram for the given selections</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+<![CDATA[
+    python '$__tool_directory__/end-to-end.py'
+        --itraj '$trajin'
+        --istr '$strin'
+        --itrajext '$trajin.ext'
+        --istrext '$strin.ext'
+        --isegid1 '$segid1'
+        --ilabel '$label1'
+        --ititle1 '$title1'
+        --output1 '$output1'
+        --o_plot '$o_plot'
+    2>&1
+]]></command>
+    <inputs>
+        <expand macro="analysis_inputs"/>
+        <param name="segid1" type="text" value="PROA" label="Segment ID of the protein" help="A valid segment ID selection for the current molecular system">
+            <validator type="regex" message="Maximum of 8 characters allowed.">^[a-zA-Z0-9]{1,8}$</validator>
+        </param>
+        <param name="label1" type="text" value="N-C" label="Data series label">
+            <validator type="regex" message="Maximum of 8 characters allowed.">^[a-zA-Z0-9\- ]{1,8}$</validator>
+        </param>
+        <param name="title1" type="text" value="End-to-End timeseries and histogram" label="Plot title" help="Plot title, to be included in image output">
+            <validator type="regex" message="Maximum of 36 characters allowed.">^[a-zA-Z0-9\- ]{1,36}$</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output1" label="timeseries raw data"/>
+        <data format="png" name="o_plot" label="End-to-End Timeseries and Histogram Plot"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="trajin" value="test.dcd" ftype="dcd"/>
+            <param name="strin" value="test.pdb" ftype="pdb"/>
+            <param name="segid1" value="PRO"/>
+            <output name="output1">
+                <assert_contents>
+                    <has_text text="3.921"/>
+                    <has_text text="3.938"/>
+                </assert_contents>
+            </output>
+            <output name="o_plot">
+                <assert_contents>
+                    <has_size value="39991" delta="3000"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+.. class:: infomark
+
+**What it does**
+
+End-to-End distance timeseries and histogram for proteins. The termini are chosen as ends with the N atom of the N-terminus and the C atom of the C-terminus chosen.
+
+_____
+
+
+.. class:: infomark
+
+**Input**
+
+       - Trajectory file (DCD).
+       - PDB file.
+       - Segment ID for the protein
+       - Graph series label and title
+
+Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
+
+_____
+
+
+.. class:: infomark
+
+**Output**
+
+       - Tab-separated file of timeseries raw data
+       - Image (as png) of the end-to-end timeseries and histogram
+
+    ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>