Mercurial > repos > chemteam > gmx_merge_topology_files

diff merge_top.xml @ 0:33ed3c26b8c2 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
author chemteam
date Thu, 28 Mar 2019 10:12:00 -0400
parents
children f2faba46d680
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_top.xml	Thu Mar 28 10:12:00 2019 -0400
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+<tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="0.1.0">
+    <description>for example, for protein and ligand files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$top_input' ./top_input.top &&
+        #for $itp_input in $itp_inputs
+            ln -s '$itp_input' ./$itp_input.element_identifier &&
+            echo '$itp_input.element_identifier' >> ./itps.txt &&
+        #end for
+
+        python '$__tool_directory__/merge_top.py' top_input.top itps.txt
+    ]]></command>
+    <inputs>
+        <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
+        <param argument="itp_inputs" type="data" format='itp' multiple="true" label="Position restraint file"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="top" from_work_dir="top_output.top"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="top_input" value="topol.top" />
+            <param name="itp_inputs" value="posres.itp" />
+            <output name="output" file="top_output.top" ftype="top" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Use this tool to combine GROMACS topologies - for example, the topology files for a ligand and protein.
+    ]]></help>
+    <expand macro="citations" />
+</tool>