Mercurial > repos > chemteam > gmx_energy

changeset 11:58c3e6711e94 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
author chemteam
date Wed, 01 Dec 2021 15:33:31 +0000
parents dae135dfd519
children fdf2cc80adb5
files energy.xml macros.xml
diffstat 2 files changed, 20 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/energy.xml	Tue Nov 30 15:30:43 2021 +0000
+++ b/energy.xml	Wed Dec 01 15:33:31 2021 +0000
@@ -1,7 +1,7 @@
 <tool id="gmx_energy" name="Extract energy components with GROMACS" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">0</token>
+        <token name="@GALAXY_VERSION@">1</token>
     </macros>
 
     <expand macro="requirements" />
@@ -76,17 +76,12 @@
             <option value="xvg">GROMACS XVG format</option>
             <option value="tabular" selected="true">Galaxy tabular</option>
         </param>
-
-    <expand macro="log" />
+        <expand macro="xvg_or_tab" />
+        <expand macro="log" />
 
     </inputs>
     <outputs>
-        <data name="output1" format="xvg" from_work_dir="energy.xvg">
-            <filter>fmt == 'xvg'</filter>
-        </data>
-        <data name="output2" format="tabular" from_work_dir="energy.tabular">
-            <filter>fmt == 'tabular'</filter>
-        </data>
+        <expand macro="xvg_or_tab_outputs" name="energy" label="GROMACS energy components on ${on_string}"/>
         <expand macro="log_outputs" />
     </outputs>
     <tests>
--- a/macros.xml	Tue Nov 30 15:30:43 2021 +0000
+++ b/macros.xml	Wed Dec 01 15:33:31 2021 +0000
@@ -77,6 +77,22 @@
         </data>
     </xml>
 
+    <xml name="xvg_or_tab">
+        <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file.">
+            <option value="xvg">GROMACS XVG format</option>
+            <option value="tabular" selected="true">Galaxy tabular</option>
+        </param>
+    </xml>
+
+    <xml name="xvg_or_tab_outputs" token_name="" token_label="">
+        <data name="output1" format="xvg" from_work_dir="@NAME@.xvg" label="@LABEL@">
+            <filter>fmt == 'xvg'</filter>
+        </data>
+        <data name="output2" format="tabular" from_work_dir="@NAME@.tabular" label="@LABEL@">
+            <filter>fmt == 'tabular'</filter>
+        </data>
+    </xml>
+
     <xml name="test_params">
         <param name="mdpfile" value="default" />
         <param name="step_length" value="0.002"/>