# HG changeset patch
# User recetox
# Date 1718697195 0
# Node ID cba7123c27413e2d09927d72486099f3a6890302
# Parent  d5633eaf355248ae831b93c4ab26a8dfbba22e52
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xtb commit 070a3fd9e44e71efcf7a4490d91d1cee5a4711ce

diff -r d5633eaf3552 -r cba7123c2741 test-data/initial_mol.xyz
--- a/test-data/initial_mol.xyz	Thu Oct 12 13:45:50 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-24
-
-O         -3.17218       -0.41637        0.20834
-C         -1.92531        0.00835       -0.27726
-C         -3.36523       -1.11584        1.43352
-C         -1.88297        0.68848       -1.50133
-C         -0.72594       -0.22648        0.42416
-O         -3.06572        0.92326       -2.20069
-C         -0.65923        1.13249       -2.01579
-C          0.50769        0.20309       -0.09384
-C          0.52725        0.89747       -1.31842
-C          1.73873       -0.06269        0.69160
-C          2.97242       -0.05540        0.17293
-C          4.16274       -0.34771        1.02917
-H         -2.81699       -2.08136        1.41259
-H         -3.01686       -0.49574        2.28636
-H         -4.44664       -1.32462        1.56502
-H         -0.74440       -0.75083        1.37062
-H         -3.06924        1.41308       -3.08782
-H         -0.62733        1.66802       -2.95623
-H          1.44772        1.28256       -1.73388
-H          1.62368       -0.31644        1.73996
-H          3.14017        0.13488       -0.87802
-H          4.23889        0.40538        1.84179
-H          5.08665       -0.30659        0.41501
-H          4.07211       -1.36208        1.47220
diff -r d5633eaf3552 -r cba7123c2741 test-data/initial_mol_molname.xyz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/initial_mol_molname.xyz	Tue Jun 18 07:53:15 2024 +0000
@@ -0,0 +1,26 @@
+24
+Benzophenone
+O         -3.17218       -0.41637        0.20834
+C         -1.92531        0.00835       -0.27726
+C         -3.36523       -1.11584        1.43352
+C         -1.88297        0.68848       -1.50133
+C         -0.72594       -0.22648        0.42416
+O         -3.06572        0.92326       -2.20069
+C         -0.65923        1.13249       -2.01579
+C          0.50769        0.20309       -0.09384
+C          0.52725        0.89747       -1.31842
+C          1.73873       -0.06269        0.69160
+C          2.97242       -0.05540        0.17293
+C          4.16274       -0.34771        1.02917
+H         -2.81699       -2.08136        1.41259
+H         -3.01686       -0.49574        2.28636
+H         -4.44664       -1.32462        1.56502
+H         -0.74440       -0.75083        1.37062
+H         -3.06924        1.41308       -3.08782
+H         -0.62733        1.66802       -2.95623
+H          1.44772        1.28256       -1.73388
+H          1.62368       -0.31644        1.73996
+H          3.14017        0.13488       -0.87802
+H          4.23889        0.40538        1.84179
+H          5.08665       -0.30659        0.41501
+H          4.07211       -1.36208        1.47220
diff -r d5633eaf3552 -r cba7123c2741 test-data/initial_mol_no_molname.xyz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/initial_mol_no_molname.xyz	Tue Jun 18 07:53:15 2024 +0000
@@ -0,0 +1,26 @@
+24
+
+O         -3.17218       -0.41637        0.20834
+C         -1.92531        0.00835       -0.27726
+C         -3.36523       -1.11584        1.43352
+C         -1.88297        0.68848       -1.50133
+C         -0.72594       -0.22648        0.42416
+O         -3.06572        0.92326       -2.20069
+C         -0.65923        1.13249       -2.01579
+C          0.50769        0.20309       -0.09384
+C          0.52725        0.89747       -1.31842
+C          1.73873       -0.06269        0.69160
+C          2.97242       -0.05540        0.17293
+C          4.16274       -0.34771        1.02917
+H         -2.81699       -2.08136        1.41259
+H         -3.01686       -0.49574        2.28636
+H         -4.44664       -1.32462        1.56502
+H         -0.74440       -0.75083        1.37062
+H         -3.06924        1.41308       -3.08782
+H         -0.62733        1.66802       -2.95623
+H          1.44772        1.28256       -1.73388
+H          1.62368       -0.31644        1.73996
+H          3.14017        0.13488       -0.87802
+H          4.23889        0.40538        1.84179
+H          5.08665       -0.30659        0.41501
+H          4.07211       -1.36208        1.47220
diff -r d5633eaf3552 -r cba7123c2741 xtb_molecular_optimization.xml
--- a/xtb_molecular_optimization.xml	Thu Oct 12 13:45:50 2023 +0000
+++ b/xtb_molecular_optimization.xml	Tue Jun 18 07:53:15 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>Semiempirical quantum mechanical molecular optimization method</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,18 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '${coordinates}' 'mol.${coordinates.ext}' &&
         xtb 'mol.${coordinates.ext}' --opt '${opt_level}' && 
-        cp 'xtbopt.${coordinates.ext}' '${output}'
+
+        #if $replace_second_line == "FALSE":
+        cp  'xtbopt.${coordinates.ext}' '${output}'
+        #end if
+
+        #if $replace_second_line == "TRUE":
+        cp  'xtbopt.${coordinates.ext}' '${output}' &&
+        awk 'NR==FNR{if(NR==2) line=$0; next} {if(FNR==2) print line; else print $0}' '${coordinates}' '${output}' > final &&
+        mv final '${output}'
+        #end if
+
+
     ]]></command>
     <inputs>
         <param label="Atomic coordinates file" type="data" name="coordinates" format="xyz" help="Initial atomic coordinates file to be optimized."/>
@@ -24,29 +35,48 @@
             <option value="vtight">vtight</option>
             <option value="extreme">extreme</option>
         </param>
+        <param type="boolean" name="replace_second_line" label = "Keep molecule name" truevalue="TRUE" falsevalue="FALSE" checked="false" help = "If YES, the molecule name from the coordinates file is preserved, if it exists. Otherwise, the energy, gnorm, and xtb version are printed." />
     </inputs>
     <outputs>
         <data name="output" format_source="coordinates"  />
     </outputs>
     <tests>
         <test>
-            <param name="coordinates" value="initial_mol.xyz" ftype="xyz"/>
+            <param name="coordinates" value="initial_mol_molname.xyz" ftype="xyz"/>
+            <param name="replace_second_line" value="TRUE" />
             <output name="output">
                 <assert_contents>
-                    <has_text text="xtb"/>
-                    <has_n_lines n="26"/> 
+                    <has_text text="Benzophenone"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="coordinates" value="initial_mol_molname.xyz" ftype="xyz"/>
+            <param name="replace_second_line" value="FALSE" />
+            <output name="output">
+                <assert_contents>
+                    <has_text text="energy"/>
                 </assert_contents>
             </output>
         </test>
-        <!-- <test>
-            <param name="coordinates" value="initial_mol.coord" ftype="coord"/>
-            <output name="output" file="optimized_mol.coord" ftype="coord">
+        <test>
+            <param name="coordinates" value="initial_mol_no_molname.xyz" ftype="xyz"/>
+            <param name="replace_second_line" value="TRUE" />
+            <output name="output">
                 <assert_contents>
-                    <has_text text="$coord"/>
-                    <has_n_lines min="26"/> 
+                    <not_has_text text="energy"/>
                 </assert_contents>
             </output>
-        </test> -->
+        </test>
+        <test>
+            <param name="coordinates" value="initial_mol_no_molname.xyz" ftype="xyz"/>
+            <param name="replace_second_line" value="FALSE" />
+            <output name="output">
+                <assert_contents>
+                    <has_text text="energy"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests> 
     <help>
         <![CDATA[