| Previous changeset 0:d5633eaf3552 (2023-10-12) Next changeset 2:6e1ef071fffc (2024-07-25) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xtb commit 070a3fd9e44e71efcf7a4490d91d1cee5a4711ce |
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modified:
xtb_molecular_optimization.xml |
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added:
test-data/initial_mol_molname.xyz test-data/initial_mol_no_molname.xyz |
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removed:
test-data/initial_mol.xyz |
| b |
| 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 |
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| @@ -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 |
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| 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 |
| b |
| @@ -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 |
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| 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 |
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| @@ -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 |
| b |
| 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[ |