Mercurial > repos > bgruening > openbabel_compound_convert
changeset 7:76254bc453a5 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
| author | bgruening |
|---|---|
| date | Tue, 07 May 2019 13:25:48 -0400 |
| parents | 9c76f3bf14af |
| children | e55fdd268109 |
| files | macros.xml ob_convert.xml test-data/2_mol.dat test-data/CO.smarts |
| diffstat | 4 files changed, 43 insertions(+), 44 deletions(-) [+] |
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--- a/macros.xml Mon Sep 03 16:35:54 2018 -0400 +++ b/macros.xml Tue May 07 13:25:48 2019 -0400 @@ -1,9 +1,10 @@ <macros> - <token name="@VERSION@">2.4.1</token> + <token name="@VERSION@">2.4.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.4.1">openbabel</requirement> + <requirement type="package" version="3">python</requirement> <yield /> </requirements> </xml> @@ -37,6 +38,3 @@ </citations> </xml> </macros> - - -
--- a/ob_convert.xml Mon Sep 03 16:35:54 2018 -0400 +++ b/ob_convert.xml Tue May 07 13:25:48 2019 -0400 @@ -1,5 +1,5 @@ -<tool id="openbabel_compound_convert" name="Compound Convert" version="@VERSION@.0"> - <description>Converts various chemistry and molecular modeling data files</description> +<tool id="openbabel_compound_convert" name="Compound conversion" version="@VERSION@.0"> + <description>- interconvert between various chemistry and molecular modeling data files</description> <!--<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> We can't use that currently, because a few output-datatypes, like the fastsearch index do not support merging. We need to patch galaxy to not abort in such a case and run the job in non-multi mode. @@ -220,23 +220,23 @@ <when value="cache" /> <when value="cacint" /> <when value="can"> - <param name="can_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" /> + <param name="can_exp_h" type="boolean" label="Explicitly include hydrogens in output (-xh)" truevalue="-xh" falsevalue="" checked="false" /> <param name="can_iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="-xi" falsevalue="" checked="false" /> - <param name="can_rad" type="boolean" label="Radicals lower case eg ethyl is Cc (-xr)" truevalue="-xr" falsevalue="" checked="false" /> - <param name="can_atomclass_out" type="boolean" label="Output atomclass like [C:2] (-xa)" truevalue="-xa" falsevalue="" checked="false" /> + <param name="can_rad" type="boolean" label="Show radicals in lower case (e.g. ethyl as Cc) (-xr)" truevalue="-xr" falsevalue="" checked="false" /> + <param name="can_atomclass_out" type="boolean" label="Output atomclass (e.g. [C:2]) (-xa)" truevalue="-xa" falsevalue="" checked="false" /> </when> <when value="cdxml" /> <when value="cht" /> <when value="cif" /> <when value="cml"> - <param name="cml_cml1" type="boolean" label="convert to CML 1 (rather than CML 2) (-x1)" truevalue="-x1" falsevalue="" checked="false" /> - <param name="cml_array" type="boolean" label="write array format for atoms and bonds (-xa)" truevalue="-xa" falsevalue="" checked="false" /> - <param name="cml_aromatic" type="boolean" label="write aromatic bonds as such, not Kekule form (-xA)" truevalue="-xA" falsevalue="" checked="false" /> - <param name="cml_hydrogen" type="boolean" label="use hydrogen Count for all hydrogens (-xh)" truevalue="-xh" falsevalue="" checked="false" /> - <param name="cml_metadata" type="boolean" label="write metadata (-xm)" truevalue="-xm" falsevalue="" checked="false" /> - <param name="cml_omit" type="boolean" label="omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" /> - <param name="cml_continuous" type="boolean" label="continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" /> - <param name="cml_properties" type="boolean" label="write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" /> + <param name="cml_cml1" type="boolean" label="Convert to CML 1 (rather than CML 2) (-x1)" truevalue="-x1" falsevalue="" checked="false" /> + <param name="cml_array" type="boolean" label="Write array format for atoms and bonds (-xa)" truevalue="-xa" falsevalue="" checked="false" /> + <param name="cml_aromatic" type="boolean" label="Write aromatic bonds as such, not Kekule form (-xA)" truevalue="-xA" falsevalue="" checked="false" /> + <param name="cml_hydrogen" type="boolean" label="Use hydrogen count for all hydrogens (-xh)" truevalue="-xh" falsevalue="" checked="false" /> + <param name="cml_metadata" type="boolean" label="Write metadata (-xm)" truevalue="-xm" falsevalue="" checked="false" /> + <param name="cml_omit" type="boolean" label="Omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" /> + <param name="cml_continuous" type="boolean" label="Continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" /> + <param name="cml_properties" type="boolean" label="Write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" /> <expand macro="2D_3D_opts" /> </when> <when value="cmlr" /> @@ -259,13 +259,13 @@ <option value="-xfFP4">FP4</option> <option value="-xfMACCS">MACCS</option> </param> - <param name="fpt_fold" type="integer" value="0" label="Fold fingerprint to the number of specifed bits (32, 64, 128, etc.)" help="Use zero for default"> + <param name="fpt_fold" type="integer" value="0" label="Fold fingerprint to the number of specified bits (32, 64, 128, etc.)" help="Use zero for default"> <validator type="in_range" min="0" /> </param> - <param name="fpt_hex_multiple" type="boolean" label="hex output when multiple molecules (-xh)" truevalue="-xh" falsevalue="" checked="false" /> - <param name="fpt_hex" type="boolean" label="hex output only (-xo)" truevalue="-xo" falsevalue="" checked="false" /> - <param name="fpt_set" type="boolean" label="describe each set bit (-xs)" truevalue="-xs" falsevalue="" checked="false" /> - <param name="fpt_unset" type="boolean" label="describe each unset bit (-xu)" truevalue="-xu" falsevalue="" checked="false" /> + <param name="fpt_hex_multiple" type="boolean" label="Hex output when multiple molecules (-xh)" truevalue="-xh" falsevalue="" checked="false" /> + <param name="fpt_hex" type="boolean" label="Hex output only (-xo)" truevalue="-xo" falsevalue="" checked="false" /> + <param name="fpt_set" type="boolean" label="Describe each set bit (-xs)" truevalue="-xs" falsevalue="" checked="false" /> + <param name="fpt_unset" type="boolean" label="Describe each unset bit (-xu)" truevalue="-xu" falsevalue="" checked="false" /> </when> <when value="fract" /> <when value="fs"> @@ -275,7 +275,7 @@ <option value="-xfFP4">FP4</option> <option value="-xfMACCS">MACCS</option> </param> - <param name="fs_fold" type="integer" value="0" label="Fold fingerprint to the number of specifed bits (32, 64, 128, etc.)" help="Use zero for default"> + <param name="fs_fold" type="integer" value="0" label="Fold fingerprint to the number of specified bits (32, 64, 128, etc.)" help="Use zero for default"> <validator type="in_range" min="0" /> </param> </when> @@ -285,11 +285,11 @@ <when value="gr96" /> <when value="hin" /> <when value="inchi"> - <param name="inchi_key" type="boolean" label="output InChIKey only (-xK)" truevalue="-xK" falsevalue="" checked="false" /> - <param name="inchi_name" type="boolean" label="add molecule name after InChI (-xt)" truevalue="-xt" falsevalue="" checked="true" /> - <param name="inchi_unique" type="boolean" label="output only unique molecules (-xu)" truevalue="-xu" falsevalue="" checked="false" /> - <param name="inchi_unique_sort" type="boolean" label="output only unique molecules and sort them (-xU)" truevalue="-xU" falsevalue="" checked="false" /> - <param name="inchi_truncate" type="select" multiple="True" display="checkboxes" label="truncate InChI according to various parameters"> + <param name="inchi_key" type="boolean" label="Output InChIKey only (-xK)" truevalue="-xK" falsevalue="" checked="false" /> + <param name="inchi_name" type="boolean" label="Add molecule name after InChI (-xt)" truevalue="-xt" falsevalue="" checked="true" /> + <param name="inchi_unique" type="boolean" label="Output only unique molecules (-xu)" truevalue="-xu" falsevalue="" checked="false" /> + <param name="inchi_unique_sort" type="boolean" label="Output only unique molecules and sort them (-xU)" truevalue="-xU" falsevalue="" checked="false" /> + <param name="inchi_truncate" type="select" multiple="True" display="checkboxes" label="Truncate InChI according to various parameters"> <option value="/formula">formula only</option> <option value="/connect">formula and connectivity only</option> <option value="/nostereo">ignore E/Z and sp3 stereochemistry</option> @@ -321,7 +321,7 @@ <when value="mmd" /> <when value="mmod" /> <when value="mol2"> - <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands" help="(-xl)" + <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands?" help="(-xl)" truevalue="-xl" falsevalue="" checked="false" /> <expand macro="2D_3D_opts" /> </when> @@ -342,27 +342,27 @@ <when value="rxn" /> <when value="sdf"> <param name="sdf_exp_h" type="boolean" truevalue="-x3" falsevalue="" checked="false" - label="output V3000 not V2000 (used for >999 atoms/bonds)" help="(-x3)" /> + label="Output V3000 not V2000 (used for >999 atoms/bonds)" help="(-x3)" /> <param name="sdf_no_prop" type="boolean" truevalue="-xm" falsevalue="" checked="false" - label="write no properties" help="(-xm)" /> + label="Do not write properties" help="(-xm)" /> <param name="sdf_wedge_bonds" type="boolean" truevalue="-xw" falsevalue="" checked="false" - label="use wedge and hash bonds from input (2D structures only)" help="(-xw)"/> + label="Use wedge and hash bonds from input (2D structures only)" help="(-xw)"/> <param name="sdf_alias_out" type="boolean" truevalue="-xA" falsevalue="" checked="false" - label="output in Alias form, e.g. Ph" help="(-xA)" /> + label="Output in alias form, e.g. Ph for phenyl" help="(-xA)" /> <expand macro="2D_3D_opts" /> </when> <when value="smi"> - <param name="smi_exp_h" type="boolean" label="Output explicit hydrogens as such" help="(-xh)" + <param name="smi_exp_h" type="boolean" label="Explicitly include hydrogens in output" help="(-xh)" truevalue="-xh" falsevalue="" checked="false" /> <param name="smi_iso_chi" type="boolean" label="Do not include isotopic or chiral markings" help="(-xi)" truevalue="-xi" falsevalue="" checked="false" /> - <param name="smi_rad" type="boolean" label="Radicals lower case eg ethyl is Cc" help="(-xr)" truevalue="-xr" + <param name="smi_rad" type="boolean" label="Show radicals in lower case (e.g. ethyl as Cc)" help="(-xr)" truevalue="-xr" falsevalue="" checked="false" /> - <param name="smi_atomclass_out" type="boolean" label="Output atomclass like [C:2]" help="(-xa)" + <param name="smi_atomclass_out" type="boolean" label="Output atomclass (e.g. [C:2])" help="(-xa)" truevalue="-xa" falsevalue="" checked="false" /> <param name="smi_can" type="boolean" label="Output in canonical form" help="(-xc)" truevalue="-xc" falsevalue="" checked="false" /> - <param name="smi_coordinates" type="boolean" label="append X/Y coordinates in canonical-SMILES order" help="(-xx)" + <param name="smi_coordinates" type="boolean" label="Append X/Y coordinates in canonical-SMILES order" help="(-xx)" truevalue="-xx" falsevalue="" checked="false" /> </when> <when value="tdd" /> @@ -380,7 +380,7 @@ <!-- Options for all formats.--> <param name="remove_h" type="boolean" truevalue="-d" falsevalue="" - label="Delete hydrogen atoms, make all hydrogen implicit" help="(-d)" /> + label="Delete hydrogen atoms, make all hydrogens implicit" help="(-d)" /> <param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH" help="-1 means deactivated (-p)"/> <param name="dative_bonds" type="boolean" truevalue="-b" falsevalue="" label="Convert dative bonds" help="e.g. [N+]([O-])=O to N(=O)=O (-b)" /> @@ -391,9 +391,9 @@ <param name="unique_opts_selector" type="select" label="Uniqueness according to"> <option value="" selected="True">No unique filter</option> <option value="inchi">InChI</option> - <option value="cansmi">canonical SMILES with stereochemical information</option> - <option value="cansmiNS">canonical SMILES without stereochemical information</option> - <option value="title">title</option> + <option value="cansmi">Canonical SMILES with stereochemical information</option> + <option value="cansmiNS">Canonical SMILES without stereochemical information</option> + <option value="title">Title</option> </param> <when value="" /> <when value="cansmi" /> @@ -470,9 +470,7 @@ **What this tool does** -The compound converter joins several `Open Babel`_ command prompt converters in an easy to use tool. It converts various chemistry and moleculare modeling data files. -The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) -others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI). +The compound converter combines several Open Babel command prompt converters into a single easy-to-use tool. It interconverts various chemistry and molecular modeling data files. The output format can be specified as well as several parameters. Some parameters are available for all tools (e.g. protonation state and pH) while others are specific for a given output format (e.g. exclude isotopes for conversion to canSMI). -----