Mercurial > repos > tduigou > molecule_signature_enumerate
changeset 0:3244fa368e7c draft
planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
| author | tduigou |
|---|---|
| date | Fri, 07 Feb 2025 10:33:51 +0000 |
| parents | |
| children | 2ed696bb6a6b |
| files | enumerate.xml macros.xml test-data/alphabet.npz test-data/enumerate.tsv test-data/signature.tsv |
| diffstat | 5 files changed, 66 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/enumerate.xml Fri Feb 07 10:33:51 2025 +0000 @@ -0,0 +1,37 @@ +<tool id="molecule_signature_enumerate" name="Molecule Signature Enumerate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT"> + <description>Enumerate Molecules from a ECFP fingerprint</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + cp '$input_alphabet_npz' 'alphabet.npz' && + molsig enumerate + --smiles '$input_smiles_str' + --alphabet 'alphabet.npz' + --output '$output_enumerate_tsv' + ]]></command> + <inputs> + <param name="input_smiles_str" type="text" label="SMILES of the molecule" /> + <param name="input_alphabet_npz" type="data" format="npz" label="Alphabet file" /> + </inputs> + <outputs> + <data name="output_enumerate_tsv" format="tabular" label="${tool.name}" /> + </outputs> + <tests> + <test> + <param name="input_smiles_str" value="CCO" /> + <param name="input_alphabet_npz" value="alphabet.npz" /> + <output name="output_enumerate_tsv" value="enumerate.tsv" ftype="tabular" compare="diff" /> + </test> + </tests> + <help><![CDATA[ +Enumerate Molecules +=================== +Enumerate Molecules from a ECFP fingerprint + +Note: Alphabet is available at `10.5281/zenodo.14760991 <https://zenodo.org/records/14760992>`_. +]]></help> + <expand macro="creator"/> + <expand macro="citation"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 07 10:33:51 2025 +0000 @@ -0,0 +1,26 @@ +<macros> + <token name="@TOOL_VERSION@">2.1.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">molecule-signature</requirement> + <yield/> + </requirements> + </xml> + <xml name="citation"> + <citations> + <citation type="bibtex"> + @unpublished{MoleculeSignature, + author = {Philippe Meyer, Thomas Duigou, Guillaume Gricourt, Jean-Loup Faulon}, + title = {{MoleculeSignature}}, + url = {https://github.com/brsynth/molecule-signature}, + } + </citation> + </citations> + </xml> + <xml name="creator"> + <creator> + <organization name="BioRetroSynth" url="https://github.com/brsynth"/> + </creator> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/enumerate.tsv Fri Feb 07 10:33:51 2025 +0000 @@ -0,0 +1,1 @@ +SMILES
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/signature.tsv Fri Feb 07 10:33:51 2025 +0000 @@ -0,0 +1,2 @@ +SMILES signature +CCO 80-1410 ## [C;H3;h3;D1;X4]-[C;H2;h2;D2;X4:1]-[O;H1;h1;D1;X2] .. 807-222 ## [C;H3;h3;D1;X4]-[C;H2;h2;D2;X4]-[O;H1;h1;D1;X2:1] .. 1057-294 ## [O;H1;h1;D1;X2]-[C;H2;h2;D2;X4]-[C;H3;h3;D1;X4:1]