Mercurial > repos > tduigou > molecule_signature_enumerate

annotate enumerate.xml @ 3:cda3af74acca draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth/molecule-signature commit f9e708319991416e6931e9acd5619c472f3d3792
author tduigou
date Fri, 14 Feb 2025 16:03:22 +0000
parents 35c07741031b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
1 <tool id="molecule_signature_enumerate" name="Molecule Signature Enumerate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT">
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
2 <description>Enumerate Molecules from a ECFP fingerprint</description>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
3 <macros>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
4 <import>macros.xml</import>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
5 </macros>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
6 <expand macro="requirements"/>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
8 cp '$input_alphabet_npz' 'alphabet.npz' &&
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
9 molsig enumerate
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
10 --smiles '$input_smiles_str'
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
11 --alphabet 'alphabet.npz'
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
12 --output '$output_enumerate_tsv'
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
13 ]]></command>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
14 <inputs>
1
2ed696bb6a6b planemo upload for repository https://github.com/brsynth/molecule-signature commit 23ed4c204be0ab50a03cbde02f1e1e2b83531965
tduigou
parents: 0
diff changeset
15 <param name="input_smiles_str" type="text" label="SMILES of the molecule">
3
cda3af74acca planemo upload for repository https://github.com/brsynth/molecule-signature commit f9e708319991416e6931e9acd5619c472f3d3792
tduigou
parents: 2
diff changeset
16 <validator type="empty_field" message="You must provide the SMILES string" />
2
35c07741031b planemo upload for repository https://github.com/brsynth/molecule-signature commit b64a61400688127dfce11f04952a368cfe2b900c
tduigou
parents: 1
diff changeset
17 <validator type="regex" message="Wildcards are not allowed">^[^*?]*$</validator>
1
2ed696bb6a6b planemo upload for repository https://github.com/brsynth/molecule-signature commit 23ed4c204be0ab50a03cbde02f1e1e2b83531965
tduigou
parents: 0
diff changeset
18 <sanitizer sanitize="false" />
2ed696bb6a6b planemo upload for repository https://github.com/brsynth/molecule-signature commit 23ed4c204be0ab50a03cbde02f1e1e2b83531965
tduigou
parents: 0
diff changeset
19 </param>
0
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
20 <param name="input_alphabet_npz" type="data" format="npz" label="Alphabet file" />
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
21 </inputs>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
22 <outputs>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
23 <data name="output_enumerate_tsv" format="tabular" label="${tool.name}" />
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
24 </outputs>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
25 <tests>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
26 <test>
1
2ed696bb6a6b planemo upload for repository https://github.com/brsynth/molecule-signature commit 23ed4c204be0ab50a03cbde02f1e1e2b83531965
tduigou
parents: 0
diff changeset
27 <param name="input_smiles_str" value="C=C1CC[C@H]2[C@]3(C)CC[C@H]4C(C)(C)CCC[C@]4(C)[C@H]3CC[C@]2(C)[C@H]1CO" />
0
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
28 <param name="input_alphabet_npz" value="alphabet.npz" />
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
29 <output name="output_enumerate_tsv" value="enumerate.tsv" ftype="tabular" compare="diff" />
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
30 </test>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
31 </tests>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
32 <help><![CDATA[
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
33 Enumerate Molecules
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
34 ===================
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
35 Enumerate Molecules from a ECFP fingerprint
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
36
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
37 Note: Alphabet is available at `10.5281/zenodo.14760991 <https://zenodo.org/records/14760992>`_.
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
38 ]]></help>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
39 <expand macro="creator"/>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
40 <expand macro="citation"/>
3244fa368e7c planemo upload for repository https://github.com/brsynth/molecule-signature commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
tduigou
parents:
diff changeset
41 </tool>