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comparison filter_compounds.xml @ 0:987357c6941c draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit ad6ca51c5fee52d533cfd6b8ccef5e44027ed298"
author recetox
date Thu, 07 Jan 2021 11:30:13 +0000
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children 686850eb1e64
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-1:000000000000 0:987357c6941c
1 <tool id="filter_orgmet_anorg" name="Filter organometallics and/or anorganics" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>from a library of compounds</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <macros>
5 <import>macros.xml</import>
6 <token name="@GALAXY_VERSION@">0</token>
7 </macros>
8 <expand macro="requirements"/>
9 <command detect_errors="aggressive">
10 <![CDATA[
11 python '$__tool_directory__/filter_compounds.py'
12 -i '${infile}'
13 -o '${outfile}'
14 $metorg
15 $anorg
16 ]]>
17 </command>
18 <inputs>
19 <param name="infile" type="data" format="smi" label="Select input file" help="Currently only SMILES identifiers are allowed as an input."/>
20 <param name="metorg" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Filter out organometallic compounds?" />
21 <param name="anorg" type="boolean" checked="false" truevalue="-a" falsevalue="" label="Filter out anorganic compounds?" />
22 </inputs>
23 <outputs>
24 <data format="smi" name="outfile"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="infile" ftype="smi" value="input_all.smi"/>
29 <param name="metorg" value="true"/>
30 <param name="anorg" value="true"/>
31 <output name="outfile" ftype="smi" file="output_all.smi" />
32 </test>
33 <test>
34 <param name="infile" ftype="smi" value="input_all_table.smi"/>
35 <param name="metorg" value="true"/>
36 <param name="anorg" value="true"/>
37 <output name="outfile" ftype="smi" file="output_all_table.smi" />
38 </test>
39 </tests>
40 <help>
41 <![CDATA[
42
43 .. class:: infomark
44
45 **What this tool does**
46
47 Filters organometallics (compounds containing atoms other than C|N|O|P|F|S|I|B|Si|Se|Cl|Br|Li|Na|H|K) or anorganics (compounds without C). Input can be either list of SMILES identifiers or indexed table of SMILES (two tab-separated columns, first column is index, second columns is SMILES).
48
49 ]]>
50 </help>
51 </tool>
52