Mercurial > repos > recetox > filter_compounds

comparison filter_compounds.xml @ 1:686850eb1e64 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:21:21 +0000
parents 987357c6941c
children 8eb6e392c92b
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0:987357c6941c 1:686850eb1e64
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism--> 3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <token name="@GALAXY_VERSION@">0</token> 6 <token name="@GALAXY_VERSION@">0</token>
7 </macros> 7 </macros>
8 <expand macro="creator"/>
8 <expand macro="requirements"/> 9 <expand macro="requirements"/>
9 <command detect_errors="aggressive"> 10 <command detect_errors="aggressive">
10 <![CDATA[ 11 <![CDATA[
11 python '$__tool_directory__/filter_compounds.py' 12 python '$__tool_directory__/filter_compounds.py'
12 -i '${infile}' 13 -i '${infile}'
13 -o '${outfile}' 14 -o '${outfile}'
14 $metorg 15 $metorg
15 $anorg 16 $anorg
16 ]]> 17 ]]>
17 </command> 18 </command>
18 <inputs> 19 <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="infile" type="data" format="smi" label="Select input file"
20 <param name="metorg" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Filter out organometallic compounds?" /> 21 help="Currently only SMILES identifiers are allowed as an input."/>
21 <param name="anorg" type="boolean" checked="false" truevalue="-a" falsevalue="" label="Filter out anorganic compounds?" /> 22 <param name="metorg" type="boolean" checked="false" truevalue="-m" falsevalue=""
23 label="Filter out organometallic compounds?"/>
24 <param name="anorg" type="boolean" checked="false" truevalue="-a" falsevalue=""
25 label="Filter out anorganic compounds?"/>
22 </inputs> 26 </inputs>
23 <outputs> 27 <outputs>
24 <data format="smi" name="outfile"/> 28 <data format="smi" name="outfile"/>
25 </outputs> 29 </outputs>
26 <tests> 30 <tests>
27 <test> 31 <test>
28 <param name="infile" ftype="smi" value="input_all.smi"/> 32 <param name="infile" ftype="smi" value="input_all.smi"/>
29 <param name="metorg" value="true"/> 33 <param name="metorg" value="true"/>
30 <param name="anorg" value="true"/> 34 <param name="anorg" value="true"/>
31 <output name="outfile" ftype="smi" file="output_all.smi" /> 35 <output name="outfile" ftype="smi" file="output_all.smi"/>
32 </test> 36 </test>
33 <test> 37 <test>
34 <param name="infile" ftype="smi" value="input_all_table.smi"/> 38 <param name="infile" ftype="smi" value="input_all_table.smi"/>
35 <param name="metorg" value="true"/> 39 <param name="metorg" value="true"/>
36 <param name="anorg" value="true"/> 40 <param name="anorg" value="true"/>
37 <output name="outfile" ftype="smi" file="output_all_table.smi" /> 41 <output name="outfile" ftype="smi" file="output_all_table.smi"/>
38 </test> 42 </test>
39 </tests> 43 </tests>
40 <help> 44 <help>
41 <![CDATA[ 45 <![CDATA[
42 46 @HELP@
43 .. class:: infomark 47 ]]>
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> 48 </help>
51 </tool> 49 </tool>
52 50