comparison ob_remIons.xml @ 14:4e3b2049a4d3 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author bgruening
date Tue, 10 Nov 2020 20:32:05 +0000
parents 3153b6f3087c
children
comparison
equal deleted inserted replaced
13:3153b6f3087c 14:4e3b2049a4d3
1 <tool id="openbabel_remIons" name="Remove counterions and fragments" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="openbabel_remIons" name="Remove counterions and fragments" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>from a library of compounds</description> 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--> 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@">1</token> 6 <token name="@GALAXY_VERSION@">2</token>
7 </macros> 7 </macros>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <command detect_errors="aggressive"> 9 <command detect_errors="aggressive">
10 <![CDATA[ 10 <![CDATA[
11 python '$__tool_directory__/ob_remIons.py' 11 python '$__tool_directory__/ob_remIons.py'
12 -i '${infile}' 12 -i '${infile}'
13 -iformat '${infile.ext}' 13 -iformat '${infile.ext}'
14 -o '${outfile}' 14 -o '${outfile}'
15 $index
15 ]]> 16 ]]>
16 </command> 17 </command>
17 <inputs> 18 <inputs>
18 <expand macro="infile_all_types"/> 19 <expand macro="infile_all_types"/>
20 <param name="index" type="boolean" checked="false" truevalue="-idx" falsevalue="" label="Output indexed tab-separated table?" help="Add an index column to the output file. This option will work only when input format is InChI or SMILES, otherwise it will be ignored." />
19 </inputs> 21 </inputs>
20 <outputs> 22 <outputs>
21 <expand macro="output_like_input"/> 23 <expand macro="output_like_input"/>
22 </outputs> 24 </outputs>
23 <tests> 25 <tests>
26 <output name="outfile" ftype="smi" file="obrmions_on_2_mol.smi" /> 28 <output name="outfile" ftype="smi" file="obrmions_on_2_mol.smi" />
27 </test> 29 </test>
28 <test> 30 <test>
29 <param name="infile" ftype="inchi" value="na-sal.inchi"/> 31 <param name="infile" ftype="inchi" value="na-sal.inchi"/>
30 <output name="outfile" ftype="inchi" file="na-sal_obrmions.inchi" /> 32 <output name="outfile" ftype="inchi" file="na-sal_obrmions.inchi" />
33 </test>
34 <test>
35 <param name="infile" ftype="inchi" value="multiple.inchi"/>
36 <param name="index" value="true"/>
37 <output name="outfile" ftype="inchi" file="multiple_obrmions.inchi" />
31 </test> 38 </test>
32 </tests> 39 </tests>
33 <help> 40 <help>
34 <![CDATA[ 41 <![CDATA[
35 42