Mercurial > repos > recetox > matchms_formatter

comparison matchms_formatter.xml @ 19:f7718efde4d5 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 19994ff091195ec6c7df791985b2a04ed5aba329
author recetox
date Mon, 04 Dec 2023 13:40:45 +0000
parents 86a45ba3d3f2
children 402620029a7a
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18:86a45ba3d3f2 19:f7718efde4d5
1 <tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy2" profile="21.09"> 1 <tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy3" profile="21.09">
2 <description>reformat scores object of matchms to long format table</description> 2 <description>reformat scores object of matchms to long format table</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>help.xml</import> 6 <import>help.xml</import>
11 </edam_operations> 11 </edam_operations>
12 <expand macro="bio.tools"/> 12 <expand macro="bio.tools"/>
13 13
14 <requirements> 14 <requirements>
15 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> 15 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
16 <requirement type="package" version="8.0.1">click</requirement>
16 <requirement type="package" version="1.1.4">pandas</requirement> 17 <requirement type="package" version="1.1.4">pandas</requirement>
17 <requirement type="package" version="8.0.1">click</requirement>
18 </requirements> 18 </requirements>
19 19
20 <command detect_errors="aggressive"><![CDATA[ 20 <command detect_errors="aggressive"><![CDATA[
21 sh ${matchms_formatter_cli} 21 sh ${matchms_formatter_cli}
22 ]]></command> 22 ]]></command>
23 23
24 <environment_variables> 24 <environment_variables>
25 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> 25 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
26 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable> 26 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
27 <environment_variable name="OPENBLAS_NUM_THREADS">4</environment_variable> 27 <environment_variable name="OPENBLAS_NUM_THREADS">4</environment_variable>
28 <environment_variable name="RLIMIT_NPROC">4</environment_variable>
28 </environment_variables> 29 </environment_variables>
29 30
30 <configfiles> 31 <configfiles>
31 <configfile name="matchms_formatter_cli"> 32 <configfile name="matchms_formatter_cli">
32 python3 ${__tool_directory__}/formatter.py \ 33 python3 ${__tool_directory__}/formatter.py \