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comparison matchms_formatter.xml @ 11:ae45992f969e draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:29:16 +0000
parents 1b09315a3f87
children 1e58bf51a0e5
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10:1b09315a3f87 11:ae45992f969e
1 <tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" 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>
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="1.1.4">pandas</requirement> 16 <requirement type="package" version="1.1.4">pandas</requirement>
17 <requirement type="package" version="8.0.1">click</requirement> 17 <requirement type="package" version="8.0.1">click</requirement>
18 </requirements> 18 </requirements>
19
20 <command detect_errors="aggressive"><![CDATA[
21 sh ${matchms_formatter_cli}
22 ]]></command>
19 23
20 <environment_variables> 24 <environment_variables>
21 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> 25 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
22 <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>
23 </environment_variables> 27 </environment_variables>
24
25 <command detect_errors="aggressive"><![CDATA[
26 sh ${matchms_formatter_cli}
27 ]]></command>
28 28
29 <configfiles> 29 <configfiles>
30 <configfile name="matchms_formatter_cli"> 30 <configfile name="matchms_formatter_cli">
31 python3 ${__tool_directory__}/formatter.py \ 31 python3 ${__tool_directory__}/formatter.py \
32 --sf '$scores' \ 32 --sf '$scores' \
55 55
56 <help> 56 <help>
57 @HELP_formatter@ 57 @HELP_formatter@
58 @HELP_matchms@ 58 @HELP_matchms@
59 </help> 59 </help>
60
61 <citations>
62 <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
63 </citations>
60 </tool> 64 </tool>