Mercurial > repos > recetox > matchms_formatter

annotate matchms_formatter.xml @ 16:2f0545b02020 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:19:32 +0000
parents 5c0e5344edf3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
1 <tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" profile="21.09">
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
2 <description>reformat scores object of matchms to long format table</description>
0
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
3
3
e2a1dbeba196 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
4 <macros>
e2a1dbeba196 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
5 <import>macros.xml</import>
16
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
6 <import>help.xml</import>
3
e2a1dbeba196 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
7 </macros>
e2a1dbeba196 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
8 <expand macro="creator"/>
16
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
9 <edam_operations>
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
10 <edam_operation>operation_0335</edam_operation>
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
11 </edam_operations>
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
12 <expand macro="bio.tools"/>
0
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
13
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
14 <requirements>
10
5c0e5344edf3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 9
diff changeset
15 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
0
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
16 <requirement type="package" version="1.1.4">pandas</requirement>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
17 <requirement type="package" version="8.0.1">click</requirement>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
18 </requirements>
10
5c0e5344edf3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 9
diff changeset
19
5c0e5344edf3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 9
diff changeset
20 <environment_variables>
5c0e5344edf3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 9
diff changeset
21 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
5c0e5344edf3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 9
diff changeset
22 <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
5c0e5344edf3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 9
diff changeset
23 </environment_variables>
0
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
24
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
25 <command detect_errors="aggressive"><![CDATA[
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
26 sh ${matchms_formatter_cli}
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
27 ]]></command>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
28
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
29 <configfiles>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
30 <configfile name="matchms_formatter_cli">
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
31 python3 ${__tool_directory__}/formatter.py \
16
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
32 --sf '$scores' \
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
33 --o '$output'
0
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
34 </configfile>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
35 </configfiles>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
36
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
37 <inputs>
16
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
38 <param label="Scores object" name="scores" type="data" format="json" help="matchms Scores json file." />
0
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
39 </inputs>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
40 <outputs>
16
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
41 <data label="${tool.name} on ${on_string}" name="output" format="tsv"/>
0
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
42 </outputs>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
43
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
44 <tests>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
45 <test>
16
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
46 <param name="scores" value="formatter/fill2_trunc_scores_with_metadata_match.json" ftype="json"/>
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
47 <output name="output" value="formatter/fill2_formatted.tsv" ftype="tsv"
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
48 checksum="md5$4f0d83da381b8a403d807d26a9dd0f34"/>
0
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
49 </test>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
50 <test>
16
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
51 <param name="scores" value="similarity/scores_test4_out.json" ftype="json"/>
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
52 <output name="output" file="formatter/test4_formatted.tsv" ftype="tsv"/>
0
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
53 </test>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
54 </tests>
0a08bed94964 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 85f60c94ccb3cb7706694cbb7ff6d59dcb41c0c9"
recetox
parents:
diff changeset
55
16
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
56 <help>
10
5c0e5344edf3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 9
diff changeset
57 @HELP_formatter@
16
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
58 @HELP_matchms@
2f0545b02020 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 10
diff changeset
59 </help>
2
52abfe76c25b "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 46191b39a711f92418f1d412065bbb3648dbf42d"
recetox
parents: 1
diff changeset
60 </tool>