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comparison riassigner.xml @ 5:4abc4359b978 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit 4b8a43b863ff8a0ff1d5a08e516068853adf358d
author recetox
date Tue, 16 Apr 2024 11:30:33 +0000
parents 8c5e65adf694
children af25aa61c611
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4:79818ce5a8bf 5:4abc4359b978
1 <tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy4" profile="21.09"> 1 <tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy5" profile="21.09">
2 <description>compute retention indices</description> 2 <description>compute retention indices</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="creator"/> 6 <expand macro="creator"/>
12 <requirements> 12 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement>
14 </requirements> 14 </requirements>
15 15
16 <command detect_errors="exit_code"><![CDATA[ 16 <command detect_errors="exit_code"><![CDATA[
17 python -m RIAssigner --reference "$reference_section.reference" "$reference_section.reference.ext" "$reference_section.reference_rt_units" --query "$query_section.query" "$query_section.query.ext" "$query_section.query_rt_units" --method "$method" --output "output.${query_section.query.ext}" && 17 python -m RIAssigner --reference "$reference_section.reference" "$reference_section.reference.ext" "$reference_section.reference_rt_units" --query "$query_section.query" "$query_section.query.ext" "$query_section.query_rt_units" --method "$method" --output "output.${output.ext}" &&
18 cp -r 'output.${query_section.query.ext}' '${output}' 18 cp -r 'output.${output.ext}' '${output}'
19 ]]> 19 ]]>
20 </command> 20 </command>
21 21
22 <inputs> 22 <inputs>
23 <section name="query_section" title="Query dataset" expanded="true"> 23 <section name="query_section" title="Query dataset" expanded="true">
53 <option value="cubicspline">CubicSpline</option> 53 <option value="cubicspline">CubicSpline</option>
54 </param> 54 </param>
55 </inputs> 55 </inputs>
56 56
57 <outputs> 57 <outputs>
58 <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query" 58 <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format="tsv"
59 metadata_source="query"/> 59 metadata_source="query">
60 <change_format>
61 <when input="query_section.query.ext" value="msp" format="msp" />
62 </change_format>
63 </data>
60 </outputs> 64 </outputs>
61 65
62 <tests> 66 <tests>
63 <test> 67 <test>
64 <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv"/> 68 <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv"/>
65 <param name="query_rt_units" value="seconds"/> 69 <param name="query_rt_units" value="seconds"/>
66 <param name="reference" value="Alkanes_20210325.csv" ftype="csv"/> 70 <param name="reference" value="Alkanes_20210325.csv" ftype="csv"/>
67 <param name="reference_rt_units" value="seconds"/> 71 <param name="reference_rt_units" value="seconds"/>
68 <param name="method" value="kovats"/> 72 <param name="method" value="kovats"/>
69 <output name="output" file="results.csv" ftype="csv"/> 73 <output name="output" file="results.tsv" ftype="tsv"/>
70 </test> 74 </test>
71 </tests> 75 </tests>
72 76
73 <help> 77 <help>
74 <![CDATA[ 78 <![CDATA[