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comparison riassigner.xml @ 3:113f5f66e6b9 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:30:37 +0000
parents 97c0aae5eb69
children d3f04719501a
comparison
equal deleted inserted replaced
2:3c396ae0a1e7 3:113f5f66e6b9
1 <tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy0" profile="19.05"> 1 <tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy0" profile="19.05">
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"/>
7
6 <requirements> 8 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement>
8 </requirements> 10 </requirements>
9 <expand macro="creator"/>
10 11
11 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
12 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}" && 13 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}" &&
13 cp -r 'output.${query_section.query.ext}' '${output}' 14 cp -r 'output.${query_section.query.ext}' '${output}'
14 ]]> 15 ]]>
35 A list of retention time and retention index pairs. 36 A list of retention time and retention index pairs.
36 Expected columns for RT (oneof): ['rt', 'retention_time']. 37 Expected columns for RT (oneof): ['rt', 'retention_time'].
37 Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index']. 38 Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index'].
38 ]]></help> 39 ]]></help>
39 </param> 40 </param>
40 <param name="reference_rt_units" type="select" display="radio" help="Retention time units in the reference file."> 41 <param name="reference_rt_units" type="select" display="radio"
42 help="Retention time units in the reference file.">
41 <option value="seconds" selected="true">Seconds</option> 43 <option value="seconds" selected="true">Seconds</option>
42 <option value="min">Minutes</option> 44 <option value="min">Minutes</option>
43 </param> 45 </param>
44 </section> 46 </section>
45 <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use."> 47 <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use.">
46 <option value="kovats" selected="true">Kovats</option> 48 <option value="kovats" selected="true">Kovats</option>
47 <option value="cubicspline">CubicSpline </option> 49 <option value="cubicspline">CubicSpline</option>
48 </param> 50 </param>
49 </inputs> 51 </inputs>
50 52
51 <outputs> 53 <outputs>
52 <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query" metadata_source="query"/> 54 <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query"
55 metadata_source="query"/>
53 </outputs> 56 </outputs>
54 57
55 <tests> 58 <tests>
56 <test> 59 <test>
57 <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv" /> 60 <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv"/>
58 <param name="query_rt_units" value="seconds" /> 61 <param name="query_rt_units" value="seconds"/>
59 <param name="reference" value="Alkanes_20210325.csv" ftype="csv" /> 62 <param name="reference" value="Alkanes_20210325.csv" ftype="csv"/>
60 <param name="reference_rt_units" value="seconds" /> 63 <param name="reference_rt_units" value="seconds"/>
61 <param name="method" value="kovats" /> 64 <param name="method" value="kovats"/>
62 <output name="output" file="results.csv" ftype="csv"/> 65 <output name="output" file="results.csv" ftype="csv"/>
63 </test> 66 </test>
64 </tests> 67 </tests>
65 68
66 <help> 69 <help>