Mercurial > repos > recetox > riassigner
comparison riassigner.xml @ 0:7cc615de435e draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit dc8ac7e3c57d6448fa8e0422e9229e10d2b4525a"
| author | recetox |
|---|---|
| date | Fri, 20 Aug 2021 12:27:54 +0000 |
| parents | |
| children | 97c0aae5eb69 |
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| -1:000000000000 | 0:7cc615de435e |
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| 1 <tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5"> | |
| 2 <description>compute retention indices</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="creator"/> | |
| 7 <expand macro="requirements" /> | |
| 8 | |
| 9 <command detect_errors="exit_code"><![CDATA[ | |
| 10 sh ${symlink_inputs} && | |
| 11 python -m RIAssigner --reference "$reference.element_identifier" --query "$query.element_identifier" --method "$method" --output "output.${query.ext}" && | |
| 12 cp -r 'output.${query.ext}' '${output}' | |
| 13 ]]></command> | |
| 14 | |
| 15 <configfiles> | |
| 16 <configfile name="symlink_inputs"> | |
| 17 ln -s '${query}' '${query.element_identifier}' | |
| 18 ln -s '${reference}' '${reference.element_identifier}' | |
| 19 </configfile> | |
| 20 </configfiles> | |
| 21 | |
| 22 <inputs> | |
| 23 <param name="reference" type="data" format="csv,tsv,msp"> | |
| 24 <label>Reference compound list</label> | |
| 25 <help><![CDATA[ | |
| 26 A list of retention time and retention index pairs. | |
| 27 Expected columns for RT (oneof): ['rt', 'retention_time']. | |
| 28 Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index']. | |
| 29 Retention time is expected to be in seconds. | |
| 30 ]]></help> | |
| 31 </param> | |
| 32 <param name="query" type="data" format="csv,tsv,msp"> | |
| 33 <label>Query compound list</label> | |
| 34 <help><![CDATA[ | |
| 35 A list of compounds with retention times for which to compute the retention index. | |
| 36 Expected columns for RT (oneof): ['rt', 'retention_time']. | |
| 37 Retention time is expected to be in seconds. | |
| 38 ]]></help> | |
| 39 </param> | |
| 40 <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use."> | |
| 41 <option value="kovats" selected="true">Kovats</option> | |
| 42 <!-- <option value="cubicspline">CubicSpline </option> --> | |
| 43 </param> | |
| 44 </inputs> | |
| 45 | |
| 46 <outputs> | |
| 47 <data label="RI using $method of ${query.element_identifier}" name="output" format_source="query" /> | |
| 48 </outputs> | |
| 49 | |
| 50 <tests> | |
| 51 <test> | |
| 52 <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv" /> | |
| 53 <param name="reference" value="Alkanes_20210325.csv" ftype="csv" /> | |
| 54 <param name="method" value="kovats" /> | |
| 55 <output name="output" file="results.csv" ftype="csv"/> | |
| 56 </test> | |
| 57 </tests> | |
| 58 | |
| 59 <help> | |
| 60 <![CDATA[ | |
| 61 @HELP@ | |
| 62 ]]> | |
| 63 </help> | |
| 64 </tool> |