Mercurial > repos > recetox > riassigner
view riassigner.xml @ 2:4e47a0fa9287 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit e8d838b42298fb282581f05397451ee450e3600e
author | recetox |
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date | Thu, 22 Jun 2023 15:19:27 +0000 |
parents | f6bf8f1f3224 |
children | 8c5e65adf694 |
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<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy2" profile="21.09"> <description>compute retention indices</description> <macros> <import>macros.xml</import> </macros> <expand macro="creator"/> <xrefs> <xref type="bio.tools">riassigner</xref> </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ 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}" && cp -r 'output.${query_section.query.ext}' '${output}' ]]> </command> <inputs> <section name="query_section" title="Query dataset" expanded="true"> <param name="query" type="data" format="csv,tsv,msp"> <label>Query compound list</label> <help><![CDATA[ A list of compounds with retention times for which to compute the retention index. Expected columns for RT (oneof): ['rt', 'retention_time']. ]]></help> </param> <param name="query_rt_units" type="select" display="radio" help="Retention time units in the query file."> <option value="seconds" selected="true">Seconds</option> <option value="min">Minutes</option> </param> </section> <section name="reference_section" title="Reference dataset" expanded="true"> <param name="reference" type="data" format="csv,tsv,msp"> <label>Reference compound list</label> <help><![CDATA[ A list of retention time and retention index pairs. Expected columns for RT (oneof): ['rt', 'retention_time']. Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index']. ]]></help> </param> <param name="reference_rt_units" type="select" display="radio" help="Retention time units in the reference file."> <option value="seconds" selected="true">Seconds</option> <option value="min">Minutes</option> </param> </section> <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use."> <option value="kovats" selected="true">Kovats</option> <option value="cubicspline">CubicSpline</option> </param> </inputs> <outputs> <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query" metadata_source="query"/> </outputs> <tests> <test> <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv"/> <param name="query_rt_units" value="seconds"/> <param name="reference" value="Alkanes_20210325.csv" ftype="csv"/> <param name="reference_rt_units" value="seconds"/> <param name="method" value="kovats"/> <output name="output" file="results.csv" ftype="csv"/> </test> </tests> <help> <![CDATA[ @HELP@ ]]> </help> </tool>