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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit e8d838b42298fb282581f05397451ee450e3600e
author recetox
date Thu, 22 Jun 2023 15:19:18 +0000
parents d3f04719501a
children
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156531829f42 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit e8d838b42298fb282581f05397451ee450e3600e
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1 <tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy2" profile="21.09">
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2 <description>compute retention indices</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creator"/>
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7
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156531829f42 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit e8d838b42298fb282581f05397451ee450e3600e
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8 <xrefs>
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9 <xref type="bio.tools">riassigner</xref>
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10 </xrefs>
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement>
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14 </requirements>
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16 <command detect_errors="exit_code"><![CDATA[
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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}" &&
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18 cp -r 'output.${query_section.query.ext}' '${output}'
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19 ]]>
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20 </command>
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22 <inputs>
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23 <section name="query_section" title="Query dataset" expanded="true">
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24 <param name="query" type="data" format="csv,tsv,msp">
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25 <label>Query compound list</label>
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26 <help><![CDATA[
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27 A list of compounds with retention times for which to compute the retention index.
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28 Expected columns for RT (oneof): ['rt', 'retention_time'].
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29 ]]></help>
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30 </param>
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31 <param name="query_rt_units" type="select" display="radio" help="Retention time units in the query file.">
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32 <option value="seconds" selected="true">Seconds</option>
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33 <option value="min">Minutes</option>
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34 </param>
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35 </section>
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36 <section name="reference_section" title="Reference dataset" expanded="true">
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37 <param name="reference" type="data" format="csv,tsv,msp">
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38 <label>Reference compound list</label>
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39 <help><![CDATA[
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40 A list of retention time and retention index pairs.
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41 Expected columns for RT (oneof): ['rt', 'retention_time'].
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42 Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index'].
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43 ]]></help>
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44 </param>
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45 <param name="reference_rt_units" type="select" display="radio"
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46 help="Retention time units in the reference file.">
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47 <option value="seconds" selected="true">Seconds</option>
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48 <option value="min">Minutes</option>
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49 </param>
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50 </section>
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51 <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use.">
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52 <option value="kovats" selected="true">Kovats</option>
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53 <option value="cubicspline">CubicSpline</option>
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54 </param>
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55 </inputs>
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57 <outputs>
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58 <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query"
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59 metadata_source="query"/>
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60 </outputs>
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62 <tests>
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63 <test>
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64 <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv"/>
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65 <param name="query_rt_units" value="seconds"/>
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66 <param name="reference" value="Alkanes_20210325.csv" ftype="csv"/>
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67 <param name="reference_rt_units" value="seconds"/>
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68 <param name="method" value="kovats"/>
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69 <output name="output" file="results.csv" ftype="csv"/>
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70 </test>
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71 </tests>
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72
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73 <help>
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74 <![CDATA[
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75 @HELP@
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76 ]]>
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77 </help>
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78 </tool>