Mercurial > repos > recetox > riassigner

annotate 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
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1 <tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy0" profile="19.05">
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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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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement>
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10 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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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}" &&
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14 cp -r 'output.${query_section.query.ext}' '${output}'
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15 ]]>
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16 </command>
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18 <inputs>
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19 <section name="query_section" title="Query dataset" expanded="true">
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20 <param name="query" type="data" format="csv,tsv,msp">
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21 <label>Query compound list</label>
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22 <help><![CDATA[
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23 A list of compounds with retention times for which to compute the retention index.
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24 Expected columns for RT (oneof): ['rt', 'retention_time'].
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25 ]]></help>
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26 </param>
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27 <param name="query_rt_units" type="select" display="radio" help="Retention time units in the query file.">
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28 <option value="seconds" selected="true">Seconds</option>
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29 <option value="min">Minutes</option>
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30 </param>
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31 </section>
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32 <section name="reference_section" title="Reference dataset" expanded="true">
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33 <param name="reference" type="data" format="csv,tsv,msp">
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34 <label>Reference compound list</label>
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35 <help><![CDATA[
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36 A list of retention time and retention index pairs.
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37 Expected columns for RT (oneof): ['rt', 'retention_time'].
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38 Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index'].
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39 ]]></help>
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40 </param>
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41 <param name="reference_rt_units" type="select" display="radio"
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42 help="Retention time units in the reference file.">
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43 <option value="seconds" selected="true">Seconds</option>
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44 <option value="min">Minutes</option>
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45 </param>
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46 </section>
0
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47 <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use.">
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48 <option value="kovats" selected="true">Kovats</option>
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49 <option value="cubicspline">CubicSpline</option>
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50 </param>
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51 </inputs>
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52
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53 <outputs>
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54 <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format_source="query"
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55 metadata_source="query"/>
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56 </outputs>
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58 <tests>
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59 <test>
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60 <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv"/>
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61 <param name="query_rt_units" value="seconds"/>
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62 <param name="reference" value="Alkanes_20210325.csv" ftype="csv"/>
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63 <param name="reference_rt_units" value="seconds"/>
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64 <param name="method" value="kovats"/>
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65 <output name="output" file="results.csv" ftype="csv"/>
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66 </test>
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67 </tests>
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68
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69 <help>
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70 <![CDATA[
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71 @HELP@
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72 ]]>
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73 </help>
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74 </tool>