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annotate riassigner.xml @ 0:7cc615de435e draft

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