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annotate isolib.xml @ 0:8a1893635ac0 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
author recetox
date Tue, 23 Apr 2024 06:39:20 +0000
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8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
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1 <tool id="isolib" name="isolib" version="1.0.0+galaxy0" profile="21.09">
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2 <description>create an isotopic pattern library for given compounds and adducts</description>
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3 <creator>
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4 <person
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5 givenName="Helge"
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6 familyName="Hecht"
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7 url="https://github.com/hechth"
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8 identifier="0000-0001-6744-996X" />
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9 <organization
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10 url="https://www.recetox.muni.cz/"
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11 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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12 name="RECETOX MUNI" />
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13 </creator>
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14 <edam_operations>
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15 <edam_operation>operation_3632</edam_operation>
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16 </edam_operations>
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17 <requirements>
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18 <requirement type="package" version="1.10.0">bioconductor-metabocoreutils</requirement>
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19 <requirement type="package" version="1.12.0">bioconductor-spectra</requirement>
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20 <requirement type="package" version="1.6.0">bioconductor-msbackendmsp</requirement>
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21 <requirement type="package" version="2.6">r-envipat</requirement>
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22 </requirements>
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23 <command detect_errors="exit_code"><![CDATA[
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24 Rscript ${__tool_directory__}/isolib.R '${input_file}' '${adducts}' '${threshold}' '${append_adduct}' '${isotope_library}'
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25 ]]></command>
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26 <inputs>
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27 <param name="input_file" type="data" format="tabular" label="Table with input compounds"/>
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28 <conditional name="ionization">
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29 <param name="ionization" type="select" label="Ionization mode" help="Ionization mode used in the experiment">
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30 <option value="negative" selected="true">negative</option>
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31 <option value="positive">positive</option>
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32 </param>
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33 <when value="positive">
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34 <param name="adducts" type="select" label="Adducts" multiple="true" help="Adducts to use">
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35 <option value="M+H" selected="true">M+H</option>
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36 </param>
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37 </when>
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38 <when value="negative">
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39 <param name="adducts" type="select" label="Adducts" multiple="true" help="Adducts to use">
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40 <option value="M-H" selected="true">M-H</option>
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41 <option value="M-2H">M-2H</option>
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42 <option value="2M-H">2M-H</option>
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43 </param>
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44 </when>
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45 </conditional>
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46 <param name="threshold" type="float" min="0" max="100" value="1" label="Threshold" help="Probability threshold to use as cutoff for isotopic pattern distribution - this can be used to remove low abundant peaks and improve computation performance." />
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47 <param name="append_adduct" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Append adduct to compound name" help="Append the adduct string to the compound name for easy identification." />
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48 </inputs>
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49 <outputs>
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50 <data format="msp" name="isotope_library"/>
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51 </outputs>
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52
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53 <tests>
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54 <test>
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55 <param name="input_file" value="lc_markers_neg.tsv"/>
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56 <output name="isotope_library" file="test0.msp"/>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 This tool computes isotopic patterns for given compounds and adduct forms.
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61 The compound table input file should contain the following columns:
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62 - name: compound name
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63 - formula: compound formula
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64 - rt (optional): retention time
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65
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66 The output is a spectral library in the MSP format.
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67 ]]></help>
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68 <citations>
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69 <citation type="doi">10.1021/acs.analchem.5b00941</citation>
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70 <citation type="doi">10.3390/metabo12020173</citation>
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71 </citations>
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72 </tool>