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1 <tool id="lookup_library" name="RIQC-Lookup RI for CAS numbers in library" version="1.0.2">
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2 <description>Lookup or estimate the RI using a "known RI values" CAS numbers library</description>
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3 <command interpreter="python">
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4 library_lookup.py
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5 $library_file
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6 $input
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7 "$col_type"
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8 "$polarity"
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9 $output
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10 #for $ctype in $pref
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11 ${ctype.columntype}
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12 #end for
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13 $regression.model
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14 </command>
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15 <inputs>
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41
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16 <!-- Regarding the <page> items: this blocks the use of this tool in Galaxy workflows. However,
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17 alternatives like wrapping this in conditionals, repeats (to force a refresh_on_change as this option
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18 is not working on its own) failed since the workflow editor does not support refreshes...not does the
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19 workflow runtime support conditionals or repeats to be set at runtime. See also
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20 galaxy-dev mail thread "when else" in <conditional> ? RE: refresh_on_change : is this a valid attribute? Any other ideas/options??" -->
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21 <page>
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22 <param format="tabular" name="input" type="data" label="NIST identifications as tabular file"
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23 help="Select a tab delimited NIST metabolite identifications file (converted from PDF)" />
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24 <param name="library_file" type="select" label="CAS x RI Library file"
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25 help="Select a library/lookup file containing RI values for CAS numbers on various chromatography columns "
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26 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/RI_DB_libraries")'/>
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41
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27 </page>
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28 <page>
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29 <param name="col_type" type="select" label="Select column type" refresh_on_change="true"
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30 display="radio" dynamic_options='get_column_type(library_file)'
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31 help="" />
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41
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32 </page>
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33 <page>
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34 <param name="polarity" type="select" label="Select polarity" refresh_on_change="true"
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35 display="radio" dynamic_options='filter_column(library_file,col_type)'
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36 help="" />
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37 </page>
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38 <page>
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39 <conditional name="regression">
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40 <param name="regression_select" type="boolean" checked="false" label="Apply regression method"
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41 help="If no data for the selected column is present in the database, selecting this option will try
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42 to convert Retention Indices using data from other GC-columns with a regression method. Please
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43 note that only the first given GC-column above will be used for this, any alternatives will be
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44 ignored" />
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45 <when value="true">
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46 <param name="model" format="tabular" type="data" label="Tabular file containing regression model"
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47 help="This file contains the coefficients used to perform the regression from one GC-column
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48 to another GC-column"/>
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49 </when>
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50 <when value="false">
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51 <param name="model" type="hidden" value="False" />
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52 </when>
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53 </conditional>
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54 <repeat name="pref" title="Select column name preference">
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55 <param name="columntype" type="select" label="Column name" refresh_on_change="true"
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56 dynamic_options='filter_column2(library_file, col_type, polarity)'
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57 help="Select one or more column names for filtering. The order defines the priority." />
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58 </repeat>
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59 </page>
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60 </inputs>
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61 <outputs>
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62 <data format="tabular" label="${tool.name} on" name="output" />
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63 </outputs>
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64 <code file="match_library.py" />
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65 <help>
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66 Performs a lookup of the RI values by matching CAS numbers from the given NIST identifications file to a library.
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67 If a direct match is NOT found for the preferred column name, a regression can be done to find
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68 the theoretical RI value based on known RI values for the CAS number on other column types (see step 4).
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69 If there is no match for the CAS number on any column type, then the record is not given a RI.
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70
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71
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72
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73 </help>
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74
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75 </tool>
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