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1 <tool id="secimtools_threshold_based_flags" name="Threshold Based Flags" version="@WRAPPER_VERSION@">
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2 <description>to flag features based on a user-specified threshold.</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="requirements" />
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7 <command><![CDATA[
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8 threshold_based_flags.py
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9 --input $input
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10 --design $design
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11 --ID $uniqID
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12 --output $output
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13 --group $group
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14
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15 #if $cutoff:
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16 --cutoff $cutoff
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17 #end if
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18 ]]></command>
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19 <inputs>
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20 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
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21 <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
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22 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
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23 <param name="group" type="text" size="30" label="Group/Treatment" help="Name of the column in your Design File that contains group classifications. The resulting indicator flags will generated for these group categories." />
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24 <param name="cutoff" type="integer" optional="true" size="6" value="30000" label="Cutoff" help="Cutoff to use for which values to flag. Defaults = 30,000."/>
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25 </inputs>
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26 <outputs>
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27 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input" value="ST000006_data.tsv"/>
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32 <param name="design" value="ST000006_design.tsv"/>
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33 <param name="uniqID" value="Retention_Index" />
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34 <param name="group" value="White_wine_type_and_source" />
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35 <param name="cutoff" value="3000" />
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36 <output name="output" file="ST000006_threshold_based_flags_output.tsv" />
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40
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41 @TIP_AND_WARNING@
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42
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43 **Tool Description**
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44
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45 This tool flags a feature in a given group with a binary indicator if, for half (or more) of the samples within the group, the feature value is below a user specified threshold or is missing.
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46 The default threshold value of 30,000 is primarily useful for peak intensities from mass spectroscopy data and should be evaluated carefully for other types of values (e.g. for peak height).
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47
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48 --------------------------------------------------------------------------------
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49
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50
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51 **Input**
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52
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53 - Two input datasets are required.
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54
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55 @WIDE@
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56
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57 **NOTE:** The sample IDs must match the sample IDs in the Design File (below).
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58 Extra columns will automatically be ignored.
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59
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60 @METADATA@
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61
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62 @UNIQID@
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63
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64 @GROUP@
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65
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66 **Cutoff Value**
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67
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68 - Cutoff to use for which values to flag. Default = 30,000.
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69
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70 --------------------------------------------------------------------------------
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71
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72 **Output**
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73
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74 This tool outputs a TSV file containing indicator flags for each group, where the number of indicator flags is determined by the number of groups.
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75
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76 ]]></help>
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77 <expand macro="citations"/>
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78 </tool>
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