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"planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
author malex
date Thu, 10 Jun 2021 15:41:17 +0000
parents 2e7d47c0b027
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2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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1 <tool id="secimtools_subset_data" name="Subset Wide Data and Design File" version="@WRAPPER_VERSION@">
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2 <description>- Based on groups.</description>
2
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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 detect_errors="exit_code"><![CDATA[
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8 subset_data.py
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9 --input $input
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10 --design $design
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11 --uniqID $uniqID
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12 #if $group
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13 --group $group
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14 #end if
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15 --drops $toDrop
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16 --out $out
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17 ]]></command>
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18 <inputs>
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19 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
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20 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
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21 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
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22 <param name="group" type="text" size="30" value="" optional="false" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications. If not provided, the drop will be performed by 'sampleID'."/>
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23 <param name="toDrop" type="text" size="30" optional="false" label="Group(s)/Sample(s) to drop" help="Name of the Group(s)/Sample(s), comma separated, that will be removed from your wide datset."/>
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24 </inputs>
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25 <outputs>
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26 <data format="tabular" name="out" label="${tool.name} on ${on_string}: Value"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input" value="ST000006_data.tsv"/>
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31 <param name="design" value="ST000006_design_names_underscore.tsv"/>
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32 <param name="uniqID" value="Retention_Index" />
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33 <param name="group" value="White_wine_type_and_source" />
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34 <param name="drops" value="Chardonnay_ Napa_ CA 2003,Riesling_ CA 2004" />
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35 <output name="out" file="ST000006_subset_data_output.tsv" />
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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40 @TIP_AND_WARNING@
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41
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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42 **Tool Description**
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2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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44 The tool creates new wide format dataset and design dataset based on the existing wide and design datasets where only groups specified by the user are present.
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45 The user chooses which group(s) to include in the new datasets.
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46
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47 --------------------------------------------------------------------------------
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48
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49 **Input**
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50
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51 - Two input datasets are required.
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52
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53 @WIDE@
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54
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55 **NOTE:** The sample IDs must match the sample IDs in the Design File
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56 (below). Extra columns will automatically be ignored.
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57
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58 @METADATA@
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60 @UNIQID@
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62 **Group/Treatment [Optional]**
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64 - Name of the column in your Design File that contains group classifications. If none provided the drop will be performed by 'sampleID'.
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65
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66 **Group(s)/Sample(s) to drop**
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68 - Name of the Group(s)/Sample(s), comma separeted, that will be removed from your wide datset.
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70 --------------------------------------------------------------------------------
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71
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72 **Output**
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74 This tool will output two TSV files: a TSV file containing the subset of the original wide format dataset and a TSV file containing the subset of the original design dataset. Both datasets will contain only the samples belonging to groups selected by the user.
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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>