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annotate modify_design_file.xml @ 1:2e7d47c0b027 draft

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"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author malex
date Mon, 08 Mar 2021 22:04:06 +0000
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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_modify_design_file" name="Modify design file" version="@WRAPPER_VERSION@">
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2 <description>to remove specified group types or sampleIDs</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 modify_design_file.py
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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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
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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14 #end if
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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15 --drops $toDrop
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16 --out $out
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17 ]]></command>
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18 <inputs>
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19 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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20 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
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21 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers.."/>
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22 <param name="group" type="text" size="30" value="" optional="false" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications. If not provided, the drop will be performed by 'sampleID'."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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23 <param name="toDrop" type="text" size="30" optional="false" label="Group(s)/Sample(s) to drop" help="Name of the Group(s) or Sample(s), comma separated, to remove from your design file."/>
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24 </inputs>
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25 <outputs>
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26 <data format="tabular" name="out" label="${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_group_name_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_no_space" />
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34 <param name="toDrop" value="Chardonnay_Napa_CA2003,Riesling_CA2004,SauvignonBlanc_LakeCounty_CA2001" />
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35 <output name="out" file="ST000006_modify_design_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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39
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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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43
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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44 The tool creates a new design file based on the existing wide dataset and design file where the specified group types or samples are removed from the existing design file.
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45
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46 --------------------------------------------------------------------------------
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47
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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48 **Input**
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49
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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50 - Two input datasets are required.
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51
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52 @WIDE@
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53
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54 **NOTE:** The sample IDs must match the sample IDs in the Design File
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55 (below). Extra columns will automatically be ignored.
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56
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57 @METADATA@
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58
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59 @UNIQID@
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60
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61 **Group/Treatment [Optional]**
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62
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63 - Name of the column in your Design File that contains group classifications. If not provided, the drop will be performed by 'sampleID's.
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64
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65 **Group(s)/Sample(s) to drop**
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66
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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67 - Name of the Group(s) or Sample(s), comma separated, to remove from the design file.
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68
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69 --------------------------------------------------------------------------------
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70
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71 **Output**
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72
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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73 This tool will output a single design file that contains only the samples not selected for removal.
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74
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75 ]]></help>
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76 <expand macro="citations"/>
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77 </tool>