annotate remove_user_specified_row_col.xml @ 1:2e7d47c0b027 draft

"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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children caba07f41453
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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_remove_user_specified_features" name="Remove User-Specified Features or Samples" version="@WRAPPER_VERSION@">
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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2 <description>from the data.</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[
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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8 remove_user_specified_row_col.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 --ID $uniqID
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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12 --outWide $outWide
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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13 --row $rowID
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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14 --col $colID
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15 ]]></command>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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16 <inputs>
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17 <param name="input" type="data" format="tabular" label="Wide Dataset"
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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18 help="Input your tab-separated wide format dataset. If file is 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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19 <param name="design" type="data" format="tabular" label="Design File"
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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20 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"
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22 help="Name of the column in your wide dataset that has unique identifiers."/>
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23 <param name="rowID" type="text" size="30" value="" label="Features to drop [Optional]."
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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24 help="Space-separated list of unique identifiers (rows) in your wide dataset to delete."/>
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25 <param name="colID" type="text" size="30" value="" label="Samples to drop [Optional]."
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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26 help="Space-separated list of unique sampleIDs (columns) to be removed from the wide dataset."/>
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27 </inputs>
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28 <outputs>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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29 <data format="tabular" name="outWide" label="${tool.name} on ${on_string}: Dropped wide"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input" value="fly_test_sbys.tsv"/>
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34 <param name="design" value="fly_test_design.tsv"/>
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35 <param name="uniqID" value="rowID" />
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36 <param name="rowID" value="_15" />
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37 <param name="colID" value="r101_V_3" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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38 <output name="outWide" file="fly_remove_specified_features_samples_wide.tsv" />
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39 </test>
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40 </tests>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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41 <help><![CDATA[
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42
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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43 @TIP_AND_WARNING@
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44
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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45 **Tool Description**
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46
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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47 The tool removes user-specified features (rows) or samples (columns) from a wide format dataset.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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48 The user manually enters space delimited rows (features) and / or columns (samples).
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49
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50 --------------------------------------------------------------------------------
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51
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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52 **Input**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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53
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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54 - Two input datasets are required.
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55
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56 @WIDE@
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57
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58 **NOTE:** The sample IDs must match the sample IDs in the Design File
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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59 (below). Extra columns will automatically be ignored.
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60
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61 @METADATA@
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62
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63 @UNIQID@
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64
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65 **Unique ID for Flag file (feature ID or sample ID).**
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66
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67 - Name of the column in your Wide dataset that contains unique Feature IDs.
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68
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69 **rowID.**
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70
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71 - Name of the row(s) in your Wide dataset to drop.
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72
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73 **colID.**
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74
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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75 - Name of the column(s) in your Wide dataset to drop.
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76
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77 --------------------------------------------------------------------------------
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78
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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79 **Output**
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80
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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81 This tool outputs one TSV file:
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82
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83 (1) A wide format dataset generated from the input wide format dataset where features and/or samples specified by the user have been removed.
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84
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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85 ]]></help>
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86 <expand macro="citations"/>
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87 </tool>