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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
children
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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_merge_flags" name="Merge Flag Files" version="@WRAPPER_VERSION@">
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2 <description>with the same unique identifiers into a single file.</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 merge_flags.py
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9 --input "$input"
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10 --output "$output"
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11 #set names = '" "'.join( [ str( $i.display_name ) for $i in $input ] )
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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12 --filename "${names}"
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13 #if $flagUniqID
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14 --flagUniqID $flagUniqID
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15 #end if
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16 ]]></command>
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17 <inputs>
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18 <param name="input" format="tabular" type="data" label="Input Flag Files" multiple="true" help="Input your tab-separated flag files. CTRL+CLICK to select multiple files. If not tab separated see TIP below." />
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19 <param name="flagUniqID" type="text" size="30" value="" label="Unique identifier in the flag files (feature or sample)" help="Name of the column in your flag file that contains unique identifiers."/>
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Flags"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="ST000006_run_order_regression_flags.tsv,ST000006_lasso_enet_var_select_flags.tsv"/>
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27 <param name="flagUniqID" value="Retention_Index" />
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28 <param name="filename" value="ST000006_run_order_regression_flags ST000006_lasso_enet_var_select_flags" />
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29 <output name="output" file="ST000006_merge_flags_output.tsv" />
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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34 @TIP_AND_WARNING@
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35
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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36 **Tool Description**
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37
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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38 The tool merges two or more flag files together. The flag files can be either in wide format or in design format.
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39
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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40 The merging requirements are:
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2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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42 (1) the number of rows should be the same in all files being merged and
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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43 (2) all files should contain the same unique ID column name to merge by.
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44
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caba07f41453 "planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
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45 **Note:** More broadly, the tool can merge non-metabolomics data as long as the above requirements are met.
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48 --------------------------------------------------------------------------------
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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 **Input**
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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 - Two or more datasets are required.
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caba07f41453 "planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
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54 **Note:** If the input flag files have the same flag column name in multiple files, the merged output file will have columns from all imputed files.
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55 To distinguish columns obtained from different files, column names will be altered by appending the corresponding file name to the end of the column name.
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56 All non-supported file name characters will be changed to ‘_’.
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58 @WIDE@
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59
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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60 **NOTE:** The sample IDs must match the sample IDs in the Design File (below).
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61 Extra columns will automatically be ignored.
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62
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63 @METADATA@
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65 **Unique ID for Flag file (feature ID or sample ID).**
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67 - Name of the column in your Flag file that contains unique IDs.
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70 --------------------------------------------------------------------------------
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71
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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72 **Output**
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74 The TSV output contains all columns from the flag files. The column with the unique row ID will be included once in the output dataset.
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77 ]]></help>
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78 <expand macro="citations"/>
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79 </tool>