annotate generate_rank_wide.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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1 <tool id="secimtools_generate_rank_wide" name="Ranked wide file" version="@WRAPPER_VERSION@">
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2 <description>Generate a wide format file with ranked columns from an input wide 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 detect_errors="exit_code"><![CDATA[
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8 addGroupRank.py
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9 --wide $wide
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10 --design $design
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11 --out $out
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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12 #if $ngroup:
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13 --ngroup $ngroup
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14 #end if
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15 --rank $rank
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16 --uniqID $uniqID
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17 ]]></command>
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18 <inputs>
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19 <param name="wide" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
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20 <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
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21 <param name="uniqID" type="text" size="30" value="rowID" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
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22 <param name="ngroup" type="integer" size="30" value="" optional="true" label="number of groups for each feature being ranked" help="number of bins/groups for each feature being ranked. If there is no input, the default behavir is ranking each column."/>
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23 <param name="rank" type="text" size="30" value="Rank" label=" Name of flag column" help="The column name in your design file that contains the flags to specify whether a sampleID will be ranked in the input wide file."/>
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24 </inputs>
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25 <outputs>
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26 <data format="tabular" name="out" label="${tool.name} on ${on_string}: Results Table"/>
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27 </outputs>
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28
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29 <help><![CDATA[
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30
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31 @TIP_AND_WARNING@
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32
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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33 **Tool Description**
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34
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35 The tool is used to generate a wide format file with each column being ranked in the input wide format dataset.
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36
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37 --------------------------------------------------------------------------------
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38
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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39 **Input**
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40
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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41 - Two input datasets are required.
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44 --------------------------------------------------------------------------------
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45
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46 **Output**
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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 The user will get a output file from the tool:
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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 (1) a wide format file with each column being ranked. The columns will be selected using the flag column in the design file.
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51
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52
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53 ]]></help>
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54 <expand macro="citations"/>
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55 </tool>