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author nml
date Mon, 13 May 2019 12:59:15 -0400
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1 <tool id="bionumeric_convert" name="biohansel2bionumerics" version="0.2.0">
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2 <description>compliant results</description>
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3 <requirements>
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4 <requirement type="package" version="0.24.1">pandas</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 $__tool_directory__/bionumeric_converter.py -f '$Input' -o '$Output'
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8 ]]></command>
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9 <inputs>
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10 <param type="data" name="Input" format="tabular"/>
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11 </inputs>
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12 <outputs>
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13 <data name="Output" format="csv" from_work_dir="output" label="Biohansel_Bionumerics"/>
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="Input" value="results.tab"/>
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18 <output name="Output" value="Biohansel_Bionumerics.csv"/>
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19 </test>
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20 </tests>
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21 <help><![CDATA[
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22 **What it does**
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23
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24 This tool is a supplementary script that takes Biohansel output data and converts it into a format compatible with Bionumerics.
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25
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26 **Inputs:**
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27
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28 - *Individual* output or *Collection* of outputs for any of the three Biohansel results files (tech_results.tab, match_results.tab, or results.tab)
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29
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30 **Outputs:**
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31
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32 - A .CSV file or a collection of .CSV files called "*Output*" that can be renamed and downloaded as required.
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33
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34 **Specific modifications done to the data**
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36 1. Converts all commas in the output to "/"
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37 2. Splits Biohansel qc_message column into multiple columns if the message is longer than 150 characters
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38 3. Converts the .tab or .tsv file to a .csv file
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39
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40 ]]></help>
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41 <citations>
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42 </citations>
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43 </tool>