Mercurial > repos > nml > biohansel_bionumeric_converter

comparison bionumeric_convert.xml @ 1:07dfb8fd47f4 draft default tip

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planemo upload commit e0d65bf0850ce95ffb89982e61f2136fcf0359ee
author nml
date Mon, 13 May 2019 12:59:15 -0400
parents b000a3130db8
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0:b000a3130db8 1:07dfb8fd47f4
1 <tool id="bionumeric_convert" name="biohansel2bionumerics" version="0.1.0"> 1 <tool id="bionumeric_convert" name="biohansel2bionumerics" version="0.2.0">
2 <description>compliant results</description> 2 <description>compliant results</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.24.1">pandas</requirement> 4 <requirement type="package" version="0.24.1">pandas</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 $__tool_directory__/bionumeric_converter.py -f '$Input' -o '$output' 7 $__tool_directory__/bionumeric_converter.py -f '$Input' -o '$Output'
8 ]]></command> 8 ]]></command>
9 <inputs> 9 <inputs>
10 <param type="data" name="Input" format="tabular"/> 10 <param type="data" name="Input" format="tabular"/>
11 </inputs> 11 </inputs>
12 <outputs> 12 <outputs>
13 <data name="output" format="csv" from_work_dir="output" label="Output.csv"/> 13 <data name="Output" format="csv" from_work_dir="output" label="Biohansel_Bionumerics"/>
14 </outputs> 14 </outputs>
15 <tests> 15 <tests>
16 <test> 16 <test>
17 <param name="Input" value="results.tab"/> 17 <param name="Input" value="results.tab"/>
18 <output name="output" value="Output.csv"/> 18 <output name="Output" value="Biohansel_Bionumerics.csv"/>
19 </test> 19 </test>
20 </tests> 20 </tests>
21 <help><![CDATA[ 21 <help><![CDATA[
22 **What it does** 22 **What it does**
23 23
24 This tool is a supplementary script that takes *only* BioHansel output data and converts it into a format compatible with bionumerics. 24 This tool is a supplementary script that takes Biohansel output data and converts it into a format compatible with Bionumerics.
25 25
26 **How to run it** 26 **Inputs:**
27 27
28 1. Input any of your BioHansel output files (tech_results.tab, match_results.tab, and results.tab) 28 - *Individual* output or *Collection* of outputs for any of the three Biohansel results files (tech_results.tab, match_results.tab, or results.tab)
29 2. Click Execute
30 29
31 **Specific modifications done on the data** 30 **Outputs:**
31
32 - A .CSV file or a collection of .CSV files called "*Output*" that can be renamed and downloaded as required.
33
34 **Specific modifications done to the data**
32 35
33 1. Converts all commas in the output to "/" 36 1. Converts all commas in the output to "/"
34 2. Shortens BioHansel qc_messages if they are over 150 characters 37 2. Splits Biohansel qc_message column into multiple columns if the message is longer than 150 characters
35 3. Converts the .tab file to a .csv file 38 3. Converts the .tab or .tsv file to a .csv file
36 39
37 ]]></help> 40 ]]></help>
38 <citations> 41 <citations>
39 </citations> 42 </citations>
40 </tool> 43 </tool>