Mercurial > repos > recetox > aplcms_to_ramclustr_converter

comparison aplcms_to_ramclustr_converter.xml @ 3:07667688735e draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 521769cd5af12987a119e6302f22e2e1e864ff9a"
author recetox
date Wed, 17 Feb 2021 15:14:33 +0000
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children 9ea34e24474f
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2:644192cf22a5 3:07667688735e
1 <tool id="aplcms_to_ramclustr_converter" name="apLCMS to RamClustR converter" version="0.0.1+galaxy0" python_template_version="3.5">
2 <description>converts aplcms HDF output to RamClustR csv input</description>
3 <requirements>
4 <requirement type="package" version="3.7">python</requirement>
5 <requirement type="package" version="1.1.5">pandas</requirement>
6 <requirement type="package" version="3.6.1">pytables</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 python $__tool_directory__/aplcms_to_ramclustr_converter.py --dataframe '${hdf_dataframe}' --table '${table_name}' '${out_file}'
10 ]]></command>
11 <inputs>
12 <param name="hdf_dataframe" type="data" format="h5" label="apLCMS Dataset"/>
13 <param name="table_name" type="select" label="Table Name">
14 <option value="peaks">peaks</option>
15 <option value="aligned_peaks">aligned peaks</option>
16 </param>
17 </inputs>
18 <outputs>
19 <data format="csv" name="out_file" label="CSV with ${table_name} from ${hdf_dataframe.name}"/>
20 </outputs>
21 <tests>
22 <test>
23 <param name="hdf_dataframe" value="test-input.h5" ftype="h5"/>
24 <param name="table_name" value="peaks"/>
25 <output name="out_file" file="test-output.csv" ftype="csv"/>
26 </test>
27 </tests>
28 <help><![CDATA[
29 Tool to convert apLCMS output to csv file formated in accordance to RamClustR (CSV) input requirements.
30
31 **Workflow position**
32
33 - Upstream tool: `apLCMS <https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms>`_ Unsupervised or Hybrid
34
35 - Downstream tool: `RamClustR <https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr>`_ (CSV)
36 ]]></help>
37 </tool>