Mercurial > repos > recetox > aplcms_to_ramclustr_converter

comparison aplcms_to_ramclustr_converter.xml @ 4:9ea34e24474f draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tools/aplcms_to_ramclustr_converter/ commit 2dd20229f0c7f43dacc0d201ea50fef3c993d30e"
author recetox
date Mon, 09 Aug 2021 15:29:08 +0000
parents 07667688735e
children b9263b8fcc1e
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3:07667688735e 4:9ea34e24474f
1 <tool id="aplcms_to_ramclustr_converter" name="apLCMS to RamClustR converter" version="0.0.1+galaxy0" python_template_version="3.5"> 1 <tool id="aplcms_to_ramclustr_converter" name="apLCMS to RamClustR converter" version="0.1.0+galaxy0" python_template_version="3.5">
2 <description>converts aplcms HDF output to RamClustR csv input</description> 2 <description>converts apLCMS parquet output to RamClustR csv input</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.7">python</requirement>
5 <requirement type="package" version="1.1.5">pandas</requirement> 4 <requirement type="package" version="1.1.5">pandas</requirement>
6 <requirement type="package" version="3.6.1">pytables</requirement> 5 <requirement type="package" version="4.0.0">pyarrow</requirement>
7 </requirements> 6 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
9 python $__tool_directory__/aplcms_to_ramclustr_converter.py --dataframe '${hdf_dataframe}' --table '${table_name}' '${out_file}' 8 python $__tool_directory__/aplcms_to_ramclustr_converter.py --dataframe '${aplcms_dataframe}' '${out_file}'
10 ]]></command> 9 ]]></command>
11 <inputs> 10 <inputs>
12 <param name="hdf_dataframe" type="data" format="h5" label="apLCMS Dataset"/> 11 <param name="aplcms_dataframe" type="data" format="parquet" label="apLCMS Dataframe"/>
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> 12 </inputs>
18 <outputs> 13 <outputs>
19 <data format="csv" name="out_file" label="CSV with ${table_name} from ${hdf_dataframe.name}"/> 14 <data format="csv" name="out_file" label="Feature-by-sample ${aplcms_dataframe.name} table (csv)"/>
20 </outputs> 15 </outputs>
21 <tests> 16 <tests>
22 <test> 17 <test>
23 <param name="hdf_dataframe" value="test-input.h5" ftype="h5"/> 18 <param name="aplcms_dataframe" value="input.parquet" ftype="parquet"/>
24 <param name="table_name" value="peaks"/> 19 <output name="out_file" file="output.csv" ftype="csv"/>
25 <output name="out_file" file="test-output.csv" ftype="csv"/>
26 </test> 20 </test>
27 </tests> 21 </tests>
28 <help><![CDATA[ 22 <help><![CDATA[
29 Tool to convert apLCMS output to csv file formated in accordance to RamClustR (CSV) input requirements. 23 Tool to convert apLCMS output to csv file formated in accordance to RamClustR (CSV) input requirements.
30 24
31 **Workflow position** 25 **Workflow position**
32 26
33 - Upstream tool: `apLCMS <https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms>`_ Unsupervised or Hybrid 27 - Upstream tool: `apLCMS <https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms>`_ Unsupervised or Hybrid
34 28
35 - Downstream tool: `RamClustR <https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr>`_ (CSV) 29 - Downstream tool: `RamClustR <https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr>`_ (CSV)
36 ]]></help> 30 ]]></help>
37 </tool> 31 </tool>