Mercurial > repos > recetox > aplcms_to_ramclustr_converter

annotate hdf_converter.xml @ 1:52470d439e50 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 9a479980d3432f6f1a4541bac75b4ccc40d189ee"
author recetox
date Wed, 16 Dec 2020 17:28:30 +0000
parents 062f4c571a24
children 644192cf22a5
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062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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1 <tool id="aplcms_to_ramclustr_converter" name="apLCMS to RamClustR converter" version="0.0.1" python_template_version="3.5">
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2 <description>converts aplcms HDF output to RamClustR csv input</description>
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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3 <requirements>
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4 <requirement type="package" version="3.7">python</requirement>
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5 <requirement type="package" version="1.1.5">pandas</requirement>
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6 <requirement type="package" version="3.6.1">pytables</requirement>
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7 </requirements>
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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8 <command detect_errors="exit_code"><![CDATA[
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9 python $__tool_directory__/hdf_converter.py --dataframe '${hdf_dataframe}' --table '${table_name}' '${out_file}'
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10 ]]></command>
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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11 <inputs>
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12 <param name="hdf_dataframe" type="data" format="h5" label="apLCMS Dataset"/>
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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13 <param name="table_name" type="select" label="Table Name">
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14 <option value="peaks">peaks</option>
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15 <option value="aligned_peaks">aligned peaks</option>
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16 </param>
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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17 </inputs>
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18 <outputs>
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19 <data format="csv" name="out_file" label="CSV with ${table_name} from ${hdf_dataframe.name}"/>
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20 </outputs>
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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21 <tests>
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22 <test>
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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23 <param name="hdf_dataframe" value="test.h5" ftype="h5"/>
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24 <param name="table_name" value="peaks"/>
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25 <output name="out_file" file="test.csv" ftype="csv"/>
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26 </test>
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27 </tests>
062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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28 <help><![CDATA[
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29 Tool to convert apLCMS output to csv file formated in accordance to RamClustR (CSV) input requirements.
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062f4c571a24 "planemo upload for repository https://github.com/RECETOX/galaxytools/tools/hdf_converter/ commit 7c15608bc9e6d0cc28daed590341b2b22f9fcedf"
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31 **Workflow position**
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33 - Upstream tool: `apLCMS <https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms>`_ Unsupervised or Hybrid
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34
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35 - Downstream tool: `RamClustR <https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr>`_ (CSV)
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36 ]]></help>
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37 </tool>