Mercurial > repos > recetox > aplcms_to_ramclustr_converter

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