Mercurial > repos > recetox > aplcms_to_ramclustr_converter

changeset 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
files hdf_converter.py hdf_converter.xml
diffstat 2 files changed, 7 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/hdf_converter.py	Tue Dec 15 17:38:07 2020 +0000
+++ b/hdf_converter.py	Wed Dec 16 17:28:30 2020 +0000
@@ -53,8 +53,8 @@
     except KeyError:
         sys.exit("Selected table does not exist in HDF dataframe")
 
-    RamClutsr_data = join_samples(aplcms_table)
-    RamClustr_data = convert_to_RamClustR(RamClutsr_data)
+    RamClustr_data = join_samples(aplcms_table)
+    RamClustr_data = convert_to_RamClustR(RamClustr_data)
     output = args[0]
     RamClustr_data.to_csv(output, sep=';')
     print("Table '{}' of HDF dataset is converted to csv for RamClutsR".format(options.table))
--- a/hdf_converter.xml	Tue Dec 15 17:38:07 2020 +0000
+++ b/hdf_converter.xml	Wed Dec 16 17:28:30 2020 +0000
@@ -11,12 +11,12 @@
     <inputs>
         <param name="hdf_dataframe" type="data" format="h5" label="apLCMS Dataset"/>
         <param name="table_name" type="select" label="Table Name">
-            <option value="peaks">Peaks</option>
-            <option value="aligned_peaks">Aligned Peaks</option>
+            <option value="peaks">peaks</option>
+            <option value="aligned_peaks">aligned peaks</option>
         </param>
     </inputs>
     <outputs>
-        <data format="csv" name="out_file" label="${hdf_dataframe.name}"/>
+        <data format="csv" name="out_file" label="CSV with ${table_name} from ${hdf_dataframe.name}"/>
     </outputs>
     <tests>
         <test>
@@ -26,12 +26,12 @@
         </test>
     </tests>
     <help><![CDATA[
-        Tool to convert apLCMS output to csv file formated in accordance to `RamClustR (CSV) <https://umsa.cerit-sc.cz/root?tool_id=testtoolshed.g2.bx.psu.edu/repos/recetox/ramclustr_csv/ramclustr_csv/1.1.0+galaxy0>`_ input requirements.
+        Tool to convert apLCMS output to csv file formated in accordance to RamClustR (CSV) input requirements.
 
         **Workflow position**
 
         - Upstream tool: `apLCMS <https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms>`_  Unsupervised or Hybrid
 
-        - Downstream tool: `RamClustR (CSV) <https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr>`_
+        - Downstream tool: `RamClustR <https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr>`_ (CSV)
     ]]></help>
 </tool>
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