view render_datatable.xml @ 7:b6ece07bec6a draft

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<tool id="PHYLO_render_datatable" name="Render CSV file" version="1.1.0">
  <description>as an interactive HTML table</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <stdio>
    <expand macro="basic_errors"/>
  </stdio>
  <command interpreter="bash">
    render_datatable-wrapper.sh $config
  </command>
  <inputs>
    <param name="input" type="data" format="csv" label="CSV file"/>
  </inputs>
  <outputs>
    <data format="html" name="output" label="Generated table"/>
  </outputs>
  <configfiles>
    <configfile name="config">
INPUT="${input}"

OUTPUT="${output}"
OUTPUT_DIR="${output.files_path}"
    </configfile>
  </configfiles>
  <!-- The contents of the help tag is parsed as reStructuredText. Please see
       help-template.rst for examples of commonly-used sections in other Galaxy
       tools. -->
  <help>

.. class:: infomark

**What it does**

This tool reformats a CSV file, like this::

    "seqname","accession","tax_id","species_name","is_type"
    "FM872653","FM872653","308994","Dialister propionicifaciens",0.0
    "AY331416","AY331416","239137","Candidate Division TM7 oral",0.0
    "DQ666092","DQ666092","95818_1","Candidate Division TM7 vaginal",0.0
    "S002223913","GQ900631","186802_3","bacterium BVAB3-Strain 1",0.0
    ...

into an interactive HTML table.

[placeholder]

+-------------+-----------+----------+---------------------------------------+----------+
|  seqname    | accession | tax_id   | species_name                          | is_type  |
+=============+===========+==========+=======================================+==========+
|  FM872653   | FM872653  | 308994   | Dialister propionicifaciens           | 0.0      |
+-------------+-----------+----------+---------------------------------------+----------+
|  AY331416   | AY331416  | 239137   | Candidate Division TM7 oral           | 0.0      |
+-------------+-----------+----------+---------------------------------------+----------+
|  DQ666092   | DQ666092  | 95818_1  | Candidate Division TM7 vaginal        | 0.0      |
+-------------+-----------+----------+---------------------------------------+----------+
|  S002223913 | GQ900631  | 186802_3 | bacterium BVAB3-Strain 1              | 0.0      |
+-------------+-----------+----------+---------------------------------------+----------+

...

  </help>
</tool>