view txt_diagnosis/txtDiagnosis.xml @ 0:e1f0194cf8fc draft

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<tool id="txt_diagnosis" name="Check data" version="1.1">
  <description> in txt-converted FCS files.</description>
  <requirements>
    <requirement type="package" version="0.17.1">pandas</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
    python $__tool_directory__/txtdiagnosis.py -i "${input}" -o "${output}" -n "${input.name}"
  ]]>
  </command>
  <inputs>
    <param format="flowtext" name="input" type="data" label="Text file to check"/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="Report on ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input_error.txt"/>
      <output name="output" file="output_error.txt">
        <assert_contents>
          <has_text_matching text="WARNING: line 6 in .* contains non-numeric results"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="input_noerror.txt"/>
      <output name="output" file="output_noerror.txt">
        <assert_contents>
          <has_text text="No errors in the file."/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[
   This tool looks for potential errors in txt-converted FCS files.

-----

**Input**

This diagnosis tools reads in text files, and checks that the data is all numeric.

**Output**

The output is a report with the errors and corresponding line numbers.

-----

**Example**

*Input*::

   Marker1 Marker2 Marker3
   34      45      12
   NaN     65      10
   34      45      12
   33      NaN     10
   34      45      12
   33      65      10
   34      45      12
   33      65      NaN
   34      45      12
   33      65      10

*Output*::

   WARNING: line 2 in example_file.txt contains non-numeric results
   WARNING: line 4 in example_file.txt contains non-numeric results
   WARNING: line 8 in example_file.txt contains non-numeric results
  ]]>
  </help>
</tool>