<tool id="filterstat" name="Filter Stats" version ="@VERSION@+galaxy1">
  <description>Identify number of positions excluded based on filtered status</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code">
      filter-stats.pl -i $tabfile
      #if $summary:
        -a
      #end if
	> $out
  </command>
  <inputs>
    <param name="tabfile" type="data"  label="SNV-alignment positions tab delimited file" format="tabular"/>
    <param name="summary" type="select" display="checkboxes" label="Summary Options" multiple="true">
        <option value="invalids">Include all entries marked as 'filtered-invalid'</option>
    </param>
  </inputs>
  <outputs>
    <data format="tabular" name="out" />
  </outputs>
  <tests>
    <test>
      <param name="tabfile" value="filter-stats-in.tsv" />
      <output name="out" file="filter-stats-out.tabular" />
    </test>
  </tests>

  <help>
What it does
============

This script prints a stat summary of the number of N's and -'s found in the SNV-alignment positions tab delimited file.


Usage
=====

**Parameters**
  - input - The SNV-alignment positions tab delimited file


**Options**
  - -all When this option is set, the summary will include all the entries marked as 'filtered-invalid'
  </help>
  <expand macro="citations"/>
</tool>