view seqtk_fqchk.xml @ 0:e0a0fd938de4 draft

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<?xml version="1.0"?>
<tool id="seqtk_fqchk" name="seqtk_fqchk" version="@WRAPPER_VERSION@.0">
  <description>fastq QC (base/quality summary)</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[seqtk fqchk
-q $q
$in_file | awk '{if(NR<4){print "#"$0}else{print $0}}'
> $default]]></command>
  <inputs>
    <expand macro="in_fq"/>
    <param name="q" type="integer" value="20" label="quality values" help="use 0 to get the distribution of all quality values (-q)"/>
  </inputs>
  <outputs>
    <data format="tabular" hidden="false" name="default" label="Quality information for $in_file.name"/>
  </outputs>
  <tests>
    <test>
      <param name="in_file" value="seqtk_fqchk.fq"/>
      <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Returns quality score information base-by-base.

::

    @SEQ_ID1
    GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
    +
    !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

each based is examined individually and information reported:

::

    #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
    #POS  #bases  %A     %C    %G     %T     %N   avgQ  errQ  %low   %high
    #ALL  60      31.7   16.7  18.3   33.3   0.0  15.1  8.7   66.7   33.3
    1     1       0.0    0.0   100.0  0.0    0.0  0.0   3.0   100.0  0.0
    2     1       100.0  0.0   0.0    0.0    0.0  6.0   6.0   100.0  0.0
    3     1       0.0    0.0   0.0    100.0  0.0  6.0   6.0   100.0  0.0
    4     1       0.0    0.0   0.0    100.0  0.0  9.0   9.0   100.0  0.0
    5     1       0.0    0.0   0.0    100.0  0.0  7.0   7.0   100.0  0.0
    6     1       0.0    0.0   100.0  0.0    0.0  7.0   7.0   100.0  0.0
    7     1       0.0    0.0   100.0  0.0    0.0  7.0   7.0   100.0  0.0
    8     1       0.0    0.0   100.0  0.0    0.0  7.0   7.0   100.0  0.0
    9     1       0.0    0.0   100.0  0.0    0.0  9.0   9.0   100.0  0.0
    10    1       0.0    0.0   0.0    100.0  0.0  9.0   9.0   100.0  0.0

@ATTRIBUTION@
]]></help>
</tool>