view seqtk_comp.xml @ 1:61718851f199 draft

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<?xml version="1.0"?>
<tool id="seqtk_comp" name="seqtk_comp" version="@WRAPPER_VERSION@.0">
  <description>get the nucleotide composition of FASTA/Q</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[seqtk comp
#if $in_bed:
-r $in_bed
#end if

$in_file | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1'

> $default]]></command>
  <inputs>
    <expand macro="in_faq"/>
    <param name="in_bed" optional="True" type="data" format="bed" label="bed file"/>
  </inputs>
  <outputs>
    <data format="tabular" hidden="false" name="default" label="Nucleotide composition of $in_file.name"/>
  </outputs>
  <tests>
    <test>
      <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
      <output name="default" file="seqtk_comp.out" ftype="tabular"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Reports composition of fasta/fastq sequences. For an example sequence like

::
    >test0
    ACTGACTGAA
    >ambig_ref
    ACGTCGTGTTVHDBN

The seqtk tool will report:

::

    #chr       length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
    test0      11     4  2  2  2  0  0  1  0    0   0   0
    ambig_ref  15     1  2  3  4  0  4  1  4    0   0   0


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