<tool id="removeFastaSubSequence" name="Remove Fasta Substring Sequence" version="1.0.0">
  <description>Removes sequences from query fasta file that are present in a reference Fasta File.</description>
  <requirements>
      <requirement type="package" version="1.70">biopython</requirement>
  </requirements>
  <command interpreter="python"><![CDATA[removeFastaSubSequence.py $ref_fastafile $query_fastafile $output]]></command>
  <inputs>
    <param name="ref_fastafile" type="data" format="fasta">
      <label>Input Reference Fasta File</label>
    </param>
    <param name="query_fastafile" type="data" format="fasta">
      <label>Input Query Fasta File</label>
    </param>
  </inputs>

  <outputs>
    <data format="fasta" name="output" label="uniqSeq_${query_fastafile.name.rsplit('.',1)[0]}.fasta" />
  </outputs>
  
  <tests> 
    <test>
      <param name="ref_fastafile" value="test_ref.fasta" />
      <param name="query_fastafile" value="test_query.fasta" />
      <output name="output" file="uniqSeq_test_query.fasta">
        <assert_contents>
            <has_text text="ENSMUST00000193003" />
        </assert_contents>
      </output>
    </test>
  </tests>
  
  
  <help>
This program removes the sequences from the query fasta file that are present in a reference fasta file (removes even those query sequences that are present as substring in reference fasta file).

EXAMPLE:

----

Ref sequences:

>reference_seq_1

TSLDKDHLELCCTLSLPFSWACSWVLVLRLSINGQLPRSRLWAAHCLWGVP

>reference_seq_2

RGLCISGLEKEVQVQSRQAEGPVHLWLRKGSTSAE

----

Query Sequences:

>query_seq_1

TKTILNYAVLSPCLSPGHVLGC


>query_seq_2

LDKDHLELCCTLSLPFSWACSWVLVL


>query_seq_3

LWGVPRGLCISG

----

Output Sequences:

>query_seq_1

TKTILNYAVLSPCLSPGHVLGC


>query_seq_3

LWGVPRGLCISG

----

Output Sequence file will have only query_seq_1 and query_seq_3. query_seq_2 is removed because query_seq_2's sequence "LDKDHLELCCTLSLPFSWACSWVLVL" is 
present as substring in reference_seq_1's sequence "TSLDKDHLELCCTLSLPFSWACSWVLVLRLSINGQLPRSRLWAAHCLWGVP".

  </help>
</tool>