<tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@+galaxy0">
  <description>
    classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data.
  </description>
  <macros>
   <token name="@VERSION@">1.0</token>
  </macros>
  <requirements>
    <requirement type="package" version ="@VERSION@">cryptogenotyper</requirement>
  </requirements>
  <version_command>cryptogenotyper --version</version_command>
  <command detect_errors="exit_code">
     <![CDATA[

     #set $ref_file=''

     #if $db
        ln -s '${db}' '${db.name}' &&
        #set $ref_file = $db.name
     #end if

     #if $primers['seqtype'] == 'contig'
        ln -s '${$primers.abi_input['forward']}' '${primers.abi_input.name}_forward.ab1' &&
        ln -s '${$primers.abi_input['reverse']}' '${primers.abi_input.name}_reverse.ab1' &&
        cryptogenotyper -i '.' -m '$marker' -t '$primers.seqtype' -f 'forward' -r 'reverse'
        #if $db
          --databasefile $ref_file
        #end if
     #else
        ln -s '${primers.abi_input}' '${primers.abi_input.element_identifier}' &&
        cryptogenotyper -i './${primers.abi_input.element_identifier}' -m '$marker' -t '$primers.seqtype'
        #if $db
          --databasefile $ref_file
        #end if
     #end if
     $outputheader
     -o 'result'
     ]]>
  </command>
  <inputs>
      <param name="marker" type="select" label="Marker">
          <option value="18S">SSU rRNA</option>
          <option value="gp60">gp60</option>
      </param>
      <param name="db" type="data" optional="true" format="fasta" label="Reference Database File (optional):"/>
      <conditional name="primers">
        <param name="seqtype" type="select" label="Type of Sequences">
            <option value="forward">Forward Only</option>
            <option value="reverse">Reverse Only</option>
            <option selected="true" value="contig">Contig</option>
        </param>
        <when value="contig">
          <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)"/>
        </when>
        <when value="forward">
          <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)"/>
        </when>
        <when value="reverse">
          <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)"/>
        </when>
     </conditional>
     <param name="outputheader" type="boolean" truevalue="" falsevalue="--noheaderline" checked="true" label="Output header line in the report?">
     </param>


  </inputs>
  <outputs>
    <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/>
    <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" label="${tool.name}:${on_string}:reports"/>
  </outputs>

  <tests>
    <test expect_num_outputs="2">
      <param name="marker" value="18S"/>
      <param name="seqtype" value="forward"/>
      <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/>
      <output name="outfile_report" ftype="tabular">
          <assert_contents>
              <has_text_matching expression="C.parvum"/>
          </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <param name="marker" value="gp60"/>
      <param name="seqtype" value="forward"/>
      <param name="abi_input"  value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>
      <output name="outfile_report" ftype="tabular" >
          <assert_contents>
              <has_text_matching expression="C.parvum"/>
          </assert_contents>
      </output>
    </test>
  </tests>


  <help>


**Syntax**

CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.
For more information please visit https://github.com/phac-nml/CryptoGenotyper.

-----

**Input:**

AB1 file(s) representing *Cryptosporidium's* SSU rRNA or gp60 locus (forward, reverse, or contig (forward and reverse paired-end reads)).
Optional: A custom reference database in .fa file format, to be used during the homology search for *Cryptosporidium* classification.


**Output:**

FASTA file containing the identification of the *Cryptosporidium* species/subtype and its corresponding sequence for each sample.
  </help>
  <citations>
    <citation type="bibtex">
  @misc{githubCryptoGenotyper,
  author = {Yanta C, Bessonov K, Robinson G, Troell K, Guy R},
  title = {CryptoGenotyper: a new bioinformatics tool to enhance Cryptosporidium identification},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/phac-nml/CryptoGenotyper}
    }</citation>
  </citations>

</tool>