kt_extract.xml

<tool id="kt_extract" name="ktoolu extract reads" version="0.1.0">
    <description>Extract reads that were assigned a chosen taxonomy id or belong to a taxonomic subtree.</description>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command interpreter="python"><![CDATA[
        kt_extract.py
         --db "${databaseChoice.fields.path}"
         --inR1 "${inputData.inputR1}"
         --outR1 "${outputR1}"

        #if $inputData.inputFormat == "pairedFastq" or $inputData.inputFormat == "pairedFasta":
          --inR2 "${inputData.inputR2}"
          --outR2 "${outputR2}"
        #end if

        #if $inputData.inputFormat == "singleFastq" or $inputData.inputFormat == "pairedFastq":
          --input-format "fq"
        #else:
          --input-format "fa"
        #end if

        --kraken-results "${kraken_results}"

        #if $includeUnclassifiedReads == "includeUnclassifiedYes":
          --include-unclassified
        #end if

        #if $keepTaxIDs != "":
          --keep-taxids "${keepTaxIDs}"
        #end if

        #if $dropTaxIDs != "":
          --drop-taxids "${dropTaxIDs}"
        #end if

        #if $vipTaxIDs != "":
          --vip-taxids "${vipTaxIDs}"
        #end if
        > ${logfile}
    ]]></command>
    <inputs>
      <param name="databaseChoice" type="select" label="Select a kraken database">
        <options from_data_table="krakenDBs">
          <filter type="sort_by" column="2" />
          <validator type="no_options" message="No databases are available" />
        </options>
      </param>
      <param name="kraken_results" type="data" format="tabular" label="Kraken classification output" />
      <conditional name="inputData">
        <param name="inputFormat" type="select" label="Please select input file type and library type.">
          <option value="singleFastq">Single-end Fastq</option>
				  <option value="pairedFastq">Paired-end Fastq</option>
          <option value="singleFasta">Single-end Fasta</option>
          <option value="pairedFasta">Paired-end Fasta</option>
        </param>
        <when value="singleFastq">
          <param name="inputR1" type="data" format="fastq,fq,fastqsanger,fastqsolexa,fastqillumina,fastq.gz,fq.gz,fastq.bz2,fq.bz2" label="Forward/single end (R1) Fastq file" />
        </when>
        <when value="pairedFastq">
          <param name="inputR1" type="data" format="fastq,fq,fastqsanger,fastqsolexa,fastqillumina,fastq.gz,fq.gz,fastq.bz2,fq.bz2" label="Forward/single end (R1) Fastq file" />
          <param name="inputR2" type="data" format="fastq,fq,fastqsanger,fastqsolexa,fastqillumina,fastq.gz,fq.gz,fastq.bz2,fq.bz2" label="Reverse (R2) Fastq file" />
        </when>
        <when value="singleFasta">
          <param name="inputR1" type="data" format="fasta,fa,fas,fasta.gz,fa.gz,fas.gz,fasta.bz2,fa.bz2,fas.bz2" label="Forward/single end (R1) Fasta file" />
        </when>
        <when value="pairedFasta">
          <param name="inputR1" type="data" format="fasta,fa,fas,fasta.gz,fa.gz,fas.gz,fasta.bz2,fa.bz2,fas.bz2" label="Forward/single end (R1) Fasta file" />
          <param name="inputR2" type="data" format="fasta,fa,fas,fasta.gz,fa.gz,fas.gz,fasta.bz2,fa.bz2,fas.bz2" label="Reverse (R2) Fasta file" />
        </when>
      </conditional>
      <param name="keepTaxIDs" type="text" value="" default="" label="Extract all reads that were classified to belong to a subtree rooted at these taxonomy IDs.">
        <sanitizer invalid_char=",">
          <valid initial="string.digits">
            <add value="," />
          </valid>
        </sanitizer>
      </param>
      <param name="dropTaxIDs" type="text" value="" default="" label="Ignore all reads that were classified to belong to a subtree rooted at these taxonomy IDs.">
        <sanitizer invalid_char=",">
          <valid initial="string.digits">
            <add value="," />
          </valid>
        </sanitizer>
      </param>
      <param name="vipTaxIDs" type="text" value="" default="" label="Extract all reads that were classified as one of these taxonomy IDs (overrides ignored subtrees).">
        <sanitizer invalid_char=",">
          <valid initial="string.digits">
            <add value="," />
          </valid>
        </sanitizer>
      </param>

      <param name="includeUnclassifiedReads" type="select" label="Include unclassified reads?">
        <option value="includeUnclassifiedNo">No</option>
        <option value="includeUnclassifiedYes">Yes</option>
      </param>
    </inputs>
    <outputs>
      <data format="tabular" name="logfile" label="${tool.name} logfile" />
      <data format="inputR1" name="outputR1" label="${tool.name} filtered R1-reads of ${on_string}" />
      <data format="inputR2" name="outputR2" label="${tool.name} filtered R2-reads of ${on_string}">
        <filter>inputFormat == "pairedFastq" or inputFormat == "pairedFasta</filter>
      </data>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>