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<tool id="pathoscope_map" name="Pathoscope Map" version="0.1.0">
  <description> Pathoscope Map </description>
  <requirements>
    <requirement type="package" version="2.0.6"> pathoscope </requirement>
  </requirements>
  <command> <![CDATA[
    pathoscope MAP
    #if str($library.type) == "single"
      -U $fastqU
    #elif str($library.type) == "paired"
      -1 $fastq1
      -2 $fastq2
    #end if
    -indexDir $targetAlignPrefixes.fields.path
    -targetAlignPrefixes $targetAlignPrefixes
    -filterAlignPrefixes $filterAlignPrefixes
    ]]>
  </command>
  <inputs>
    <conditional name="library">
      <param name="type" type="select" label="Is this single or paired library" help="">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
      </param>
      <when value="single">
        <param name="fastqU" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
      </when>
      <when value="paired">
        <param name="fastq1" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
        <param name="fastq2" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
      </when>
    </conditional>
    <param name="targetAlignPrefixes" type="select" label="targetAlignPrefixes" help="Target Index Prefixes">
        <options from_data_table="pathoscope_indexes">
          <column name="value" index="0"/>
          <column name="name" index="0"/>
          <column name="path" index="0"/>
        </options>
    </param>
    <param name="filterAlignPrefixes" type="select" label="filterAlignPrefixes" help="Filter Alignment Files Prefixes">
      <options from_data_table="pathoscope_indexes">
        <column name="value" index="0"/>
        <column name="name" index="0"/>
        <column name="path" index="0"/>
      </options>
    </param>
  </inputs>
  <outputs>
  </outputs>
  <help>
    This module will take your reads and map them against a target library. Then it will map the mapping reads
against a filter library. All the reads that map to the filter library with a score equal or greater than the mapping
score to the target library will be discarded. The reads mapping with a better score to the target library will be
used downstream by the PathoID module.
  </help>
  <citations>
    <citation type="doi">10.1101/gr.150151.112</citation>
    <citation type="doi">10.1186/2049-2618-2-33</citation>
    <citation type="doi">10.1186/1471-2105-15-262</citation>
    <citation type="doi">10.4137/CIN.S13890</citation>
  </citations>
</tool>