<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[
    #from os import listdir
    #set path=$targetIndexPrefixes.fields.path.split(',')[0]
    #set prefixes=[f for f in listdir(path) if f.endswith(".3.bt2")]
    #set targetRefs=str($targetIndexPrefixes)
    #set targetR=targetRefs.split(',')
    #set p=[]
    #for $f in prefixes
      #for $t in targetR
        #if $t in f
          #set p = p + [f[:-6]]
        #end if
      #end for
    #end for
    #set target=','.join(p)
    pathoscope MAP
    #if str($reads.type) == "single"
      -U $fastqU
    #elif str($reads.type) == "paired"
      -1 $fastq1
      -2 $fastq2
    #end if
    -indexDir $path
    -targetIndexPrefixes $target
    -filterIndexPrefixes $filterIndexPrefixes 2>&1
    && mv outalign.sam "$outalign"
    && mv pathomap-appendAlign.fq "$pathomap_appendAlign"
    ]]>
  </command>
  <inputs>
    <conditional name="reads">
      <param name="type" type="select" label="Is this single or paired reads" 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="targetIndexPrefixes" multiple="true" type="select" label="targetIndexPrefixes" help="Target Index Prefixes">
        <options from_data_table="pathoscope_indexes">
          <filter type="sort_by" column="2"/>
          <validator type="no_options" message="No indexes are available for the selected input dataset"/>
        </options>
    </param>
    <param name="filterIndexPrefixes" multiple="true" type="select" label="filterIndexPrefixes" help="Filter Index Prefixes">
      <options from_data_table="pathoscope_indexes">
        <filter type="sort_by" column="2"/>
        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
      </options>
    </param>
  </inputs>
  <outputs>
    <data format="sam" name="outalign" label="outalign.sam" />
    <data format="fastqsanger" name="pathomap_appendAlign" label="pathomap_appendAlign.fastq" />
  </outputs>

  <help>
  IMPORTANT: The name and the path of the reference database (with bowtie indexed)
  should be added to the pathoscope.loc entry.
  </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>