view LINE_html_4_1.xml @ 0:4060fe70a3e8 draft

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<tool name="chimericLineFinder4" id="LINE mosaic transcripts finder4" version="0.4.1">
  <description>Find chimerics transcripts containing LINEs sequences</description>
  <command interpreter="perl">
   
   LINE_html4.1.pl
  
    --first ${first}
    --name ${first.name}
    --second ${second}
    

    #if $Genome.refGenomeSource == "history":
    --ref "${Genome.ownFile}"
    --build_index
    #else:
    --ref "${Genome.indices.fields.path}"
    #end if
   
    #if $TE.refGenomeSource == "history":
    --TE "${TE.ownFile}"
    --build_TE
    #else:
    --TE "${TE.indices.fields.path}"
    #end if


    #for $input_file in $input_files:
      --first ${input_file.first}
      --name ${input_file.first.name}
      --second ${input_file.second}
    #end for
    --html $chimerae
    --html_path ${chimerae.files_path}
    --size_insert $size_insert
    --size_read $size
    --pourcentage $prct
    --image $image
    --BDir $BDir
    --minL1 $minL1
    --mis_L1 $mis_L1
    
  
  </command>
  
   <requirements>
        <requirement type="package" version="3.1.0">R</requirement>
        <requirement type="package" version="0.7.12">bwa</requirement>
        <requirement type="package" version="2.17.0">bedTools</requirement>
    </requirements>
  
  <inputs>
    <param format="fastqsanger" name="first" type="data" label="first set of paired-end reads" help=""/>
    <param format="fastqsanger" name="second" type="data" label="second set of paired-end reads" help=""/>
    <repeat name="input_files" title="Additional Fastq Files">
      <param name="first" type="data" format="fastqsanger" label="FASTQ file" help="first set of paired-end reads" />
      <param name="second" type="data" format="fastqsanger" label="FASTQ file" help="second set of paired-end reads" />
    </repeat>

  <conditional name="Genome">
    <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
      <option value="indexed">Use a built-in index</option>
      <option value="history">Use one from the history</option>
    </param>
    <when value="indexed">
      <param name="indices" type="select" label="Select a reference genome">
        <options from_data_table="bwa_indexes">
          <filter type="sort_by" column="2" />
          <validator type="no_options" message="No indexes are available" />
        </options>
      </param>
    </when>
    <when value="history">
      <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
    </when>
  </conditional>


  <conditional name="TE">
    <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?">
      <option value="indexed">Use a built-in index</option>
      <option value="history">Use one from the history</option>
    </param>
    <when value="indexed">
      <param name="indices" type="select" label="Select a TE reference">
        <options from_data_table="bwa_indexes">
          <filter type="sort_by" column="2" />
          <validator type="no_options" message="No indexes are available" />
        </options>
      </param>
    </when>
    <when value="history">
      <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
    </when>
  </conditional>

    <param name="BDir" type="select" >
        <option value="0">Undirectional libraries</option>
        <option value="1">TEs sequences in first read in pair</option>
        <option value="2">TEs sequences in second read in pair</option>
    </param>

    <param name="size" type="integer" value="100" label="reads size"/>
    <param name="size_insert" type="integer" value="250" label="maximum insert size (bp)"/>
    <param name ="minL1" type="integer" value="50" label="minimun bp mapping on selected TEs database"/>
    <param name ="mis_L1" type="integer" value="2" label="number of mismatches tolerated in TEs mapping sequences"/>
    <param name="prct" type="integer" value="33" label="minimum consecutive bp corresponding to a unique sequence"/>
  </inputs>
  <outputs>
    <data format="html" name="chimerae" label="${tool.name}_on_${on_string}"/>
  </outputs>
</tool>