annotate alignTophat.xml @ 13:cc676ee7fe40 draft

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<tool id="alignTophat" name="align RNAseq" version="0.0.1">
  <description>Align directionnal RNAseq to obtain bedgraphs and raw count file</description>
  <command interpreter="perl">
    
    ./alignTophat.pl
    
    --fastq ${first_input}
    --fastq_n ${first_input.name}
    
    #if $Genome.refGenomeSource == "history":
    --ref "${Genome.ownFile}"
    --build_ref
    #else:
    --ref "${Genome.indices.fields.path}"
    #end if
    
    #if $contaminants.refGenomeSource == "history":
    --contaminants "${contaminants.ownFile}"
    --build_contaminant
    #else:
    --contaminants "${contaminants.indices.fields.path}"
    #end if
    #if $anno.bedpipe == "history":
      --anno "${anno.ownFile}"
    #else:
      --anno "${anno.indices.fields.path}"
    #end if

    --mis  $mis
    --ma $ma
    
    --dirbam $dirbam
    --dirbamCont $dirbamcont
    --dirbedgraph $dirbedgraph
    
    --text $text
    
    --random_w $rand
    --find $idDir.find
    --direction $idDir.direc
  </command>
  <inputs>
    
    <param format="fastqsanger" name="first_input" type="data" label="fastq produced by fasteris" help=""/>
    
    
    <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="bowtie2_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="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="bowtie2_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="contaminants">
      <param name="refGenomeSource" type="select" label="Will you select contaminants 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 contaminants reference">
          <options from_data_table="bowtie2_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="anno">
      <param name="bedpipe" type="select" label="Will you select an annotation file from your history or use a built-in index?" help="tab file format, (chr start end id score strand type description1 description2 description3">
        <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 annotation file">
          <options from_data_table="bed_pipe">
            <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="bed" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>
    
    
    <param name="mis" type="integer" value="0" label="mismatches"/>
    <param name="ma" type="integer" value="0" label="normalization value" help="e.g number of mappers (if 0 auto)"/> 
    <param name="rand" type="boolean" checked="false" label="work on multi-mappers randomly assigned"/>


    <conditional name="idDir">
      <param name="direc" type="boolean" checked="true" label="directional library"/>
      <when value="false">
        <param name="find" type="hidden" value="false"/>
      </when>
      <when value="true">
        <param name="find" type="boolean" checked="true" label="auto sens finder"/>
      </when>
     </conditional>
  </inputs>
  
  <outputs>
    <data format="tar" name="dirbam" label="alignement_zip_${first_input.name}"/>
    <data format="tar" name="dirbamcont" label="contaminant_zip_${first_input.name}"/>
    <data format="tar" name="dirbedgraph" label="bedgraph_zip_${first_input.name}"/>
    <data format="tabular" name="text" label="raw_count_tabular_${first_input.name}_rand_${rand}"/>
  </outputs>
  
  <requirements>
    <requirement type="package" version="2.2.6">bowtie2</requirement>
    <requirement type="package" version="2.1.0">tophat</requirement>
    <requirement type="package" version="2.24.0">bedtools</requirement>
    <requirement type="package" version="1.2">samtools</requirement>
   </requirements>
  
</tool>