<tool id="FeaturesParser" name="Parse GFF3 features" version="0.9.1">
  <description>in sRbowtie alignment</description>
  <requirements><requirement type='package'>bowtie-inspect</requirement></requirements>
  <parallelism method="basic"></parallelism>
<command interpreter="python">
        FeaturesParser.py 
	          #if $refGenomeSource.genomeSource == "history":
                    $refGenomeSource.ownFile ## index source  ## 1
         	    --do_not_extract_index  ## 2
          	  #else:
		    #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
            	    $reference   ## index source ## 1
            	    --extract_index  ## 2
          	  #end if
		  $output ## 3
		  $gff3 ## 4
		  #for $i in $refGenomeSource.input_list
    		    $i $i.ext "$i.name"
		  #end for

</command>
  <inputs>
       <conditional name="refGenomeSource">
           <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
               <option value="indexed">Use a built-in index</option>
               <option value="history">Use one from the history</option>
           </param>
           <when value="indexed">
               <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true">
                  <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
               </param>
           </when>
           <when value="history">
                <param name="ownFile" type="data" format="fasta"  label="Select the fasta reference" />
	        <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/>
           </when>
       </conditional>  <!-- refGenomeSource -->
       <param name="gff3" type="data" format="gff3" label="A GFF3 with features' coordinates"/>
   </inputs>
   <outputs>
   <data format="tabular" name="output" label="Feature Counts  Lists"/>
   </outputs>
  <help>

**What it does**

Parses Features Counts from one or several sRBowtie alignments (in tabular, Sam or Bam format).

Both sense and antisense alignments are counted

The library labels are infered from the input dataset names in the galaxy history.

**It is thus essential that input datasets are appropriately renamed**

**it is preferable that you do not put any space in this input dataset names. You may edit these names in the history**



  </help>
</tool>