<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.0">
  <description>by iterative alignments with sRbowtie</description>
  <requirements>
        <requirement type="package" version="1.1.2">bowtie</requirement>
  </requirements>
  <command  detect_errors="exit_code"><![CDATA[
        #if $refGenomeSource1.genomeSource == "history":
            bowtie-build -f $refGenomeSource1.ownFile genome  1>/dev/null &&
            ln -s -f '$refGenomeSource1.ownFile' genome.fa &&
            #set index_path = 'genome'
        #else:
            #set index_path = $refGenomeSource1.index.fields.path
        #end if
        #if $input.extension == "fasta":
            #set format = "-f"
        #elif $input.extension == "fastq":
            #set format = "-q"
        #end if
        #if $format == '-f':
            input_nbr_read=\$(( \$(wc -l < $input)/2)) &&
        #elif $format == '-q':
            input_nbr_read=\$(( \$(wc -l < $input)/4)) &&
        #end if
        #set method_prefix = "-v %s -k 1 --best" % str($mismatches)
        bowtie -p \${GALAXY_SLOTS:-4}
               $method_prefix
               --al matched.fa
               --un unmatched.fa
               --suppress 6,7,8
               $index_path $format '$input' > tabular_bowtie_output.tab &&
        genome_aligned=\$(wc -l < matched.fa) &&
        genome_aligned=\$(( \$genome_aligned/2)) &&
        echo -e "$refGenomeSource1.ownFile.name Matched\t\${genome_aligned}\n" > $output &&
        #set counter = 0
        #for $i in $AdditionalQueries:
            rm genome.fa &&
            #set $counter += 1
            #if $counter != 1:
                #set input = "class_unmatched.fa"
            #else:
                #set input = "matched.fa"
            #end if
            touch temp_class_matched.fa temp_class_unmatched.fa &&
            bowtie-build -f $i.ownFile genome  1>/dev/null &&
            ln -s -f '$i.ownFile' genome.fa &&
            #set index_path = 'genome'
            bowtie -p \${GALAXY_SLOTS:-4}
                $method_prefix
                --al temp_class_matched.fa
                --un temp_class_unmatched.fa
                --suppress 6,7,8
                $index_path $format '$input' > tabular_bowtie_output.tab &&
            class_aligned=\$(( \$(wc -l < temp_class_matched.fa)/2)) &&
            class_unaligned=\$(( \$(wc -l < temp_class_unmatched.fa)/2)) &&
            mv temp_class_unmatched.fa class_unmatched.fa &&
            echo -e "$i.ownFile.name Matched\t\${class_aligned}\n" >> $output &&
        #end for
        remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
        echo -e "Unmatched to previous indexes\t\${remaining}\n" >> $output
        ]]></command>
  <inputs>
      <param name="input" type="data" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/>
    <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
        <option value="0">0</option>
        <option value="1" selected="true">1</option>
        <option value="2">2</option>
        <option value="3">3</option>
    </param>
<!-- First bowtie index selection -->
    <conditional name="refGenomeSource1">
      <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Bowtie 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="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact instance administrator">
          <options from_data_table="bowtie_indexes"/>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
      </when>
    </conditional>
<!-- End of first bowtie index selection -->
<!-- other  bowtie index selections from fasta in history (mandatory) -->
    <repeat name="AdditionalQueries" title="Additional Alignment Step">
        <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
    </repeat>
<!-- End of other bowtie index selections -->
   </inputs>
   <outputs>
   <data format="tabular" name="output" label="Cascade Annotation Analysis">
       <actions>
           <action name="column_names" type="metadata" default="Reference Index,Number of reads" />
       </actions>
    </data>
   </outputs>
    <tests>
        <test>
            <param name="input" value ="sample1.fa" ftype="fasta" />
            <param name="genomeSource" value="history" />
            <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
            <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
            <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
            <output name="output" ftype="tabular" file="sample1_output.tab" />
        </test>
        <test>
            <param name="input" value ="sample.fastq" ftype="fastq" />
            <param name="genomeSource" value="history" />
            <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
            <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
            <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
            <output name="output" ftype="tabular" file="sample_output.tab" />
        </test>
    </tests>
  <help>

**Introduction**

Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient.
A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.

Here The sRbowtie wrapper specifically works with short reads FASTA or FASTQ inputs
(-v bowtie mode, with -k 1) which has to be clipped from adapter before alignment.

.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml


------

**What it does**

.. class:: infomark

This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes.
Read that aligned to the first reference are realigned to the second reference.
From this point, unaligned reads are taken as input for alignment to the third reference, etc.


Reads are Matched on DNA references (both strands) as fast as possible, without taking care of mapping issues

*-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*

unaligned reads at step N are used as input for sRbowtie at step N+1

-----

**Input formats**

.. class:: warningmark

*Reads must be clipped from their adapter and provided in a FASTA or FASTQ format*

-----

**OUTPUTS**

**Annotation table in a tabular format**

  </help>
</tool>