annotate sRbowtie_wrapper.xml @ 0:05ae11c21834 draft

Uploaded

<tool id="sRbowtie" name="GED bowtie" version="1.0.0">
  <description>small RNA oriented</description>
  <requirements><requirement type='package'>bowtie</requirement></requirements>
  <parallelism method="basic"></parallelism>
  <command interpreter="python"> sRbowtie_wrapper.py $input
                                                    $method
                                                    $v_mismatches
                                                    $output_type
                                                    $refGenomeSource.genomeSource
                                                    ## the very source of the index (indexed or fasta file)
                                                    #if $refGenomeSource.genomeSource == "history":
                                                        $refGenomeSource.ownFile
                                                    #else:
                                                        $refGenomeSource.index
                                                    #end if
                                                    ##
                                                    $output
                                                    $aligned
                                                    $unaligned
  </command>
  <inputs>
      <param name="input" type="data" format="fasta" label="Input fasta file: reads clipped from their adapter" help="Only with clipped, raw fasta files"/>
<!-- which method will be used --> 
      <param name="method" type="select" label="What kind of matching do you want to do?" help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand">
        <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
        <option value="unique">Match unique mappers on DNA reference index</option>
        <option value="multiple" selected="true">Match on DNA, multiple mappers randomly matched at a single position</option>
        <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>
        <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
        <option value="a_option">Match and report all valid alignments</option>
      </param>

<!-- END of which method will be used -->

    <param name="v_mismatches" type="select" label="Number of mismatches allowed" help="specify the -v bowtie option">
        <option value="0">0</option>
        <option value="1" selected="true">1</option>
        <option value="2">2</option>
        <option value="3">3</option>
    </param>


<!-- nouvel index in dev below -->
    <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="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team">
          <options from_data_table="ged_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>
<!-- nouvel index input FIN -->
       <param name="output_type" type="select" label="Select output format" help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below">
          <option value="tabular" select="true">tabular</option>
          <option value="sam">sam</option>
          <option value="bam">bam</option>
       </param>
      
     <param name="additional_fasta" type="select" label="additional fasta output" help="to get aligned and unaligned reads in fasta format">
        <option value="No" select="true">No</option>
        <option value="al">aligned</option>
        <option value="unal">unaligned</option>
        <option value="al_and_unal">both aligned and unaligned</option>
     </param>

   </inputs>
   <outputs>
   <data format="tabular" name="output" label="Bowtie Output">
        <change_format>
            <when input="output_type" value="sam" format="sam" />
            <when input="output_type" value="bam" format="bam" />
        </change_format>
   </data>

   <data format="fasta" name="aligned" label="Matched reads">
	<filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
   </data>
   <data format="fasta" name="unaligned" label ="Unmatched reads">
        <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
   </data>
   </outputs>

  <help>

**What it does**

Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.

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

A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.

However, this useful Bowtie wrapper tool only takes as inputs FASTQ files.

Our sRbowtie wrapper is intented to work specifically with short reads FASTA inputs and to serve downstream small RNA sequencing analyses

------

**OPTIONS**

.. class:: infomark

This script uses Bowtie to match reads on a reference index.

Depending on the type of matching, different bowtie options are used:

**Match on sense strand RNA reference index, multiple mappers randomly matched at a single position**

Match on RNA reference, SENSE strand, randomly attributing multiple mapper to target with least mismatches, the polarity column is suppressed in the bowtie tabular report:

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

**Match unique mappers on DNA reference index**

Match ONLY unique mappers on DNA reference index

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

Note that using this option with -v values other than 0 is questionnable...

**Match on DNA, multiple mappers randomly matched at a single position**

Match multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:

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

**Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)**

Match with highest speed, not guaranteeing best hit for speed gain:

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


-----

**Input formats**

.. class:: warningmark

*The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*

-----

**OUTPUTS**

If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns::

    Column    Description
  --------    --------------------------------------------------------
   1 FastaID  fasta identifier
   2 polarity + or - depending whether the match was reported on the forward or reverse strand
   3 target     name of the matched target
   4 Offset   O-based coordinate of the miR on the miRBase pre-miR sequence
   5 Seq      sequence of the matched Read

If you choose SAM, you will get the output in unordered SAM format.

.. class:: warningmark

if you choose BAM, the output will be in sorted BAM format.
To be viewable in Trackster, several condition must be fulfilled:

.. class:: infomark

Reads must have been matched to a FULL genome whose chromosome names are compatible with Trackster genome indexes

.. class:: infomark

the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.

Please contact the GED galaxy team is your reference genome is not referenced properly in GED galaxy

**Optionnal matched and unmatched fasta reads can be obtained, for further annotations**

  </help>
</tool>