<tool id="cuffquant" name="Cuffquant" version="@VERSION@.1">
    <!-- Wrapper supports Cuffdiff versions 2.2.1 -->
    <description>Precompute gene expression levels</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command><![CDATA[cuffquant 2>&1 | head -n 1]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        cuffquant
            --no-update-check
            --num-threads=\${GALAXY_SLOTS:-4}
            ## Set advanced SE data parameters?
            #if $additional.sAdditional == "Yes":
                -m $additional.frag_mean_len
                -s $additional.frag_len_std_dev
            #end if

            ## Multi-read correct?
            #if $multiread_correct :
            -u
            #end if

            ## Bias correction?
            #if $bias_correction.do_bias_correction == "Yes":
               -b
                #if $bias_correction.seq_source.index_source == "history":
                    ## Custom genome from history.
                    '$bias_correction.seq_source.ref_file'
                #else:
                    ## Built-in genome.
                    '${bias_correction.seq_source.index.fields.path}'
                #end if
            #end if

            $length_correction

            ## Set advanced parameters for cufflinks
            #if $advanced_settings.sAdvanced == "Yes":
                #if str($advanced_settings.library_type) != 'auto':
                    --library-type=$advanced_settings.library_type
                #end if
                #if $advanced_settings.mask_file:
                    --mask-file '$advanced_settings.mask_file'
                #end if
                --max-mle-iterations=$advanced_settings.max_mle_iterations
                --max-bundle-frags=$advanced_settings.max_bundle_frags
            #end if
            ## Inputs.
            '$gtf_input'
            #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] )
            '$samplestring'
    ]]></command>
    <inputs>
        <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts"
            help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/>

        <repeat name="samples" title="Replicate" min="1">
            <param name="sample" label="Add replicate" type="data" format="sam,bam"/>
        </repeat>

        <param name="multiread_correct" type="boolean" label="Use multi-read correct"
            help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." />

        <conditional name="bias_correction">
            <param name="do_bias_correction" type="select" label="Perform Bias Correction"
                help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
                <option value="No">No</option>
                <option value="Yes">Yes</option>
            </param>
            <when value="Yes">
                <conditional name="seq_source">
                  <param name="index_source" type="select" label="Reference sequence data">
                    <option value="cached">Locally cached</option>
                    <option value="history">History</option>
                  </param>
                  <when value="cached">
                    <param name="index" type="select" label="Using reference genome">
                      <options from_data_table="fasta_indexes">
                        <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
                        <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
                      </options>
                    </param>
                  </when>
                  <when value="history">
                      <param name="ref_file" type="data" format="fasta" label="Using reference file" />
                  </when>
                </conditional>
            </when>
            <when value="No"></when>
        </conditional>

        <param name="length_correction" type="select" label="apply length correction" help="mode of length normalization to transcript fpkm.">
            <option value="" selected="true">cufflinks effective length correction</option>
            <option value="--no-effective-length-correction">standard length correction</option>
            <option value="--no-length-correction">no length correction at all (use raw counts)</option>
        </param>

        <conditional name="additional">
            <param name="sAdditional" type="select" label="Set Additional Parameters for single end reads? (not recommended for paired-end reads)">
                <option value="No" selected="True">No</option>
                <option value="Yes">Yes</option>
            </param>
            <when value="No"></when>
            <when value="Yes">
                <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/>
                <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/>
            </when>
        </conditional>

        <conditional name="advanced_settings">
            <param name="sAdvanced" type="select" label="Set Advanced Cuffquant parameters? ">
                    <option value="No" selected="True">No</option>
                    <option value="Yes">Yes</option>
                </param>
        <when value="No"></when>
        <when value="Yes">
            <param type="select" name="library_type" label="Library prep used for input reads" help="">
                <option value="auto" selected="True">Auto Detect</option>
                <option value="ff-firststrand">ff-firststrand</option>
                <option value="ff-secondstrand">ff-secondstrand</option>
                <option value="ff-unstranded">ff-unstranded</option>
                <option value="fr-firststrand">fr-firststrand</option>
                <option value="fr-secondstrand">fr-secondstrand</option>
                <option value="fr-unstranded" >fr-unstranded</option>
                <option value="transfrags">transfrags</option>
            </param>
            <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" />
            <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" />
            <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus"
                help="Sets the maximum number of fragments a locus may have before being skipped. Default: 500,000" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <!-- Standard datasets. -->
        <data format="cxb" name="out_file" label="${tool.name} on ${on_string}: Abundances.cxb" from_work_dir="abundances.cxb" />
    </outputs>
    <tests>
        <test>
            <!--
                cuffquant cuffcompare_out5.gtf cuffdiff_in1.sam,cuffdiff_in2.sam
            -->
            <param name="gtf_input" value="cuffquant_in.gtf" ftype="gtf" />
            <repeat name="samples">
                <param name="sample" value="cuffquant_in1.sam" ftype="sam" />
            </repeat>
            <repeat name="samples">
                <param name="sample" value="cuffquant_in2.sam" ftype="sam" />
            </repeat>
            <param name="length_correction" value="" />
            <param name="do_bias_correction" value="No" />
            <param name="multiread_correct" value="No"/>
            <param name="sAdditional" value="No"/>
            <param name="sAdvanced" value="No" />
            <output name="out_file" file="cuffquant_out1.cxb" compare="sim_size" />
        </test>
    </tests>

    <help>
**Cuffquant Overview**

Cuffquant is part of Cufflinks_. Cuffquant provides pre-calculation of gene expression levels. The resulting file can be provided to cuffdiff or cuffnorm for further processing.  Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621

.. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/

------

**Know what you are doing**

.. class:: warningmark

There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.

.. __: http://cole-trapnell-lab.github.io/cufflinks/cuffquant/

------

**Input format**

Cuffquant takes Cufflinks or Cuffcompare GTF files as input along with two or more SAM files containing the fragment alignments for two or more samples.

------

**Outputs**

Cuffquant produces one output file:

1. Transcript expression values in binary format.

-------

**Settings**

All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here.

------

**Cuffdiff parameter list**

This is a list of implemented Cuffdiff options::

  -m INT                         Average fragment length (SE reads); default 200
  -s INT                         Fragment legnth standard deviation (SE reads); default 80
  --max-mle-iterations INT       Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000
  -u                             Multi read correction tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.
  -b ref.fasta             bias correction. Bias detection and correction can significantly improve accuracy of transcript abundance estimates.
  --no-effective-length-correction  Use standard length correction
  --no-length-correction         Disable all length correction.
  --library-type                 ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
  --mask-file (gff3/gtf)         Ignore all alignment within transcripts in this file
  --max-bundle-frags             Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.
    </help>
    <expand macro="citations"/>
</tool>