<tool id="sailfish" name="Sailfish" version="0.10.1">
    <description>transcript quantification from RNA-seq data</description>
    <macros>
        <xml name="strandedness">
            <param name="strandedness" type="select" label="Specify the strandedness of the reads">
                <option value="U" selected="True">Not stranded (U)</option>
                <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
                <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
            </param>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="0.10.1">sailfish</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
        <regex match="Exception :" />
    </stdio>
    <version_command>sailfish -version</version_command>
    <command>
<![CDATA[
        #if $refTranscriptSource.TranscriptSource == "history":
            sailfish index
                --transcripts $refTranscriptSource.ownFile
                --kmerSize $refTranscriptSource.kmerSize
                --out ./index_dir
                --threads "\${GALAXY_SLOTS:-4}"
            #set $index_path = './index_dir'
        #else:
            #set $index_path = $refTranscriptSource.index.fields.path
        #end if
        &&
        #if $single_or_paired.single_or_paired_opts == 'single':
            #if $single_or_paired.input_singles.ext == 'fasta':
                #set $ext = 'fasta'
            #else:
                #set $ext = 'fastq'
            #end if
            ln -s $single_or_paired.input_singles ./single.$ext &&
        #else:
            #if $single_or_paired.input_mate1.ext == 'fasta':
                #set $ext = 'fasta'
            #else:
                #set $ext = 'fastq'
            #end if
            ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
            ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
        #end if
        #if $geneMap:
            ln -s "$geneMap" ./geneMap.$geneMap.ext &&
        #end if
        sailfish quant
            --index $index_path
            #if $single_or_paired.single_or_paired_opts == 'single':
                --libType ${single_or_paired.strandedness}
                --unmatedReads ./single.$ext
            #else:
                --mates1 ./mate1.$ext
                --mates2 ./mate2.$ext
                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
            #end if
            --output ./results
            $biasCorrect
            $gcBiasCorrect
            --threads "\${GALAXY_SLOTS:-4}"
            $dumpEq
            #if str($gcSizeSamp):
                --gcSizeSamp $gcSizeSamp
            #end if
            #if str($gcSpeedSamp):
                --gcSpeedSamp $gcSpeedSamp
            #end if
            #if str($fldMean):
                --fldMean $fldMean
            #end if
            #if str($fldSD):
                --fldSD $fldSD
            #end if
            #if $maxReadOcc:
                --maxReadOcc $maxReadOcc
            #end if
            #if $geneMap:
                --geneMap ./geneMap.${geneMap.ext}
            #end if
            $strictIntersect
            $noEffectiveLengthCorrection
            $useVBOpt
            $discardOrphans
            $unsmoothedFLD
            --maxFragLen ${maxFragLen}
            --txpAggregationKey '${txpAggregationKey}'
            $ignoreLibCompat
            $enforceLibCompat
            $allowDovetail
            #if str($numBiasSamples):
                --numBiasSamples $numBiasSamples
            #end if
            #if str($numFragSamples):
                --numFragSamples $numFragSamples
            #end if
            #if str($numGibbsSamples):
                --numGibbsSamples $numGibbsSamples
            #end if
            #if str($numBootstraps):
                --numBootstraps $numBootstraps
            #end if
]]>
    </command>
    <inputs>
        <conditional name="refTranscriptSource">
            <param name="TranscriptSource" type="select" label="Select a reference transcriptome 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" selected="True">Use one from the history</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
                    <options from_data_table="sailfish_indexes">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                    </options>
                </param>
            </when>  <!-- build-in -->
            <when value="history">
                <param name="ownFile" type="data" format="fasta"  label="Select the reference transcriptome" help="in FASTA format" />
                <param argument="kmerSize" type="integer" value="21" max="32" label="The size of the k-mer on which the index is built"
                    help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors.
                        The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers,
                        the more distinct they will be.  We generally recommend using a k-mer size of at least 20."/>
            </when>  <!-- history -->
        </conditional>  <!-- refTranscriptSource -->

        <conditional name="single_or_paired">
            <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
                <option value="single">Single-end</option>
                <option value="paired">Paired-end</option>
            </param>
            <when value="single">
                <param name="input_singles" type="data" format="fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
                <expand macro="strandedness" />
            </when>
            <when value="paired">
                <param name="input_mate1" type="data" format="fastq,fasta" label="Mate pair 1" help="FASTQ file." />
                <param name="input_mate2" type="data" format="fastq,fasta" label="Mate pair 2" help="FASTQ file." />
                <param name="orientation" type="select" label="Relative orientation of reads within a pair">
                    <option value="M">Mates are oriented in the same direction (M = matching)</option>
                    <option value="O">Mates are oriented away from each other (O = outward)</option>
                    <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
                </param>
                <expand macro="strandedness" />
            </when>
        </conditional>

        <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True" label="File containing a mapping of transcripts to genes"
            help="Calculates the aggregated gene-level abundance estimations. This file should be eiher a GTF file or tab-delimited format
            where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />

        <param argument="--biasCorrect" type="boolean" truevalue="--biasCorrect" falsevalue="" checked="False"
            label="Perform sequence-specific bias correction" help=""/>

        <param argument="--gcBiasCorrect" type="boolean" truevalue="--gcBiasCorrect" falsevalue="" checked="False"
            label="Perform fragment GC bias correction" help=""/>

        <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
            label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>

        <param argument="--gcSizeSamp" type="integer" value="1" optional="True"
            label="The value by which to down-sample transcripts when representing the GC content"
            help="Larger values will reduce memory usage, but may decrease the fidelity of bias modeling results."/>

        <param argument="--gcSpeedSamp" type="integer" value="1" optional="True"
            label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias."
            help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/>

        <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False"
            label="Strict Intersect." help="When this flag is set, if the intersection of the
            quasi-mappings for the left and right is empty, then all mappings for the left and all mappings
            for the right read are reported as orphaned quasi-mappings."/>

        <param argument="--fldMean" type="integer" value="200" optional="True" label="Calculate effective lengths"
            help="If single end reads are being used for quantification, or there are an insufficient number of uniquely
            mapping reads when performing paired-end quantification
            to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/>

        <param argument="--fldSD" type="integer" value="80" optional="True" label="Standard deviation"
            help="The standard deviation used in the fragment length distribution for single-end quantification or
            when an empirical distribution cannot be learned."/>

        <param argument="--maxReadOcc" type="integer" value="200" optional="True" label="Maximal read mapping occurence"
            help="Reads mapping to more than this many places won't be considered."/>

        <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
            label="Disable effective length correction" help="Disables effective length correction when computing the probability
            that a fragment was generated from a transcript.
            If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/>

        <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
            label="Use Variational Bayesian EM algorithm for optimization" help="Use Variational Bayesian EM algorithm rather
            than the traditional EM angorithm for optimization"/>

        <param argument="--discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False"
            label="Discard orphaned reads as valid hits when performing lightweight-alignment"
            help="This option will discard orphaned fragments. This only has an effect on paired-end input, but enabling this option will discard, rather than count, any reads where only one of the paired fragments maps to a transcript."/>

        <param argument="--unsmoothedFLD" type="boolean" truevalue="--unsmoothedFLD" falsevalue="" checked="False"
            label="Use the un-smoothed approach to effective length correction" help="This traditional approach works by convolving the FLD with the
            characteristic function over each transcript."/>

        <param argument="--maxFragLen" type="integer" value="1000" optional="True"
            label="The maximum length of a fragment to consider when building the empirical fragment length distribution"
            help=""/>

        <param argument="--txpAggregationKey" value="gene_id" type="text" label="The key for aggregating transcripts during gene-level estimates">
            <help>
              <![CDATA[
              When generating the gene-level estimates, use the provided key for aggregating transcripts. The default is the "gene_id" field,
              but other fields (e.g. "gene_name") might be useful depending on the specifics of the annotation being used. Note: this option only
              affects aggregation when using a GTF annotation; not an annotation in "simple" format.]]>
            </help>
        </param>
        <param argument="--ignoreLibCompat" type="boolean" truevalue="--ignoreLibCompat" falsevalue="" checked="False"
                label="Disables strand-aware processing completely.">
            <help>
                <![CDATA[
                All hits are considered "Valid".]]>
            </help>
        </param>
        <param argument="--enforceLibCompat" type="boolean" truevalue="--enforceLibCompat" falsevalue="" checked="False"
                label="Enforces strict library compatibility.">
            <help>
                <![CDATA[
                Fragments that map in a manner other than what is specified by the expected library type will be discarded,
                even if there are no mappings that agree with the expected library type.]]>
            </help>
        </param>
        <param argument="--allowDovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False"
                label="Allow paired-end reads from the same fragment to dovetail.">
            <help>
                <![CDATA[
                Allow paired-end reads from the same fragment to "dovetail", such that the ends of the mapped reads can extend past each other.]]>
            </help>
        </param>
        <param argument="--numBiasSamples" type="integer" value="1000000" optional="True"
          label="Number of fragment mappings to use when learning the sequene-specific bias model"
          help=""/>
        <param argument="--numFragSamples" type="integer" value="10000" optional="True"
          label="Number of fragments from unique alignments to sample when building the fragment length distribution"
          help=""/>
        <param argument="--numGibbsSamples" type="integer" value="0" optional="True"
          label="Number of Gibbs sampling rounds to perform."
          help=""/>
        <param argument="--numBootstraps" type="integer" value="0" optional="True"
          label="Number of bootstrap samples to generate."
          help="This is mutually exclusive with Gibbs"/>
    </inputs>


    <outputs>
        <data name="output_quant" format="tabular" from_work_dir="results/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
        <data name="output_gene_quant" format="tabular" from_work_dir="results/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
            <filter>geneMap</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="single_or_paired_opts" value="paired" />
            <param name="input_mate1" value="reads_1.fastq" />
            <param name="input_mate2" value="reads_2.fastq" />
            <param name="biasCorrect" value="False" />
            <param name="TranscriptSource" value="history" />
            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
            <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />
        </test>
        <test>
            <param name="single_or_paired_opts" value="paired" />
            <param name="input_mate1" value="reads_1.fastq" />
            <param name="input_mate2" value="reads_2.fastq" />
            <param name="biasCorrect" value="True" />
            <param name="TranscriptSource" value="history" />
            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
            <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" />
        </test>
        <test>
            <param name="single_or_paired_opts" value="paired" />
            <param name="input_mate1" value="reads_1.fastq" />
            <param name="input_mate2" value="reads_2.fastq" />
            <param name="biasCorrect" value="True" />
            <param name="TranscriptSource" value="history" />
            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
            <param name="geneMap" value="gene_map.tab" ftype="tabular" />
            <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" />
            <output file="sailfish_genMap_result1.tab" ftype="tabular" name="output_gene_quant" />
        </test>
    </tests>
    <help><![CDATA[

**What it does**

Sailfish is a tool for transcript quantification from RNA-seq data.  It
requires a set of target transcripts (either from a reference or de-novo
assembly) to quantify.  All you need to run Sailfish is a fasta file containing
your reference transcripts and a (set of) fasta/fastq file(s) containing your
reads.  Sailfish runs in two phases; indexing and quantification.  The indexing
step is independent of the reads, and only need to be run one for a particular
set of reference transcripts and choice of k (the k-mer size). The
quantification step, obviously, is specific to the set of RNA-seq reads and is
thus run more frequently.

When the quantification output contains a number of columns:
(1) Transcript ID,
(2) Transcript Length,
(3) Transcripts per Million (TPM) and
(4) Estimated number of reads (an estimate of the number of reads drawn from this transcript given the transcript’s relative abundance and length).

The first two columns are self-explanatory, the next four are measures of transcript abundance and the final is a commonly used input for differential expression tools.
The Transcripts per Million quantification number is computed as described in [1], and is meant as an estimate of the number of transcripts, per million observed transcripts,
originating from each isoform. Its benefit over the F/RPKM measure is that it is independent of the mean expressed transcript length
(i.e. if the mean expressed transcript length varies between samples, for example, this alone can affect differential analysis based on the K/RPKM.).



Fragment Library Types
======================

There are numerous library preparation protocols for RNA-seq that result in
sequencing reads with different characteristics.  For example, reads can be
single end (only one side of a fragment is recorded as a read) or paired-end
(reads are generated from both ends of a fragment).  Further, the sequencing
reads themselves may be unstraned or strand-specific.  Finally, paired-end
protocols will have a specified relative orientation.  To characterize the
various different typs of sequencing libraries, we've created a miniature
"language" that allows for the succinct description of the many different types
of possible fragment libraries.  For paired-end reads, the possible
orientations, along with a graphical description of what they mean, are
illustrated below:

.. image:: ReadLibraryIllustration.png

The library type string consists of three parts: the relative orientation of
the reads, the strandedness of the library, and the directionality of the
reads.

The first part of the library string (relative orientation) is only provided if
the library is paired-end. The possible options are:

::

    I = inward
    O = outward
    M = matching

The second part of the read library string specifies whether the protocol is
stranded or unstranded; the options are:

::

    S = stranded
    U = unstranded

If the protocol is unstranded, then we're done.  The final part of the library
string specifies the strand from which the read originates in a strand-specific
protocol — it is only provided if the library is stranded (i.e. if the
library format string is of the form S).  The possible values are:

::

    F = read 1 (or single-end read) comes from the forward strand
    R = read 1 (or single-end read) comes from the reverse strand

So, for example, if you wanted to specify a fragment library of strand-specific
paired-end reads, oriented toward each other, where read 1 comes from the
forward strand and read 2 comes from the reverse strand, you would specify ``-l
ISF`` on the command line.  This designates that the library being processed has
the type "ISF" meaning, **I**\ nward (the relative orientation), **S**\ tranted
(the protocol is strand-specific), **F**\ orward (read 1 comes from the forward
strand).

The single end library strings are a bit simpler than their pair-end counter
parts, since there is no relative orientation of which to speak.  Thus, the
only possible library format types for single-end reads are ``U`` (for
unstranded), ``SF`` (for strand-specific reads coming from the forward strand)
and ``SR`` (for strand-specific reads coming from the reverse strand).

A few more examples of some library format strings and their interpretations are:

::

    IU (an unstranded paired-end library where the reads face each other)

::

    SF (a stranded single-end protocol where the reads come from the forward strand)

::

    OSR (a stranded paired-end protocol where the reads face away from each other,
         read1 comes from reverse strand and read2 comes from the forward strand)

.. note:: Correspondence to TopHat library types

   The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq
   read aligner has a different convention for specifying the format of the library.
   Below is a table that provides the corresponding sailfish/salmon library format
   string for each of the potential TopHat library types:


   +---------------------+-------------------------+
   | TopHat              | Salmon (and Sailfish)   |
   +=====================+============+============+
   |                     | Paired-end | Single-end |
   +---------------------+------------+------------+
   |``-fr-unstranded``   |``-l IU``   |``-l U``    |
   +---------------------+------------+------------+
   |``-fr-firststrand``  |``-l ISR``  |``-l SR``   |
   +---------------------+------------+------------+
   |``-fr-secondstrand`` |``-l ISF``  |``-l SF``   |
   +---------------------+------------+------------+

   The remaining salmon library format strings are not directly expressible in terms
   of the TopHat library types, and so there is no direct mapping for them.


    ]]></help>
    <citations>
        <citation type="doi">10.1038/nbt.2862</citation>
    </citations>
</tool>