diff salmon.xml @ 0:91f3a2147127 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit d7607abc9feea09f0f8a227ead4da09323e167bb
author bgruening
date Tue, 15 Nov 2016 11:36:41 -0500
parents
children c1d822f84e1a
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+<tool id="salmon" name="Salmon" version="0.7.2">
+
+    <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="0.7.2">salmon</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="Exception:" />
+        <regex match="Exception :" />
+    </stdio>
+    <version_command>salmon -version</version_command>
+    <command><![CDATA[
+        mkdir ./index
+        &&
+        mkdir ./output
+        &&
+        #if $refTranscriptSource.TranscriptSource == "history":
+            salmon index
+                --transcripts $refTranscriptSource.ownFile
+                --kmerLen $refTranscriptSource.kmerLen
+                --threads "\${GALAXY_SLOTS:-4}"
+                --index './index'
+                --type '$quasi_orphans.type'
+                $perfectHash
+                #if str($sasamp):
+                    --sasamp $sasamp
+                #end if
+            #set $index_path = './index'
+        #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
+        salmon 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 ./output
+            #if str($quasi_orphans.type) == 'quasi':
+                --allowOrphans
+            #else:
+                $quasi_orphans.allowOrphans
+            #end if
+            $seqBias
+            $gcBias
+            --threads "\${GALAXY_SLOTS:-4}"
+            --incompatPrior $adv.incompatPrior
+            $adv.consistentHits
+            $adv.dumpEq
+            #if str($adv.gcSizeSamp):
+                --gcSizeSamp $adv.gcSizeSamp
+            #end if
+            #if str($adv.biasSpeedSamp):
+                --biasSpeedSamp $adv.biasSpeedSamp
+            #end if
+            $adv.strictIntersect
+            #if str($adv.fldMax):
+                --fldMax $adv.fldMax
+            #end if
+            #if str($adv.fldMean):
+                --fldMean $adv.fldMean
+            #end if
+            #if str($adv.fldSD):
+                --fldSD $adv.fldSD
+            #end if
+            #if $adv.forgettingFactor:
+                --forgettingFactor $adv.forgettingFactor
+            #end if
+            $adv.writeMappings
+            #if str($adv.maxOcc):
+                --maxOcc $adv.maxOcc
+            #end if
+            $adv.initUniform
+            $adv.noFragLengthDist
+            $adv.noBiasLengthThreshold
+            #if str($adv.maxReadOcc):
+                --maxReadOcc $adv.maxReadOcc
+            #end if
+            #if $geneMap:
+                --geneMap ./geneMap.${geneMap.ext}
+            #end if
+            $adv.noEffectiveLengthCorrection
+            $adv.useVBOpt
+            #if str($adv.numBiasSamples):
+                --numBiasSamples $adv.numBiasSamples
+            #end if
+            #if str($adv.numAuxModelSamples):
+                --numAuxModelSamples $adv.numAuxModelSamples
+            #end if
+            #if str($adv.numPreAuxModelSamples):
+                --numPreAuxModelSamples $adv.numPreAuxModelSamples
+            #end if
+            #if str($adv.numGibbsSamples):
+                --numGibbsSamples $adv.numGibbsSamples
+            #end if
+            #if str($adv.numBootstraps):
+                --numBootstraps $adv.numBootstraps
+            #end if
+            $adv.perTranscriptPrior
+            #if $adv.vbPrior:
+                --vbPrior $adv.vbPrior
+            #end if
+            $adv.writeUnmappedNames
+]]>
+    </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="salmon_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="kmerLen" type="integer" value="31" label="The size should be odd number."/>
+            </when>  <!-- history -->
+        </conditional>
+        <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>
+        <conditional name="quasi_orphans">
+            <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
+                <option value="quasi" selected="True">quasi</option>
+                <option value="fmd">fmd</option>
+            </param>
+            <when value="quasi">
+            </when>  <!-- build-in -->
+            <when value="fmd">
+                <param argument="--allowOrphans" type="boolean" truevalue="--allowOrphans" falsevalue="" checked="True"
+                    label="Consider orphaned reads as valid hits when performing lightweight-alignment"
+                    help="This option will increase sensitivity (allow more reads to map and more transcripts to be detected), but may decrease specificity as orphaned alignments are more likely to be spurious."/>
+            </when>  <!-- history -->
+        </conditional>
+        <param argument="--perfectHash" type="boolean" truevalue="--perfectHash" falsevalue="" checked="False"
+            label="Perfect Hash"
+            help="Build the index using a perfect hash rather than a dense hash.  This will require  less memory (especially during quantification), but will take longer to construct "/>
+        <param argument="--sasamp" type="integer" value="1" optional="True" label="Suffix Array"
+            help="The interval at which the suffix array should be sampled. Smaller values are faster, but produce a larger index. The default should be OK, unless your transcriptome is huge. This value should be a power of 2."/>
+        <param argument="--seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
+            label="Perform sequence-specific bias correction"
+            help=""/>
+        <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
+            label="Perform fragment GC bias correction"
+            help=""/>
+        <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
+            label="File containing a mapping of transcripts to genes.  If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />
+        <section name="adv" title="Additional Options">
+            <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
+                label="Write Mappings"
+                help=" Setting this option then the quasi-mapping results will be written out in SAM-cpmpatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead." />
+            <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"
+                label="Incompatible Prior"
+                help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" />
+            <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="--biasSpeedSamp" 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="Modifies how orphans are assigned." 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="--minLen" type="integer" value="19" optional="True"
+                label=" (S)MEMs smaller than this size won't be considered." help="" />
+            <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="False"
+                label="Perform sensitive quantification"
+                help=" Setting this option enables the splitting of SMEMs that are larger than 1.5 times the minimum seed length (minLen/k above).  This may reveal high scoring chains of MEMs that are masked by long SMEMs.  However, this option makes lightweight-alignment a bit slower and is usually not necessary if the reference is of reasonable quality." />
+            <param argument="--consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
+                label="Force hits gathered during quasi-mapping to be consistent"
+                help="" />
+            <param argument="--extraSensitive" type="boolean" truevalue="--extraSensitive" falsevalue="" checked="False"
+                label="Perform extra sensitive quantification"
+                help="Setting this option enables an extra pass of 'seed' search. Enabling this option may improve sensitivity (the number of reads having sufficient coverage), but will typically slow down quantification by ~40%.  Consider enabling this option if you find the mapping rate to be significantly lower than expected."/>
+            <param argument="--coverage" type="float" value="0.69999999999999996" optional="True"
+                label="Required coverage of read by union of SMEMs to consider it a hit"
+                help="" />
+            <param argument="--fldMax" type="integer" value="1000" optional="True"
+                label="The maximum fragment length to consider when building the empirical distribution."
+                help=""/>
+            <param argument="--fldMean" type="integer" value="200" optional="True"
+                label="The mean used in the fragment length distribution prior"
+                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 prior."/>
+            <param argument="--forgettingFactor" type="float" value="0.65000000000000002" optional="True"
+                label="The forgetting factor used in the online learning schedule."
+                help=" A smaller value results in quicker learning, but higher variance and may be unstable. A larger value results in slower learning but may be more stable.  Value should be in the interval (0.5, 1.0]." />
+            <param argument="--maxOcc" type="integer" value="200" optional="True"
+                label="(S)MEMs occuring more than this many times won't be considered"
+                help=""/>
+            <param argument="--initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
+                label="Initialization with uniform parameters"
+                help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
+            <param argument="--maxReadOcc" type="integer" value="100" 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="--noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False"
+                label="Ignore fragment length distribution"
+                help="[experimental] : Don't consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location.  Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment's a priori probability." />
+            <param argument="--noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
+                label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
+                help="This can increase the precision of bias correction, but harm robustness. The difault correction applies a threshold." />
+            <param argument="--numBiasSamples" type="integer" value="2000000" optional="True"
+                label="Number of fragment mappings to use when learning the sequence-specific bias model."
+                help="" />
+            <param argument="--numAuxModelSamples" type="integer" value="5000000" optional="True"
+                label="The first numAuxModelSamples are used to train the auxiliary model parameters."
+                help="(e.g. fragment length distribution, bias, etc.). After ther first numAuxModelSamples observations the auxiliary model parameters will be assumed to have converged and will be fixed." />
+            <param argument="--numPreAuxModelSamples" type="integer" value="1000000" optional="True"
+                label="The first numPreAuxModelSamples will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models."
+                help=" The purpose of ignoring the auxiliary models for the first numPreAuxModelSamples observations is to avoid applying these models before thier parameters have been learned sufficiently well." />
+            <param argument="--splitWidth" type="integer" value="0" optional="True"
+                label=" If (S)MEM occurs fewer than this many times, search for smaller, contained  MEMs"
+                help="The default value will not split (S)MEMs, a higher value will result in more MEMs being explore and, thus, will result in increased running time." />
+            <param argument="--splitSpanningSeeds" type="boolean" truevalue="--splitSpanningSeeds" falsevalue="" checked="False"
+                label="Attempt to split seeds that happen to fall on the boundary between two transcripts."
+                help="This can improve the fragment hit-rate, but is usually not necessary."/>
+            <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
+                label="Use the Variational Bayesian EM rather than the traditional EM algorithm for optimization in the batch passes."
+                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. Note: This is mutually exclusive with Gibbs sampling."
+                help="" />
+            <param argument="--perTranscriptPrior" type="boolean" truevalue="--perTranscriptPrior" falsevalue="" checked="False"
+                label="The prior will be interpreted as a transcript-level prior."
+                help="either the default or the argument provided via --vbPrior" />
+            <param argument="--vbPrior" type="float" value="0.001" optional="True"
+                label="The prior that will be used in the VBEM algorithm."
+                help="This is interpreted as a per-nucleotide prior, unless the --perTranscriptPrior flag is also given, in which case this is used as a transcript-level prior." />
+            <param argument="--writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
+                label="Write the names of un-mapped reads to the file unmapped_names.txt."
+                help=""/>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
+        <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${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 name="output_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </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="TranscriptSource" value="history" />
+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
+            <param name="geneMap" value="gene_map.tab" ftype="tabular" />
+            <output name="output_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+            <output name="output_gene_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="baz" />
+                    <has_text text="bar" />
+                    <has_text text="2283" />
+                    <has_text text="1640" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+salmon 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 Salmon is a fasta file containing
+your reference transcripts and a (set of) fasta/fastq file(s) containing your
+reads.  Salmon 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 Salmon/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">10.1101/021592</citation>
+    </citations>
+</tool>