Mercurial > repos > bgruening > salmon
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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/salmon.xml Tue Nov 15 11:36:41 2016 -0500 @@ -0,0 +1,486 @@ +<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>