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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
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1 <tool id="salmon" name="Salmon" version="0.7.2">
2
3 <description>Transcript Quantification from RNA-seq data</description>
4
5 <macros>
6 <xml name="strandedness">
7 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
8 <option value="U" selected="True">Not stranded (U)</option>
9 <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
10 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
11 </param>
12 </xml>
13 </macros>
14
15 <requirements>
16 <requirement type="package" version="0.7.2">salmon</requirement>
17 </requirements>
18
19 <stdio>
20 <exit_code range="1:" />
21 <exit_code range=":-1" />
22 <regex match="Error:" />
23 <regex match="Exception:" />
24 <regex match="Exception :" />
25 </stdio>
26 <version_command>salmon -version</version_command>
27 <command><![CDATA[
28 mkdir ./index
29 &&
30 mkdir ./output
31 &&
32 #if $refTranscriptSource.TranscriptSource == "history":
33 salmon index
34 --transcripts $refTranscriptSource.ownFile
35 --kmerLen $refTranscriptSource.kmerLen
36 --threads "\${GALAXY_SLOTS:-4}"
37 --index './index'
38 --type '$quasi_orphans.type'
39 $perfectHash
40 #if str($sasamp):
41 --sasamp $sasamp
42 #end if
43 #set $index_path = './index'
44 #else:
45 #set $index_path = $refTranscriptSource.index.fields.path
46 #end if
47 &&
48 #if $single_or_paired.single_or_paired_opts == 'single':
49 #if $single_or_paired.input_singles.ext == 'fasta':
50 #set $ext = 'fasta'
51 #else:
52 #set $ext = 'fastq'
53 #end if
54 ln -s $single_or_paired.input_singles ./single.$ext &&
55 #else:
56 #if $single_or_paired.input_mate1.ext == 'fasta':
57 #set $ext = 'fasta'
58 #else:
59 #set $ext = 'fastq'
60 #end if
61 ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
62 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
63 #end if
64 #if $geneMap:
65 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
66 #end if
67 salmon quant
68 --index $index_path
69 #if $single_or_paired.single_or_paired_opts == 'single':
70 --libType ${single_or_paired.strandedness}
71 --unmatedReads ./single.$ext
72 #else:
73 --mates1 ./mate1.$ext
74 --mates2 ./mate2.$ext
75 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
76 #end if
77 --output ./output
78 #if str($quasi_orphans.type) == 'quasi':
79 --allowOrphans
80 #else:
81 $quasi_orphans.allowOrphans
82 #end if
83 $seqBias
84 $gcBias
85 --threads "\${GALAXY_SLOTS:-4}"
86 --incompatPrior $adv.incompatPrior
87 $adv.consistentHits
88 $adv.dumpEq
89 #if str($adv.gcSizeSamp):
90 --gcSizeSamp $adv.gcSizeSamp
91 #end if
92 #if str($adv.biasSpeedSamp):
93 --biasSpeedSamp $adv.biasSpeedSamp
94 #end if
95 $adv.strictIntersect
96 #if str($adv.fldMax):
97 --fldMax $adv.fldMax
98 #end if
99 #if str($adv.fldMean):
100 --fldMean $adv.fldMean
101 #end if
102 #if str($adv.fldSD):
103 --fldSD $adv.fldSD
104 #end if
105 #if $adv.forgettingFactor:
106 --forgettingFactor $adv.forgettingFactor
107 #end if
108 $adv.writeMappings
109 #if str($adv.maxOcc):
110 --maxOcc $adv.maxOcc
111 #end if
112 $adv.initUniform
113 $adv.noFragLengthDist
114 $adv.noBiasLengthThreshold
115 #if str($adv.maxReadOcc):
116 --maxReadOcc $adv.maxReadOcc
117 #end if
118 #if $geneMap:
119 --geneMap ./geneMap.${geneMap.ext}
120 #end if
121 $adv.noEffectiveLengthCorrection
122 $adv.useVBOpt
123 #if str($adv.numBiasSamples):
124 --numBiasSamples $adv.numBiasSamples
125 #end if
126 #if str($adv.numAuxModelSamples):
127 --numAuxModelSamples $adv.numAuxModelSamples
128 #end if
129 #if str($adv.numPreAuxModelSamples):
130 --numPreAuxModelSamples $adv.numPreAuxModelSamples
131 #end if
132 #if str($adv.numGibbsSamples):
133 --numGibbsSamples $adv.numGibbsSamples
134 #end if
135 #if str($adv.numBootstraps):
136 --numBootstraps $adv.numBootstraps
137 #end if
138 $adv.perTranscriptPrior
139 #if $adv.vbPrior:
140 --vbPrior $adv.vbPrior
141 #end if
142 $adv.writeUnmappedNames
143 ]]>
144 </command>
145
146 <inputs>
147 <conditional name="refTranscriptSource">
148 <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">
149 <option value="indexed">Use a built-in index</option>
150 <option value="history" selected="True">Use one from the history</option>
151 </param>
152 <when value="indexed">
153 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
154 <options from_data_table="salmon_indexes">
155 <filter type="sort_by" column="2"/>
156 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
157 </options>
158 </param>
159 </when> <!-- build-in -->
160 <when value="history">
161 <param name="ownFile" type="data" format="fasta" label="Select the reference transcriptome" help="in FASTA format" />
162 <param argument="kmerLen" type="integer" value="31" label="The size should be odd number."/>
163 </when> <!-- history -->
164 </conditional>
165 <conditional name="single_or_paired">
166 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
167 <option value="single">Single-end</option>
168 <option value="paired">Paired-end</option>
169 </param>
170 <when value="single">
171 <param name="input_singles" type="data" format="fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
172 <expand macro="strandedness" />
173 </when>
174 <when value="paired">
175 <param name="input_mate1" type="data" format="fastq,fasta" label="Mate pair 1" help="FASTQ file." />
176 <param name="input_mate2" type="data" format="fastq,fasta" label="Mate pair 2" help="FASTQ file." />
177 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
178 <option value="M">Mates are oriented in the same direction (M = matching)</option>
179 <option value="O">Mates are oriented away from each other (O = outward)</option>
180 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
181 </param>
182 <expand macro="strandedness" />
183 </when>
184 </conditional>
185 <conditional name="quasi_orphans">
186 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
187 <option value="quasi" selected="True">quasi</option>
188 <option value="fmd">fmd</option>
189 </param>
190 <when value="quasi">
191 </when> <!-- build-in -->
192 <when value="fmd">
193 <param argument="--allowOrphans" type="boolean" truevalue="--allowOrphans" falsevalue="" checked="True"
194 label="Consider orphaned reads as valid hits when performing lightweight-alignment"
195 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."/>
196 </when> <!-- history -->
197 </conditional>
198 <param argument="--perfectHash" type="boolean" truevalue="--perfectHash" falsevalue="" checked="False"
199 label="Perfect Hash"
200 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 "/>
201 <param argument="--sasamp" type="integer" value="1" optional="True" label="Suffix Array"
202 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."/>
203 <param argument="--seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
204 label="Perform sequence-specific bias correction"
205 help=""/>
206 <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
207 label="Perform fragment GC bias correction"
208 help=""/>
209 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
210 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." />
211 <section name="adv" title="Additional Options">
212 <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
213 label="Write Mappings"
214 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." />
215 <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"
216 label="Incompatible Prior"
217 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" />
218 <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
219 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
220 <param argument="--gcSizeSamp" type="integer" value="1" optional="True"
221 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."/>
222 <param argument="--biasSpeedSamp" type="integer" value="1" optional="True"
223 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."/>
224 <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False"
225 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."/>
226 <param argument="--minLen" type="integer" value="19" optional="True"
227 label=" (S)MEMs smaller than this size won't be considered." help="" />
228 <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="False"
229 label="Perform sensitive quantification"
230 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." />
231 <param argument="--consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
232 label="Force hits gathered during quasi-mapping to be consistent"
233 help="" />
234 <param argument="--extraSensitive" type="boolean" truevalue="--extraSensitive" falsevalue="" checked="False"
235 label="Perform extra sensitive quantification"
236 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."/>
237 <param argument="--coverage" type="float" value="0.69999999999999996" optional="True"
238 label="Required coverage of read by union of SMEMs to consider it a hit"
239 help="" />
240 <param argument="--fldMax" type="integer" value="1000" optional="True"
241 label="The maximum fragment length to consider when building the empirical distribution."
242 help=""/>
243 <param argument="--fldMean" type="integer" value="200" optional="True"
244 label="The mean used in the fragment length distribution prior"
245 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."/>
246 <param argument="--fldSD" type="integer" value="80" optional="True"
247 label="Standard deviation"
248 help="The standard deviation used in the fragment length distribution prior."/>
249 <param argument="--forgettingFactor" type="float" value="0.65000000000000002" optional="True"
250 label="The forgetting factor used in the online learning schedule."
251 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]." />
252 <param argument="--maxOcc" type="integer" value="200" optional="True"
253 label="(S)MEMs occuring more than this many times won't be considered"
254 help=""/>
255 <param argument="--initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
256 label="Initialization with uniform parameters"
257 help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
258 <param argument="--maxReadOcc" type="integer" value="100" optional="True"
259 label="Maximal read mapping occurence"
260 help="Reads mapping to more than this many places won't be considered."/>
261 <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
262 label="Disable effective length correction"
263 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."/>
264 <param argument="--noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False"
265 label="Ignore fragment length distribution"
266 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." />
267 <param argument="--noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
268 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
269 help="This can increase the precision of bias correction, but harm robustness. The difault correction applies a threshold." />
270 <param argument="--numBiasSamples" type="integer" value="2000000" optional="True"
271 label="Number of fragment mappings to use when learning the sequence-specific bias model."
272 help="" />
273 <param argument="--numAuxModelSamples" type="integer" value="5000000" optional="True"
274 label="The first numAuxModelSamples are used to train the auxiliary model parameters."
275 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." />
276 <param argument="--numPreAuxModelSamples" type="integer" value="1000000" optional="True"
277 label="The first numPreAuxModelSamples will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models."
278 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." />
279 <param argument="--splitWidth" type="integer" value="0" optional="True"
280 label=" If (S)MEM occurs fewer than this many times, search for smaller, contained MEMs"
281 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." />
282 <param argument="--splitSpanningSeeds" type="boolean" truevalue="--splitSpanningSeeds" falsevalue="" checked="False"
283 label="Attempt to split seeds that happen to fall on the boundary between two transcripts."
284 help="This can improve the fragment hit-rate, but is usually not necessary."/>
285 <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
286 label="Use the Variational Bayesian EM rather than the traditional EM algorithm for optimization in the batch passes."
287 help=""/>
288 <param argument="--numGibbsSamples" type="integer" value="0" optional="True"
289 label=" Number of Gibbs sampling rounds to perform."
290 help="" />
291 <param argument="--numBootstraps" type="integer" value="0" optional="True"
292 label="Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling."
293 help="" />
294 <param argument="--perTranscriptPrior" type="boolean" truevalue="--perTranscriptPrior" falsevalue="" checked="False"
295 label="The prior will be interpreted as a transcript-level prior."
296 help="either the default or the argument provided via --vbPrior" />
297 <param argument="--vbPrior" type="float" value="0.001" optional="True"
298 label="The prior that will be used in the VBEM algorithm."
299 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." />
300 <param argument="--writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
301 label="Write the names of un-mapped reads to the file unmapped_names.txt."
302 help=""/>
303 </section>
304 </inputs>
305
306 <outputs>
307 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
308 <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
309 <filter>geneMap</filter>
310 </data>
311 </outputs>
312
313 <tests>
314 <test>
315 <param name="single_or_paired_opts" value="paired" />
316 <param name="input_mate1" value="reads_1.fastq" />
317 <param name="input_mate2" value="reads_2.fastq" />
318 <param name="biasCorrect" value="False" />
319 <param name="TranscriptSource" value="history" />
320 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
321 <output name="output_quant">
322 <assert_contents>
323 <has_text text="EffectiveLength" />
324 <has_text text="TPM" />
325 <has_text text="NM_001168316" />
326 <has_text text="NM_174914" />
327 <has_text text="NM_018953" />
328 <has_text text="NR_003084" />
329 <has_text text="NM_017410" />
330 <has_text text="NM_153693" />
331 <has_text text="NR_031764" />
332 <has_n_columns n="5" />
333 </assert_contents>
334 </output>
335 </test>
336 <test>
337 <param name="single_or_paired_opts" value="paired" />
338 <param name="input_mate1" value="reads_1.fastq" />
339 <param name="input_mate2" value="reads_2.fastq" />
340 <param name="TranscriptSource" value="history" />
341 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
342 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
343 <output name="output_quant">
344 <assert_contents>
345 <has_text text="EffectiveLength" />
346 <has_text text="TPM" />
347 <has_text text="NM_001168316" />
348 <has_text text="NM_174914" />
349 <has_text text="NM_018953" />
350 <has_text text="NR_003084" />
351 <has_text text="NM_017410" />
352 <has_text text="NM_153693" />
353 <has_text text="NR_031764" />
354 <has_n_columns n="5" />
355 </assert_contents>
356 </output>
357 <output name="output_gene_quant">
358 <assert_contents>
359 <has_text text="EffectiveLength" />
360 <has_text text="TPM" />
361 <has_text text="baz" />
362 <has_text text="bar" />
363 <has_text text="2283" />
364 <has_text text="1640" />
365 <has_n_columns n="5" />
366 </assert_contents>
367 </output>
368 </test>
369 </tests>
370
371 <help><![CDATA[
372 **What it does**
373 salmon is a tool for transcript quantification from RNA-seq data. It
374 requires a set of target transcripts (either from a reference or de-novo
375 assembly) to quantify. All you need to run Salmon is a fasta file containing
376 your reference transcripts and a (set of) fasta/fastq file(s) containing your
377 reads. Salmon runs in two phases; indexing and quantification. The indexing
378 step is independent of the reads, and only need to be run one for a particular
379 set of reference transcripts and choice of k (the k-mer size). The
380 quantification step, obviously, is specific to the set of RNA-seq reads and is
381 thus run more frequently.
382 When the quantification output contains a number of columns:
383 (1) Transcript ID,
384 (2) Transcript Length,
385 (3) Transcripts per Million (TPM) and
386 (4) Estimated number of reads (an estimate of the number of reads drawn from this transcript given the transcript’s relative abundance and length).
387 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.
388 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,
389 originating from each isoform. Its benefit over the F/RPKM measure is that it is independent of the mean expressed transcript length
390 (i.e. if the mean expressed transcript length varies between samples, for example, this alone can affect differential analysis based on the K/RPKM.).
391
392
393 Fragment Library Types
394 ======================
395
396 There are numerous library preparation protocols for RNA-seq that result in
397 sequencing reads with different characteristics. For example, reads can be
398 single end (only one side of a fragment is recorded as a read) or paired-end
399 (reads are generated from both ends of a fragment). Further, the sequencing
400 reads themselves may be unstraned or strand-specific. Finally, paired-end
401 protocols will have a specified relative orientation. To characterize the
402 various different typs of sequencing libraries, we've created a miniature
403 "language" that allows for the succinct description of the many different types
404 of possible fragment libraries. For paired-end reads, the possible
405 orientations, along with a graphical description of what they mean, are
406 illustrated below:
407 .. image:: ReadLibraryIllustration.png
408 The library type string consists of three parts: the relative orientation of
409 the reads, the strandedness of the library, and the directionality of the
410 reads.
411 The first part of the library string (relative orientation) is only provided if
412 the library is paired-end. The possible options are:
413 ::
414
415 I = inward
416 O = outward
417 M = matching
418
419 The second part of the read library string specifies whether the protocol is
420 stranded or unstranded; the options are:
421 ::
422
423 S = stranded
424 U = unstranded
425
426 If the protocol is unstranded, then we're done. The final part of the library
427 string specifies the strand from which the read originates in a strand-specific
428 protocol — it is only provided if the library is stranded (i.e. if the
429 library format string is of the form S). The possible values are:
430 ::
431
432 F = read 1 (or single-end read) comes from the forward strand
433 R = read 1 (or single-end read) comes from the reverse strand
434
435 So, for example, if you wanted to specify a fragment library of strand-specific
436 paired-end reads, oriented toward each other, where read 1 comes from the
437 forward strand and read 2 comes from the reverse strand, you would specify ``-l
438 ISF`` on the command line. This designates that the library being processed has
439 the type "ISF" meaning, **I**\ nward (the relative orientation), **S**\ tranted
440 (the protocol is strand-specific), **F**\ orward (read 1 comes from the forward
441 strand).
442 The single end library strings are a bit simpler than their pair-end counter
443 parts, since there is no relative orientation of which to speak. Thus, the
444 only possible library format types for single-end reads are ``U`` (for
445 unstranded), ``SF`` (for strand-specific reads coming from the forward strand)
446 and ``SR`` (for strand-specific reads coming from the reverse strand).
447 A few more examples of some library format strings and their interpretations are:
448 ::
449
450 IU (an unstranded paired-end library where the reads face each other)
451
452 ::
453
454 SF (a stranded single-end protocol where the reads come from the forward strand)
455
456 ::
457
458 OSR (a stranded paired-end protocol where the reads face away from each other,
459 read1 comes from reverse strand and read2 comes from the forward strand)
460
461 .. note:: Correspondence to TopHat library types
462
463 The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq
464 read aligner has a different convention for specifying the format of the library.
465 Below is a table that provides the corresponding Salmon/salmon library format
466 string for each of the potential TopHat library types:
467
468 +---------------------+-------------------------+
469 | TopHat | Salmon (and Sailfish) |
470 +=====================+============+============+
471 | | Paired-end | Single-end |
472 +---------------------+------------+------------+
473 |``-fr-unstranded`` |``-l IU`` |``-l U`` |
474 +---------------------+------------+------------+
475 |``-fr-firststrand`` |``-l ISR`` |``-l SR`` |
476 +---------------------+------------+------------+
477 |``-fr-secondstrand`` |``-l ISF`` |``-l SF`` |
478 +---------------------+------------+------------+
479
480 The remaining salmon library format strings are not directly expressible in terms
481 of the TopHat library types, and so there is no direct mapping for them.
482 ]]> </help>
483 <citations>
484 <citation type="doi">10.1101/021592</citation>
485 </citations>
486 </tool>