comparison salmon.xml @ 8:6b0ba6de1424 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56
author bgruening
date Thu, 23 Aug 2018 15:58:26 -0400
parents e7e885f718fb
children 2c0ca397d302
comparison
equal deleted inserted replaced
7:e7e885f718fb 8:6b0ba6de1424
15 <option value="M">Mates are oriented in the same direction (M = matching)</option> 15 <option value="M">Mates are oriented in the same direction (M = matching)</option>
16 <option value="O">Mates are oriented away from each other (O = outward)</option> 16 <option value="O">Mates are oriented away from each other (O = outward)</option>
17 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option> 17 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
18 </param> 18 </param>
19 </xml> 19 </xml>
20 <token name="@VERSION@">0.9.1</token> 20 <token name="@VERSION@">0.11.2</token>
21 </macros> 21 </macros>
22 22
23 <requirements> 23 <requirements>
24 <requirement type="package" version="1.0.6">bzip2</requirement> 24 <requirement type="package" version="1.0.6">bzip2</requirement>
25 <requirement type="package" version="@VERSION@">salmon</requirement> 25 <requirement type="package" version="@VERSION@">salmon</requirement>
45 --kmerLen $refTranscriptSource.kmerLen 45 --kmerLen $refTranscriptSource.kmerLen
46 --threads "\${GALAXY_SLOTS:-4}" 46 --threads "\${GALAXY_SLOTS:-4}"
47 --index './index' 47 --index './index'
48 --type '$quasi_orphans.type' 48 --type '$quasi_orphans.type'
49 $perfectHash 49 $perfectHash
50 #if str($sasamp):
51 --sasamp $sasamp
52 #end if
53 #set $index_path = './index' 50 #set $index_path = './index'
54 #else: 51 #else:
55 #set $index_path = $refTranscriptSource.index.fields.path 52 #set $index_path = $refTranscriptSource.index.fields.path
56 #end if 53 #end if
57 && 54 &&
120 --unmatedReads <(bzcat < ./single.$ext) 117 --unmatedReads <(bzcat < ./single.$ext)
121 #else: 118 #else:
122 --unmatedReads ./single.$ext 119 --unmatedReads ./single.$ext
123 #end if 120 #end if
124 #else: 121 #else:
122 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
125 #if $single_or_paired.single_or_paired_opts == 'paired_interleaved': 123 #if $single_or_paired.single_or_paired_opts == 'paired_interleaved':
126 #if $compressed == 'BZ2': 124 #if $compressed == 'BZ2':
127 --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1) 125 --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1)
128 --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2) 126 --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2)
129 #else: 127 #else:
140 #else: 138 #else:
141 --mates1 ./mate1.$ext 139 --mates1 ./mate1.$ext
142 --mates2 ./mate2.$ext 140 --mates2 ./mate2.$ext
143 #end if 141 #end if
144 #end if 142 #end if
145 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
146 #end if 143 #end if
147 --output ./output 144 --output ./output
148 #if str($quasi_orphans.type) == 'quasi': 145 #if str($quasi_orphans.type) == 'quasi':
149 --allowOrphans 146 --allowOrphans
150 #else: 147 $quasi_orphans.validateMappings
151 $quasi_orphans.allowOrphans 148 --ma $quasi_orphans.matchScore
149 --mp $quasi_orphans.mismatchPenalty
150 --go $quasi_orphans.gapOpenPenalty
151 --ge $quasi_orphans.gapExtensionPenalty
152 --minScoreFraction $quasi_orphans.minScoreFraction
152 #end if 153 #end if
153 $seqBias 154 $seqBias
154 $gcBias 155 $gcBias
156 $noErrorModel
155 --threads "\${GALAXY_SLOTS:-4}" 157 --threads "\${GALAXY_SLOTS:-4}"
156 --incompatPrior $adv.incompatPrior 158 --incompatPrior $adv.incompatPrior
157 $adv.consistentHits 159 $adv.consistentHits
158 $adv.dumpEq 160 $adv.dumpEq
159 $adv.reduceGCMemory 161 $adv.reduceGCMemory
171 --fldSD $adv.fldSD 173 --fldSD $adv.fldSD
172 #end if 174 #end if
173 #if $adv.forgettingFactor: 175 #if $adv.forgettingFactor:
174 --forgettingFactor $adv.forgettingFactor 176 --forgettingFactor $adv.forgettingFactor
175 #end if 177 #end if
176 #if str($adv.maxOcc):
177 --maxOcc $adv.maxOcc
178 #end if
179 $adv.initUniform 178 $adv.initUniform
180 $adv.noFragLengthDist 179 $adv.noFragLengthDist
181 $adv.noBiasLengthThreshold 180 $adv.noBiasLengthThreshold
182 #if str($adv.maxReadOcc): 181 #if str($adv.maxReadOcc):
183 --maxReadOcc $adv.maxReadOcc 182 --maxReadOcc $adv.maxReadOcc
184 #end if 183 #end if
185 #if $geneMap: 184 #if $geneMap:
186 --geneMap ./geneMap.${geneMap.ext} 185 --geneMap ./geneMap.${geneMap.ext}
187 #end if 186 #end if
188 $adv.noEffectiveLengthCorrection 187 $adv.noEffectiveLengthCorrection
189 $adv.useVBOpt 188 $adv.useEM
190 #if str($adv.numBiasSamples): 189 #if str($adv.numBiasSamples):
191 --numBiasSamples $adv.numBiasSamples 190 --numBiasSamples $adv.numBiasSamples
192 #end if 191 #end if
193 #if str($adv.numAuxModelSamples): 192 #if str($adv.numAuxModelSamples):
194 --numAuxModelSamples $adv.numAuxModelSamples 193 --numAuxModelSamples $adv.numAuxModelSamples
199 #if str($adv.numGibbsSamples): 198 #if str($adv.numGibbsSamples):
200 --numGibbsSamples $adv.numGibbsSamples 199 --numGibbsSamples $adv.numGibbsSamples
201 #end if 200 #end if
202 #if str($adv.numBootstraps): 201 #if str($adv.numBootstraps):
203 --numBootstraps $adv.numBootstraps 202 --numBootstraps $adv.numBootstraps
203 #end if
204 #if str($adv.consensusSlack):
205 --consensusSlack $adv.consensusSlack
206 #else:
207 #if $quasi_orphans.validateMappings:
208 --consensusSlack 1
209 #else:
210 --consensusSlack 0
211 #end if
204 #end if 212 #end if
205 $adv.perTranscriptPrior 213 $adv.perTranscriptPrior
206 #if $adv.vbPrior: 214 #if $adv.vbPrior:
207 --vbPrior $adv.vbPrior 215 --vbPrior $adv.vbPrior
208 #end if 216 #end if
209 $adv.writeUnmappedNames 217 $adv.writeUnmappedNames
218 --sigDigits $adv.sigDigits
210 #if str($adv.writeMappings): 219 #if str($adv.writeMappings):
211 $adv.writeMappings > ${output_sam} 220 $adv.writeMappings > ${output_sam}
212 #end if 221 #end if
213 ]]> 222 ]]>
214 </command> 223 </command>
261 </when> 270 </when>
262 </conditional> 271 </conditional>
263 <conditional name="quasi_orphans"> 272 <conditional name="quasi_orphans">
264 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment."> 273 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
265 <option value="quasi" selected="True">quasi</option> 274 <option value="quasi" selected="True">quasi</option>
266 <option value="fmd">fmd</option>
267 </param> 275 </param>
268 <when value="quasi"> 276 <when value="quasi">
277 <param argument="--validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
278 label="Validate mappings"
279 help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/>
280 <param name="matchScore" argument="--ma" type="integer" value="2"
281 label="Match Score"
282 help="The value given to a match between read and reference nucleotides in an alignment."/>
283 <param name="mismatchPenalty" argument="--mp" type="integer" value="4"
284 label="Mismatch Penalty"
285 help="The value given to a mis-match between read and reference nucleotides in an alignment. This will be cast to a negative value."/>
286 <param name="gapOpenPenalty" argument="--go" type="integer" value="5"
287 label="Gap Open Penalty"
288 help="The value given to a gap opening in an alignment."/>
289 <param name="gapExtensionPenalty" argument="--ge" type="integer" value="3"
290 label="Gap Extension Penalty"
291 help="The value given to a gap extension in an alignment."/>
292 <param argument="--minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
293 label="Min Score Fraction"
294 help="The fraction of the optimal possible alignment score that a mapping must achieve in order to be considered valid. Should be in (0,1]."/>
269 </when> <!-- build-in --> 295 </when> <!-- build-in -->
270 <when value="fmd">
271 <param argument="--allowOrphans" type="boolean" truevalue="--allowOrphans" falsevalue="" checked="True"
272 label="Consider orphaned reads as valid hits when performing lightweight-alignment"
273 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."/>
274 </when> <!-- history -->
275 </conditional> 296 </conditional>
276 <param argument="--perfectHash" type="boolean" truevalue="--perfectHash" falsevalue="" checked="False" 297 <param argument="--perfectHash" type="boolean" truevalue="--perfectHash" falsevalue="" checked="False"
277 label="Perfect Hash" 298 label="Perfect Hash"
278 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 "/> 299 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 "/>
279 <param argument="--sasamp" type="integer" value="1" optional="True" label="Suffix Array"
280 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."/>
281 <param argument="--seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False" 300 <param argument="--seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
282 label="Perform sequence-specific bias correction" 301 label="Perform sequence-specific bias correction"
283 help=""/> 302 help=""/>
284 <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False" 303 <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
285 label="Perform fragment GC bias correction" 304 label="Perform fragment GC bias correction"
286 help=""/> 305 help=""/>
287 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True" 306 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
288 label="File containing a mapping of transcripts to genes" 307 label="File containing a mapping of transcripts to genes"
289 help="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." /> 308 help="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." />
309 <param argument="--noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False"
310 label="No Error Model"
311 help="Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment. Turning this off can speed up alignment-based salmon, but can harm quantification accuracy."/>
290 <section name="adv" title="Additional Options"> 312 <section name="adv" title="Additional Options">
291 <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False" 313 <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
292 label="Write Mappings" 314 label="Write Mappings"
293 help="If this option is set to 'Yes', then the quasi-mapping results will be written out in SAM-compatible format. By default, output is directed to stdout." /> 315 help="If this option is set to 'Yes', then the quasi-mapping results will be written out in SAM-compatible format. By default, output is directed to stdout." />
294 <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21" 316 <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"
327 label="Standard deviation" 349 label="Standard deviation"
328 help="The standard deviation used in the fragment length distribution prior."/> 350 help="The standard deviation used in the fragment length distribution prior."/>
329 <param argument="--forgettingFactor" type="float" value="0.65000000000000002" optional="True" 351 <param argument="--forgettingFactor" type="float" value="0.65000000000000002" optional="True"
330 label="The forgetting factor used in the online learning schedule." 352 label="The forgetting factor used in the online learning schedule."
331 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]." /> 353 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]." />
332 <param argument="--maxOcc" type="integer" value="200" optional="True"
333 label="(S)MEMs occuring more than this many times won't be considered"
334 help=""/>
335 <param argument="--initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False" 354 <param argument="--initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
336 label="Initialization with uniform parameters" 355 label="Initialization with uniform parameters"
337 help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." /> 356 help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
338 <param argument="--maxReadOcc" type="integer" value="100" optional="True" 357 <param argument="--maxReadOcc" type="integer" value="100" optional="True"
339 label="Maximal read mapping occurence" 358 label="Maximal read mapping occurence"
344 <param argument="--noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False" 363 <param argument="--noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False"
345 label="Ignore fragment length distribution" 364 label="Ignore fragment length distribution"
346 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." /> 365 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." />
347 <param argument="--noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False" 366 <param argument="--noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
348 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths." 367 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
349 help="This can increase the precision of bias correction, but harm robustness. The difault correction applies a threshold." /> 368 help="This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold." />
350 <param argument="--numBiasSamples" type="integer" value="2000000" optional="True" 369 <param argument="--numBiasSamples" type="integer" value="2000000" optional="True"
351 label="Number of fragment mappings to use when learning the sequence-specific bias model." 370 label="Number of fragment mappings to use when learning the sequence-specific bias model."
352 help="" /> 371 help="" />
353 <param argument="--numAuxModelSamples" type="integer" value="5000000" optional="True" 372 <param argument="--numAuxModelSamples" type="integer" value="5000000" optional="True"
354 label="The first numAuxModelSamples are used to train the auxiliary model parameters." 373 label="The first numAuxModelSamples are used to train the auxiliary model parameters."
360 label=" If (S)MEM occurs fewer than this many times, search for smaller, contained MEMs" 379 label=" If (S)MEM occurs fewer than this many times, search for smaller, contained MEMs"
361 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." /> 380 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." />
362 <param argument="--splitSpanningSeeds" type="boolean" truevalue="--splitSpanningSeeds" falsevalue="" checked="False" 381 <param argument="--splitSpanningSeeds" type="boolean" truevalue="--splitSpanningSeeds" falsevalue="" checked="False"
363 label="Attempt to split seeds that happen to fall on the boundary between two transcripts." 382 label="Attempt to split seeds that happen to fall on the boundary between two transcripts."
364 help="This can improve the fragment hit-rate, but is usually not necessary."/> 383 help="This can improve the fragment hit-rate, but is usually not necessary."/>
365 <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False" 384 <param argument="--useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False"
366 label="Use the Variational Bayesian EM rather than the traditional EM algorithm for optimization in the batch passes." 385 label="Use the traditional EM algorithm for optimization in the batch passes."
367 help=""/> 386 help=""/>
368 <param argument="--numGibbsSamples" type="integer" value="0" optional="True" 387 <param argument="--numGibbsSamples" type="integer" value="0" optional="True"
369 label=" Number of Gibbs sampling rounds to perform." 388 label=" Number of Gibbs sampling rounds to perform."
370 help="" /> 389 help="" />
371 <param argument="--numBootstraps" type="integer" value="0" optional="True" 390 <param argument="--numBootstraps" type="integer" value="0" optional="True"
378 label="The prior that will be used in the VBEM algorithm." 397 label="The prior that will be used in the VBEM algorithm."
379 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." /> 398 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." />
380 <param argument="--writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False" 399 <param argument="--writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
381 label="Write the names of un-mapped reads to the file unmapped_names.txt." 400 label="Write the names of un-mapped reads to the file unmapped_names.txt."
382 help=""/> 401 help=""/>
402 <param argument="--sigDigits" type="integer" value="3"
403 label="Significant Digits"
404 help="The number of significant digits to write when outputting the EffectiveLength and NumReads columns."/>
405 <param argument="--consensusSlack" type="integer" optional="True"
406 label="Consensus Slack"
407 help="The amount of slack allowed in the quasi-mapping consensus mechanism. Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate. The default value of this option is 1 if --validateMappings is given and 0 otherwise."/>
383 </section> 408 </section>
384 </inputs> 409 </inputs>
385 410
386 <outputs> 411 <outputs>
387 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" /> 412 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
544 </collection> 569 </collection>
545 </param> 570 </param>
546 <param name="TranscriptSource" value="history" /> 571 <param name="TranscriptSource" value="history" />
547 <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> 572 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
548 <param name="geneMap" value="gene_map.tab" ftype="tabular" /> 573 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
574 <output name="output_quant">
575 <assert_contents>
576 <has_text text="EffectiveLength" />
577 <has_text text="TPM" />
578 <has_text text="NM_001168316" />
579 <has_text text="NM_174914" />
580 <has_text text="NM_018953" />
581 <has_text text="NR_003084" />
582 <has_text text="NM_017410" />
583 <has_text text="NM_153693" />
584 <has_text text="NR_031764" />
585 <has_n_columns n="5" />
586 </assert_contents>
587 </output>
588 <output name="output_gene_quant">
589 <assert_contents>
590 <has_text text="EffectiveLength" />
591 <has_text text="TPM" />
592 <has_text text="baz" />
593 <has_text text="bar" />
594 <has_text text="2283" />
595 <has_text text="1640" />
596 <has_n_columns n="5" />
597 </assert_contents>
598 </output>
599 </test>
600 <test>
601 <param name="single_or_paired_opts" value="paired" />
602 <param name="input_mate1" value="reads_1.fastq" />
603 <param name="input_mate2" value="reads_2.fastq" />
604 <param name="TranscriptSource" value="history" />
605 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
606 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
607 <param name="validateMappings" value="True" />
608 <output name="output_quant">
609 <assert_contents>
610 <has_text text="EffectiveLength" />
611 <has_text text="TPM" />
612 <has_text text="NM_001168316" />
613 <has_text text="NM_174914" />
614 <has_text text="NM_018953" />
615 <has_text text="NR_003084" />
616 <has_text text="NM_017410" />
617 <has_text text="NM_153693" />
618 <has_text text="NR_031764" />
619 <has_n_columns n="5" />
620 </assert_contents>
621 </output>
622 <output name="output_gene_quant">
623 <assert_contents>
624 <has_text text="EffectiveLength" />
625 <has_text text="TPM" />
626 <has_text text="baz" />
627 <has_text text="bar" />
628 <has_text text="2283" />
629 <has_text text="1640" />
630 <has_n_columns n="5" />
631 </assert_contents>
632 </output>
633 </test>
634 <test>
635 <param name="single_or_paired_opts" value="paired_collection" />
636 <param name="input_1">
637 <collection type="paired">
638 <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
639 <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
640 </collection>
641 </param>
642 <param name="TranscriptSource" value="history" />
643 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
644 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
645 <param name="validateMappings" value="True" />
646 <output name="output_quant">
647 <assert_contents>
648 <has_text text="EffectiveLength" />
649 <has_text text="TPM" />
650 <has_text text="NM_001168316" />
651 <has_text text="NM_174914" />
652 <has_text text="NM_018953" />
653 <has_text text="NR_003084" />
654 <has_text text="NM_017410" />
655 <has_text text="NM_153693" />
656 <has_text text="NR_031764" />
657 <has_n_columns n="5" />
658 </assert_contents>
659 </output>
660 <output name="output_gene_quant">
661 <assert_contents>
662 <has_text text="EffectiveLength" />
663 <has_text text="TPM" />
664 <has_text text="baz" />
665 <has_text text="bar" />
666 <has_text text="2283" />
667 <has_text text="1640" />
668 <has_n_columns n="5" />
669 </assert_contents>
670 </output>
671 </test>
672 <test>
673 <param name="single_or_paired_opts" value="paired" />
674 <param name="input_mate1" value="reads_1.fastq" />
675 <param name="input_mate2" value="reads_2.fastq" />
676 <param name="TranscriptSource" value="history" />
677 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
678 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
679 <param name="useEM" value="True" />
680 <output name="output_quant">
681 <assert_contents>
682 <has_text text="EffectiveLength" />
683 <has_text text="TPM" />
684 <has_text text="NM_001168316" />
685 <has_text text="NM_174914" />
686 <has_text text="NM_018953" />
687 <has_text text="NR_003084" />
688 <has_text text="NM_017410" />
689 <has_text text="NM_153693" />
690 <has_text text="NR_031764" />
691 <has_n_columns n="5" />
692 </assert_contents>
693 </output>
694 <output name="output_gene_quant">
695 <assert_contents>
696 <has_text text="EffectiveLength" />
697 <has_text text="TPM" />
698 <has_text text="baz" />
699 <has_text text="bar" />
700 <has_text text="2283" />
701 <has_text text="1640" />
702 <has_n_columns n="5" />
703 </assert_contents>
704 </output>
705 </test>
706 <test>
707 <param name="single_or_paired_opts" value="paired_collection" />
708 <param name="input_1">
709 <collection type="paired">
710 <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
711 <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
712 </collection>
713 </param>
714 <param name="TranscriptSource" value="history" />
715 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
716 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
717 <param name="useEM" value="True" />
549 <output name="output_quant"> 718 <output name="output_quant">
550 <assert_contents> 719 <assert_contents>
551 <has_text text="EffectiveLength" /> 720 <has_text text="EffectiveLength" />
552 <has_text text="TPM" /> 721 <has_text text="TPM" />
553 <has_text text="NM_001168316" /> 722 <has_text text="NM_001168316" />