Mercurial > repos > bgruening > sailfish
comparison sailfish.xml @ 5:1b4ed566a41c draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 03edb751808fef8bce744ebcbad5661a32373211
author | bgruening |
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date | Wed, 02 Nov 2016 10:30:36 -0400 |
parents | 03c74355227f |
children | 5bc9cd008ceb |
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4:03c74355227f | 5:1b4ed566a41c |
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1 <tool id="sailfish" name="Sailfish" version="0.7.6.1"> | 1 <tool id="sailfish" name="Sailfish" version="0.10.1"> |
2 <description>transcript quantification from RNA-seq data</description> | 2 <description>transcript quantification from RNA-seq data</description> |
3 <requirements> | |
4 <requirement type="package" version="0.7.6">sailfish</requirement> | |
5 <requirement type="package" version="1.57.0">boost</requirement> | |
6 </requirements> | |
7 <macros> | 3 <macros> |
8 <xml name="strandedness"> | 4 <xml name="strandedness"> |
9 <param name="strandedness" type="select" label="Specify the strandedness of the reads"> | 5 <param name="strandedness" type="select" label="Specify the strandedness of the reads"> |
10 <option value="U" selected="True">Not stranded (U)</option> | 6 <option value="U" selected="True">Not stranded (U)</option> |
11 <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option> | 7 <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option> |
12 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option> | 8 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option> |
13 </param> | 9 </param> |
14 </xml> | 10 </xml> |
15 </macros> | 11 </macros> |
12 <requirements> | |
13 <requirement type="package" version="0.10.1">sailfish</requirement> | |
14 </requirements> | |
16 <stdio> | 15 <stdio> |
17 <exit_code range="1:" /> | 16 <exit_code range="1:" /> |
18 <exit_code range=":-1" /> | 17 <exit_code range=":-1" /> |
19 <regex match="Error:" /> | 18 <regex match="Error:" /> |
20 <regex match="Exception:" /> | 19 <regex match="Exception:" /> |
21 <regex match="Exception :" /> | 20 <regex match="Exception :" /> |
22 </stdio> | 21 </stdio> |
23 <version_command>sailfish -version</version_command> | 22 <version_command>sailfish -version</version_command> |
24 <command> | 23 <command> |
25 <![CDATA[ | 24 <![CDATA[ |
26 | |
27 #if $refTranscriptSource.TranscriptSource == "history": | 25 #if $refTranscriptSource.TranscriptSource == "history": |
28 sailfish index | 26 sailfish index |
29 --transcripts $refTranscriptSource.ownFile | 27 --transcripts $refTranscriptSource.ownFile |
30 --kmerSize $refTranscriptSource.kmerSize | 28 --kmerSize $refTranscriptSource.kmerSize |
31 --out ./index_dir | 29 --out ./index_dir |
32 --threads "\${GALAXY_SLOTS:-4}" | 30 --threads "\${GALAXY_SLOTS:-4}" |
33 #set $index_path = './index_dir' | 31 #set $index_path = './index_dir' |
34 #else: | 32 #else: |
35 #set $index_path = $refTranscriptSource.index.fields.path | 33 #set $index_path = $refTranscriptSource.index.fields.path |
36 #end if | 34 #end if |
37 | |
38 && | 35 && |
39 | |
40 #if $single_or_paired.single_or_paired_opts == 'single': | 36 #if $single_or_paired.single_or_paired_opts == 'single': |
41 | |
42 #if $single_or_paired.input_singles.ext == 'fasta': | 37 #if $single_or_paired.input_singles.ext == 'fasta': |
43 #set $ext = 'fasta' | 38 #set $ext = 'fasta' |
44 #else: | 39 #else: |
45 #set $ext = 'fastq' | 40 #set $ext = 'fastq' |
46 #end if | 41 #end if |
47 | |
48 ln -s $single_or_paired.input_singles ./single.$ext && | 42 ln -s $single_or_paired.input_singles ./single.$ext && |
49 #else: | 43 #else: |
50 | |
51 #if $single_or_paired.input_mate1.ext == 'fasta': | 44 #if $single_or_paired.input_mate1.ext == 'fasta': |
52 #set $ext = 'fasta' | 45 #set $ext = 'fasta' |
53 #else: | 46 #else: |
54 #set $ext = 'fastq' | 47 #set $ext = 'fastq' |
55 #end if | 48 #end if |
56 | |
57 ln -s $single_or_paired.input_mate1 ./mate1.$ext && | 49 ln -s $single_or_paired.input_mate1 ./mate1.$ext && |
58 ln -s $single_or_paired.input_mate2 ./mate2.$ext && | 50 ln -s $single_or_paired.input_mate2 ./mate2.$ext && |
59 #end if | 51 #end if |
60 | |
61 | |
62 #if $geneMap: | 52 #if $geneMap: |
63 ln -s "$geneMap" ./geneMap.$geneMap.ext && | 53 ln -s "$geneMap" ./geneMap.$geneMap.ext && |
64 #end if | 54 #end if |
65 | |
66 sailfish quant | 55 sailfish quant |
67 --index $index_path | 56 --index $index_path |
68 #if $single_or_paired.single_or_paired_opts == 'single': | 57 #if $single_or_paired.single_or_paired_opts == 'single': |
69 --libType ${single_or_paired.strandedness} | 58 --libType ${single_or_paired.strandedness} |
70 --unmatedReads ./single.$ext | 59 --unmatedReads ./single.$ext |
71 #else: | 60 #else: |
72 --mates1 ./mate1.$ext | 61 --mates1 ./mate1.$ext |
73 --mates2 ./mate2.$ext | 62 --mates2 ./mate2.$ext |
74 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" | 63 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" |
75 #end if | 64 #end if |
76 --output ./ | 65 --output ./results |
77 $biasCorrect | 66 $biasCorrect |
67 $gcBiasCorrect | |
78 --threads "\${GALAXY_SLOTS:-4}" | 68 --threads "\${GALAXY_SLOTS:-4}" |
79 | 69 $dumpEq |
80 #if $fldMean: | 70 #if str($gcSizeSamp): |
71 --gcSizeSamp $gcSizeSamp | |
72 #end if | |
73 #if str($gcSpeedSamp): | |
74 --gcSpeedSamp $gcSpeedSamp | |
75 #end if | |
76 #if str($fldMean): | |
81 --fldMean $fldMean | 77 --fldMean $fldMean |
82 #end if | 78 #end if |
83 | 79 #if str($fldSD): |
84 #if $fldSD: | |
85 --fldSD $fldSD | 80 --fldSD $fldSD |
86 #end if | 81 #end if |
87 | |
88 #if $maxReadOcc: | 82 #if $maxReadOcc: |
89 --maxReadOcc $maxReadOcc | 83 --maxReadOcc $maxReadOcc |
90 #end if | 84 #end if |
91 | |
92 #if $geneMap: | 85 #if $geneMap: |
93 --geneMap ./geneMap.${geneMap.ext} | 86 --geneMap ./geneMap.${geneMap.ext} |
94 #end if | 87 #end if |
95 | 88 $strictIntersect |
96 $noEffectiveLengthCorrection | 89 $noEffectiveLengthCorrection |
97 $useVBOpt | 90 $useVBOpt |
98 $allowOrphans | 91 $discardOrphans |
99 | |
100 $unsmoothedFLD | 92 $unsmoothedFLD |
101 --maxFragLen ${maxFragLen} | 93 --maxFragLen ${maxFragLen} |
102 --txpAggregationKey "${txpAggregationKey}" | 94 --txpAggregationKey '${txpAggregationKey}' |
103 | 95 $ignoreLibCompat |
96 $enforceLibCompat | |
97 $allowDovetail | |
98 #if str($numBiasSamples): | |
99 --numBiasSamples $numBiasSamples | |
100 #end if | |
101 #if str($numFragSamples): | |
102 --numFragSamples $numFragSamples | |
103 #end if | |
104 #if str($numGibbsSamples): | |
105 --numGibbsSamples $numGibbsSamples | |
106 #end if | |
107 #if str($numBootstraps): | |
108 --numBootstraps $numBootstraps | |
109 #end if | |
104 ]]> | 110 ]]> |
105 </command> | 111 </command> |
106 <inputs> | 112 <inputs> |
107 <conditional name="refTranscriptSource"> | 113 <conditional name="refTranscriptSource"> |
108 <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"> | 114 <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"> |
116 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | 122 <validator type="no_options" message="No indexes are available for the selected input dataset"/> |
117 </options> | 123 </options> |
118 </param> | 124 </param> |
119 </when> <!-- build-in --> | 125 </when> <!-- build-in --> |
120 <when value="history"> | 126 <when value="history"> |
121 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference transcriptome" help="in FASTA format" /> | 127 <param name="ownFile" type="data" format="fasta" label="Select the reference transcriptome" help="in FASTA format" /> |
122 <param argument="kmerSize" type="integer" value="21" max="32" label="The size of the k-mer on which the index is built" | 128 <param argument="kmerSize" type="integer" value="21" max="32" label="The size of the k-mer on which the index is built" |
123 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. | 129 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. |
124 The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, | 130 The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, |
125 the more distinct they will be. We generally recommend using a k-mer size of at least 20."/> | 131 the more distinct they will be. We generally recommend using a k-mer size of at least 20."/> |
126 </when> <!-- history --> | 132 </when> <!-- history --> |
150 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True" label="File containing a mapping of transcripts to genes" | 156 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True" label="File containing a mapping of transcripts to genes" |
151 help="Calculates the aggregated gene-level abundance estimations. This file should be eiher a GTF file or tab-delimited format | 157 help="Calculates the aggregated gene-level abundance estimations. This file should be eiher a GTF file or tab-delimited format |
152 where each line contains the name of a transcript and the gene to which it belongs separated by a tab." /> | 158 where each line contains the name of a transcript and the gene to which it belongs separated by a tab." /> |
153 | 159 |
154 <param argument="--biasCorrect" type="boolean" truevalue="--biasCorrect" falsevalue="" checked="False" | 160 <param argument="--biasCorrect" type="boolean" truevalue="--biasCorrect" falsevalue="" checked="False" |
155 label="Perform bias correction" help=""/> | 161 label="Perform sequence-specific bias correction" help=""/> |
162 | |
163 <param argument="--gcBiasCorrect" type="boolean" truevalue="--gcBiasCorrect" falsevalue="" checked="False" | |
164 label="Perform fragment GC bias correction" help=""/> | |
165 | |
166 <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False" | |
167 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/> | |
168 | |
169 <param argument="--gcSizeSamp" type="integer" value="1" optional="True" | |
170 label="The value by which to down-sample transcripts when representing the GC content" | |
171 help="Larger values will reduce memory usage, but may decrease the fidelity of bias modeling results."/> | |
172 | |
173 <param argument="--gcSpeedSamp" type="integer" value="1" optional="True" | |
174 label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias." | |
175 help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/> | |
176 | |
177 <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False" | |
178 label="Strict Intersect." help="When this flag is set, if the intersection of the | |
179 quasi-mappings for the left and right is empty, then all mappings for the left and all mappings | |
180 for the right read are reported as orphaned quasi-mappings."/> | |
156 | 181 |
157 <param argument="--fldMean" type="integer" value="200" optional="True" label="Calculate effective lengths" | 182 <param argument="--fldMean" type="integer" value="200" optional="True" label="Calculate effective lengths" |
158 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 | 183 help="If single end reads are being used for quantification, or there are an insufficient number of uniquely |
159 to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/> | 184 mapping reads when performing paired-end quantification |
185 to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/> | |
160 | 186 |
161 <param argument="--fldSD" type="integer" value="80" optional="True" label="Standard deviation" | 187 <param argument="--fldSD" type="integer" value="80" optional="True" label="Standard deviation" |
162 help="The standard deviation used in the fragment length distribution for single-end quantification or when an empirical distribution cannot be learned."/> | 188 help="The standard deviation used in the fragment length distribution for single-end quantification or |
189 when an empirical distribution cannot be learned."/> | |
163 | 190 |
164 <param argument="--maxReadOcc" type="integer" value="200" optional="True" label="Maximal read mapping occurence" | 191 <param argument="--maxReadOcc" type="integer" value="200" optional="True" label="Maximal read mapping occurence" |
165 help="Reads mapping to more than this many places won't be considered."/> | 192 help="Reads mapping to more than this many places won't be considered."/> |
166 | 193 |
167 <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False" | 194 <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False" |
168 label="Disable effective length correction" help="Disables effective length correction when computing the probability that a fragment was generated from a transcript. | 195 label="Disable effective length correction" help="Disables effective length correction when computing the probability |
196 that a fragment was generated from a transcript. | |
169 If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/> | 197 If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/> |
170 | 198 |
171 <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False" | 199 <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False" |
172 label="Use Variational Bayesian EM algorithm for optimization" help=""/> | 200 label="Use Variational Bayesian EM algorithm for optimization" help="Use Variational Bayesian EM algorithm rather |
173 | 201 than the traditional EM angorithm for optimization"/> |
174 <param argument="--allowOrphans" type="boolean" truevalue="--allowOrphans" falsevalue="" checked="False" | 202 |
175 label="Consider orphaned reads as valid hits when performing lightweight-alignment" | 203 <param argument="--discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False" |
176 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."/> | 204 label="Discard orphaned reads as valid hits when performing lightweight-alignment" |
205 help="This option will discard orphaned fragments. This only has an effect on paired-end input, but enabling this option will discard, rather than count, any reads where only one of the paired fragments maps to a transcript."/> | |
177 | 206 |
178 <param argument="--unsmoothedFLD" type="boolean" truevalue="--unsmoothedFLD" falsevalue="" checked="False" | 207 <param argument="--unsmoothedFLD" type="boolean" truevalue="--unsmoothedFLD" falsevalue="" checked="False" |
179 label="Use the un-smoothed approach to effective length correction" help="This traditional approach works by convolving the FLD with the characteristic function over each transcript."/> | 208 label="Use the un-smoothed approach to effective length correction" help="This traditional approach works by convolving the FLD with the |
209 characteristic function over each transcript."/> | |
180 | 210 |
181 <param argument="--maxFragLen" type="integer" value="1000" optional="True" | 211 <param argument="--maxFragLen" type="integer" value="1000" optional="True" |
182 label="The maximum length of a fragment to consider when building the empirical fragment length distribution" | 212 label="The maximum length of a fragment to consider when building the empirical fragment length distribution" |
183 help=""/> | 213 help=""/> |
184 | 214 |
185 <param argument="--txpAggregationKey" value="gene_id" type="text" label="The key for aggregating transcripts during gene-level estimates" | 215 <param argument="--txpAggregationKey" value="gene_id" type="text" label="The key for aggregating transcripts during gene-level estimates"> |
186 help="The default is the gene_id field, but other fields (e.g. gene_name) might be useful depending on the specifics of the annotation being used." /> | 216 <help> |
187 | 217 <![CDATA[ |
218 When generating the gene-level estimates, use the provided key for aggregating transcripts. The default is the "gene_id" field, | |
219 but other fields (e.g. "gene_name") might be useful depending on the specifics of the annotation being used. Note: this option only | |
220 affects aggregation when using a GTF annotation; not an annotation in "simple" format.]]> | |
221 </help> | |
222 </param> | |
223 <param argument="--ignoreLibCompat" type="boolean" truevalue="--ignoreLibCompat" falsevalue="" checked="False" | |
224 label="Disables strand-aware processing completely."> | |
225 <help> | |
226 <![CDATA[ | |
227 All hits are considered "Valid".]]> | |
228 </help> | |
229 </param> | |
230 <param argument="--enforceLibCompat" type="boolean" truevalue="--enforceLibCompat" falsevalue="" checked="False" | |
231 label="Enforces strict library compatibility."> | |
232 <help> | |
233 <![CDATA[ | |
234 Fragments that map in a manner other than what is specified by the expected library type will be discarded, | |
235 even if there are no mappings that agree with the expected library type.]]> | |
236 </help> | |
237 </param> | |
238 <param argument="--allowDovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False" | |
239 label="Allow paired-end reads from the same fragment to dovetail."> | |
240 <help> | |
241 <![CDATA[ | |
242 Allow paired-end reads from the same fragment to "dovetail", such that the ends of the mapped reads can extend past each other.]]> | |
243 </help> | |
244 </param> | |
245 <param argument="--numBiasSamples" type="integer" value="1000000" optional="True" | |
246 label="Number of fragment mappings to use when learning the sequene-specific bias model" | |
247 help=""/> | |
248 <param argument="--numFragSamples" type="integer" value="10000" optional="True" | |
249 label="Number of fragments from unique alignments to sample when building the fragment length distribution" | |
250 help=""/> | |
251 <param argument="--numGibbsSamples" type="integer" value="0" optional="True" | |
252 label="Number of Gibbs sampling rounds to perform." | |
253 help=""/> | |
254 <param argument="--numBootstraps" type="integer" value="0" optional="True" | |
255 label="Number of bootstrap samples to generate." | |
256 help="This is mutually exclusive with Gibbs"/> | |
188 </inputs> | 257 </inputs> |
258 | |
259 | |
189 <outputs> | 260 <outputs> |
190 <data name="output_quant" format="tabular" from_work_dir="quant.sf" label="${tool.name} on ${on_string} (Quantification)" /> | 261 <data name="output_quant" format="tabular" from_work_dir="results/quant.sf" label="${tool.name} on ${on_string} (Quantification)" /> |
191 <data name="output_bias_corrected_quant" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)"> | 262 <data name="output_gene_quant" format="tabular" from_work_dir="results/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)"> |
192 <filter>biasCorrect is True</filter> | 263 <filter>geneMap</filter> |
193 </data> | |
194 <data name="output_gene_quant" format="tabular" from_work_dir="quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)"> | |
195 <filter>geneMap is True</filter> | |
196 </data> | 264 </data> |
197 </outputs> | 265 </outputs> |
198 <tests> | 266 <tests> |
199 <test> | 267 <test> |
200 <param name="single_or_paired_opts" value="paired" /> | 268 <param name="single_or_paired_opts" value="paired" /> |
201 <param name="input_mate1" value="reads_1.fastq" /> | 269 <param name="input_mate1" value="reads_1.fastq" /> |
202 <param name="input_mate2" value="reads_2.fastq" /> | 270 <param name="input_mate2" value="reads_2.fastq" /> |
271 <param name="biasCorrect" value="False" /> | |
272 <param name="TranscriptSource" value="history" /> | |
273 <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> | |
274 <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" /> | |
275 </test> | |
276 <test> | |
277 <param name="single_or_paired_opts" value="paired" /> | |
278 <param name="input_mate1" value="reads_1.fastq" /> | |
279 <param name="input_mate2" value="reads_2.fastq" /> | |
203 <param name="biasCorrect" value="True" /> | 280 <param name="biasCorrect" value="True" /> |
204 <param name="TranscriptSource" value="history" /> | 281 <param name="TranscriptSource" value="history" /> |
205 <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> | 282 <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> |
206 <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" /> | 283 <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" /> |
207 <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_bias_corrected_quant" /> | 284 </test> |
285 <test> | |
286 <param name="single_or_paired_opts" value="paired" /> | |
287 <param name="input_mate1" value="reads_1.fastq" /> | |
288 <param name="input_mate2" value="reads_2.fastq" /> | |
289 <param name="biasCorrect" value="True" /> | |
290 <param name="TranscriptSource" value="history" /> | |
291 <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> | |
292 <param name="geneMap" value="gene_map.tab" ftype="tabular" /> | |
293 <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" /> | |
294 <output file="sailfish_genMap_result1.tab" ftype="tabular" name="output_gene_quant" /> | |
208 </test> | 295 </test> |
209 </tests> | 296 </tests> |
210 <help> | 297 <help><![CDATA[ |
211 <![CDATA[ | |
212 | 298 |
213 **What it does** | 299 **What it does** |
214 | 300 |
215 Sailfish is a tool for transcript quantification from RNA-seq data. It | 301 Sailfish is a tool for transcript quantification from RNA-seq data. It |
216 requires a set of target transcripts (either from a reference or de-novo | 302 requires a set of target transcripts (either from a reference or de-novo |
334 | 420 |
335 The remaining salmon library format strings are not directly expressible in terms | 421 The remaining salmon library format strings are not directly expressible in terms |
336 of the TopHat library types, and so there is no direct mapping for them. | 422 of the TopHat library types, and so there is no direct mapping for them. |
337 | 423 |
338 | 424 |
339 ]]> | 425 ]]></help> |
340 </help> | 426 <citations> |
427 <citation type="doi">10.1038/nbt.2862</citation> | |
428 </citations> | |
341 </tool> | 429 </tool> |