Mercurial > repos > bgruening > salmon
changeset 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 |
| files | README.rst salmon.xml |
| diffstat | 2 files changed, 202 insertions(+), 27 deletions(-) [+] |
line wrap: on
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--- a/README.rst Wed May 30 03:19:09 2018 -0400 +++ b/README.rst Thu Aug 23 15:58:26 2018 -0400 @@ -1,10 +1,10 @@ Galaxy wrappers for salmon ===================================== -These wrappers are copyright 2014, updated 2016 by Björn Grüning, Mhd Ramez Alrawas and additional contributors. +These wrappers are copyright 2014, updated 2018 by Björn Grüning, Mhd Ramez Alrawas and additional contributors. All rights reserved. See the licence text below. -Currently tested with salmon 0.7.2. +Currently tested with salmon 0.11.2. Automated Installation @@ -23,6 +23,12 @@ v0.6.3.0 - First release -------- ---------------------------------------------------------------------- v0.7.2 - Second release +-------- ---------------------------------------------------------------------- +v0.8.2 - Third release +-------- ---------------------------------------------------------------------- +v0.9.1 - Fourth release +-------- ---------------------------------------------------------------------- +v0.11.2 - Fifth release ======== ======================================================================
--- a/salmon.xml Wed May 30 03:19:09 2018 -0400 +++ b/salmon.xml Thu Aug 23 15:58:26 2018 -0400 @@ -17,7 +17,7 @@ <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option> </param> </xml> - <token name="@VERSION@">0.9.1</token> + <token name="@VERSION@">0.11.2</token> </macros> <requirements> @@ -47,9 +47,6 @@ --index './index' --type '$quasi_orphans.type' $perfectHash - #if str($sasamp): - --sasamp $sasamp - #end if #set $index_path = './index' #else: #set $index_path = $refTranscriptSource.index.fields.path @@ -122,6 +119,7 @@ --unmatedReads ./single.$ext #end if #else: + --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" #if $single_or_paired.single_or_paired_opts == 'paired_interleaved': #if $compressed == 'BZ2': --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1) @@ -142,16 +140,20 @@ --mates2 ./mate2.$ext #end if #end if - --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" #end if --output ./output #if str($quasi_orphans.type) == 'quasi': --allowOrphans - #else: - $quasi_orphans.allowOrphans + $quasi_orphans.validateMappings + --ma $quasi_orphans.matchScore + --mp $quasi_orphans.mismatchPenalty + --go $quasi_orphans.gapOpenPenalty + --ge $quasi_orphans.gapExtensionPenalty + --minScoreFraction $quasi_orphans.minScoreFraction #end if $seqBias $gcBias + $noErrorModel --threads "\${GALAXY_SLOTS:-4}" --incompatPrior $adv.incompatPrior $adv.consistentHits @@ -173,9 +175,6 @@ #if $adv.forgettingFactor: --forgettingFactor $adv.forgettingFactor #end if - #if str($adv.maxOcc): - --maxOcc $adv.maxOcc - #end if $adv.initUniform $adv.noFragLengthDist $adv.noBiasLengthThreshold @@ -186,7 +185,7 @@ --geneMap ./geneMap.${geneMap.ext} #end if $adv.noEffectiveLengthCorrection - $adv.useVBOpt + $adv.useEM #if str($adv.numBiasSamples): --numBiasSamples $adv.numBiasSamples #end if @@ -202,11 +201,21 @@ #if str($adv.numBootstraps): --numBootstraps $adv.numBootstraps #end if + #if str($adv.consensusSlack): + --consensusSlack $adv.consensusSlack + #else: + #if $quasi_orphans.validateMappings: + --consensusSlack 1 + #else: + --consensusSlack 0 + #end if + #end if $adv.perTranscriptPrior #if $adv.vbPrior: --vbPrior $adv.vbPrior #end if $adv.writeUnmappedNames + --sigDigits $adv.sigDigits #if str($adv.writeMappings): $adv.writeMappings > ${output_sam} #end if @@ -263,21 +272,31 @@ <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"> + <param argument="--validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False" + label="Validate mappings" + 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."/> + <param name="matchScore" argument="--ma" type="integer" value="2" + label="Match Score" + help="The value given to a match between read and reference nucleotides in an alignment."/> + <param name="mismatchPenalty" argument="--mp" type="integer" value="4" + label="Mismatch Penalty" + help="The value given to a mis-match between read and reference nucleotides in an alignment. This will be cast to a negative value."/> + <param name="gapOpenPenalty" argument="--go" type="integer" value="5" + label="Gap Open Penalty" + help="The value given to a gap opening in an alignment."/> + <param name="gapExtensionPenalty" argument="--ge" type="integer" value="3" + label="Gap Extension Penalty" + help="The value given to a gap extension in an alignment."/> + <param argument="--minScoreFraction" type="float" value="0.65" min="0.0" max="0.99" + label="Min Score Fraction" + 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]."/> </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=""/> @@ -287,6 +306,9 @@ <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True" label="File containing a mapping of transcripts to genes" 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." /> + <param argument="--noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False" + label="No Error Model" + 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."/> <section name="adv" title="Additional Options"> <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False" label="Write Mappings" @@ -329,9 +351,6 @@ <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." /> @@ -346,7 +365,7 @@ 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." /> + help="This can increase the precision of bias correction, but harm robustness. The default 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="" /> @@ -362,8 +381,8 @@ <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." + <param argument="--useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False" + label="Use 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." @@ -380,6 +399,12 @@ <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=""/> + <param argument="--sigDigits" type="integer" value="3" + label="Significant Digits" + help="The number of significant digits to write when outputting the EffectiveLength and NumReads columns."/> + <param argument="--consensusSlack" type="integer" optional="True" + label="Consensus Slack" + 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."/> </section> </inputs> @@ -572,6 +597,150 @@ </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" /> + <param name="validateMappings" value="True" /> + <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> + <test> + <param name="single_or_paired_opts" value="paired_collection" /> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="reads_1.fastq" ftype="fastqsanger" /> + <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" /> + </collection> + </param> + <param name="TranscriptSource" value="history" /> + <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> + <param name="geneMap" value="gene_map.tab" ftype="tabular" /> + <param name="validateMappings" value="True" /> + <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> + <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" /> + <param name="useEM" value="True" /> + <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> + <test> + <param name="single_or_paired_opts" value="paired_collection" /> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="reads_1.fastq" ftype="fastqsanger" /> + <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" /> + </collection> + </param> + <param name="TranscriptSource" value="history" /> + <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> + <param name="geneMap" value="gene_map.tab" ftype="tabular" /> + <param name="useEM" value="True" /> + <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[