| Previous changeset 11:7643953b19f9 (2025-10-29) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 |
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modified:
macros.xml |
| b |
| diff -r 7643953b19f9 -r 71ce24befa24 macros.xml --- a/macros.xml Wed Oct 29 10:46:47 2025 +0000 +++ b/macros.xml Fri Oct 31 19:18:11 2025 +0000 |
| [ |
| b'@@ -1,6 +1,6 @@\n <macros>\n <token name="@TOOL_VERSION@">1.10.1</token>\n- <token name="@VERSION_SUFFIX@">3</token>\n+ <token name="@VERSION_SUFFIX@">4</token>\n <token name="@IDX_VERSION@">q7</token>\n <token name="@PROFILE_VERSION@">24.1</token>\n <xml name="xrefs">\n@@ -26,7 +26,7 @@\n <param argument="--libType" name="orientation" type="select" label="Relative orientation of reads within a pair">\n <option value="M">Mates are oriented in the same direction (M = matching)</option>\n <option value="O">Mates are oriented away from each other (O = outward)</option>\n- <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>\n+ <option value="I" selected="true">Mates are oriented toward each other (I = inward)</option>\n </param>\n </xml>\n <xml name="stranded">\n@@ -68,7 +68,7 @@\n <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?"\n help="Built-ins were indexed using default options">\n <option value="indexed">Use a built-in index</option>\n- <option value="history" selected="True">Use one from the history</option>\n+ <option value="history" selected="true">Use one from the history</option>\n </param>\n <when value="indexed">\n <param argument="--index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">\n@@ -91,7 +91,7 @@\n </conditional>\n </xml>\n <xml name="reads">\n- <section name="input" title="Data input" expanded="True">\n+ <section name="input" title="Data input" expanded="true">\n <conditional name="single_or_paired">\n <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">\n <option value="single">Single-end</option>\n@@ -108,188 +108,95 @@\n </conditional>\n </section>\n <!--Salmon quant type select: reads-based or alignment-based-->\n- <param argument="--discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="False"\n- label="Discard orphan quasi"\n- help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist."/>\n+ <param argument="--discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="false" label="Discard orphan quasi" help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist."/>\n <conditional name="validmap">\n <param name="validateMappings" type="select" 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.">\n <option value="--validateMappings">True</option>\n <option value="" selected="true">False</option>\n </param>\n <when value="--validateMappings">\n- <param argument="--minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"\n- label="Min Score Fraction"\n- 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]."/>\n- <param argument="--maxMMPExtension" type="integer" optional="True"\n- label="Sets the maximum allowable MM'..b'.gapExtensionPenalty}\'\n ${$quant_type.validmap.mimicBT2}\n ${$quant_type.validmap.mimicStrictBT2}\n ${$quant_type.validmap.hardFilter}\n #end if\n- #if $quant_type.consensusSlack:\n- --consensusSlack \'${quant_type.consensusSlack}\'\n- #end if\n+ --consensusSlack \'${quant_type.consensusSlack}\'\n ${quant_type.dovetail}\n ${quant_type.recoverOrphans}\n ${quant_type.bam_options.writeMappings}\n@@ -422,9 +314,6 @@\n ${quant_type.bam_options.writeQualities}\n #end if\n ${quant_type.consistentHits}\n- #if $quant_type.quasiCoverage:\n- --quasiCoverage \'${quant_type.quasiCoverage}\'\n- #end if\n ]]>\n </token>\n <token name="@salalign@"><![CDATA[\n@@ -439,9 +328,7 @@\n --threads "\\$SLOTS"\n ${quant_type.discardOrphans}\n ${quant_type.noErrorModel}\n- #if $quant_type.numErrorBins:\n- --numErrorBins \'${quant_type.numErrorBins}\'\n- #end if\n+ --numErrorBins \'${quant_type.numErrorBins}\'\n ${quant_type.sampleOut}\n ${quant_type.sampleUnaligned}\n ${quant_type.gencode}\n@@ -464,24 +351,12 @@\n ${adv.skipQuant}\n ${adv.dumpEq}\n ${adv.dumpEqWeights}\n- #if $adv.minAssignedFrags:\n- --minAssignedFrags \'${adv.minAssignedFrags}\'\n- #end if\n- #if $adv.biasSpeedSamp:\n- --biasSpeedSamp \'${adv.biasSpeedSamp}\'\n- #end if\n- #if $adv.fldMax:\n- --fldMax \'${adv.fldMax}\'\n- #end if\n- #if $adv.fldMean:\n- --fldMean \'${adv.fldMean}\'\n- #end if\n- #if $adv.fldSD:\n- --fldSD \'${adv.fldSD}\'\n- #end if\n- #if $adv.forgettingFactor:\n- --forgettingFactor \'${adv.forgettingFactor}\'\n- #end if\n+ --minAssignedFrags \'${adv.minAssignedFrags}\'\n+ --biasSpeedSamp \'${adv.biasSpeedSamp}\'\n+ --fldMax \'${adv.fldMax}\'\n+ --fldMean \'${adv.fldMean}\'\n+ --fldSD \'${adv.fldSD}\'\n+ --forgettingFactor \'${adv.forgettingFactor}\'\n ${adv.initUniform}\n #if str($adv.maxReadOcc):\n --maxReadOcc \'${adv.maxReadOcc}\'\n@@ -490,35 +365,19 @@\n ${adv.noEffectiveLengthCorrection}\n ${adv.noFragLengthDist}\n ${adv.noBiasLengthThreshold}\n- #if str($adv.numBiasSamples):\n- --numBiasSamples \'${adv.numBiasSamples}\'\n- #end if\n- #if str($adv.numAuxModelSamples):\n- --numAuxModelSamples \'${adv.numAuxModelSamples}\'\n- #end if\n- #if str($adv.numPreAuxModelSamples):\n- --numPreAuxModelSamples \'${adv.numPreAuxModelSamples}\'\n- #end if\n+ --numBiasSamples \'${adv.numBiasSamples}\'\n+ --numAuxModelSamples \'${adv.numAuxModelSamples}\'\n+ --numPreAuxModelSamples \'${adv.numPreAuxModelSamples}\'\n ${adv.useEM}\n- #if $adv.rangeFactorizationBins:\n- --rangeFactorizationBins \'${adv.rangeFactorizationBins}\'\n- #end if\n- #if str($adv.numGibbsSamples):\n- --numGibbsSamples \'${adv.numGibbsSamples}\'\n- #end if\n+ --rangeFactorizationBins \'${adv.rangeFactorizationBins}\'\n+ --numGibbsSamples \'${adv.numGibbsSamples}\'\n ${adv.noGammaDraw}\n- #if str($adv.numBootstraps):\n- --numBootstraps \'${adv.numBootstraps}\'\n- #end if\n+ --numBootstraps \'${adv.numBootstraps}\'\n ${adv.bootstrapReproject}\n- #if $adv.thinningFactor:\n- --thinningFactor \'${adv.thinningFactor}\'\n- #end if\n+ --thinningFactor \'${adv.thinningFactor}\'\n ${adv.perTranscriptPrior}\n --sigDigits \'${adv.sigDigits}\'\n- #if $adv.vbPrior:\n- --vbPrior \'${adv.vbPrior}\'\n- #end if\n+ --vbPrior \'${adv.vbPrior}\'\n ${adv.writeOrphanLinks}\n ${adv.writeUnmappedNames}\n -o ./output\n' |