| Previous changeset 7:e7e885f718fb (2018-05-30) Next changeset 9:2c0ca397d302 (2019-07-27) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56 |
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modified:
README.rst salmon.xml |
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| diff -r e7e885f718fb -r 6b0ba6de1424 README.rst --- a/README.rst Wed May 30 03:19:09 2018 -0400 +++ b/README.rst Thu Aug 23 15:58:26 2018 -0400 |
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| @@ -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 ======== ====================================================================== |
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| diff -r e7e885f718fb -r 6b0ba6de1424 salmon.xml --- a/salmon.xml Wed May 30 03:19:09 2018 -0400 +++ b/salmon.xml Thu Aug 23 15:58:26 2018 -0400 |
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| b'@@ -17,7 +17,7 @@\n <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>\n </param>\n </xml>\n- <token name="@VERSION@">0.9.1</token>\n+ <token name="@VERSION@">0.11.2</token>\n </macros>\n \n <requirements>\n@@ -47,9 +47,6 @@\n --index \'./index\'\n --type \'$quasi_orphans.type\'\n $perfectHash\n- #if str($sasamp):\n- --sasamp $sasamp\n- #end if\n #set $index_path = \'./index\'\n #else:\n #set $index_path = $refTranscriptSource.index.fields.path\n@@ -122,6 +119,7 @@\n --unmatedReads ./single.$ext\n #end if\n #else:\n+ --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"\n #if $single_or_paired.single_or_paired_opts == \'paired_interleaved\':\n #if $compressed == \'BZ2\':\n --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1)\n@@ -142,16 +140,20 @@\n --mates2 ./mate2.$ext\n #end if\n #end if\n- --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"\n #end if\n --output ./output\n #if str($quasi_orphans.type) == \'quasi\':\n --allowOrphans\n- #else:\n- $quasi_orphans.allowOrphans\n+ $quasi_orphans.validateMappings\n+ --ma $quasi_orphans.matchScore\n+ --mp $quasi_orphans.mismatchPenalty\n+ --go $quasi_orphans.gapOpenPenalty\n+ --ge $quasi_orphans.gapExtensionPenalty\n+ --minScoreFraction $quasi_orphans.minScoreFraction\n #end if\n $seqBias\n $gcBias\n+ $noErrorModel\n --threads "\\${GALAXY_SLOTS:-4}"\n --incompatPrior $adv.incompatPrior\n $adv.consistentHits\n@@ -173,9 +175,6 @@\n #if $adv.forgettingFactor:\n --forgettingFactor $adv.forgettingFactor\n #end if\n- #if str($adv.maxOcc):\n- --maxOcc $adv.maxOcc\n- #end if\n $adv.initUniform\n $adv.noFragLengthDist\n $adv.noBiasLengthThreshold\n@@ -186,7 +185,7 @@\n --geneMap ./geneMap.${geneMap.ext}\n #end if\n $adv.noEffectiveLengthCorrection\n- $adv.useVBOpt\n+ $adv.useEM\n #if str($adv.numBiasSamples):\n --numBiasSamples $adv.numBiasSamples\n #end if\n@@ -202,11 +201,21 @@\n #if str($adv.numBootstraps):\n --numBootstraps $adv.numBootstraps\n #end if\n+ #if str($adv.consensusSlack):\n+ --consensusSlack $adv.consensusSlack\n+ #else:\n+ #if $quasi_orphans.validateMappings:\n+ --consensusSlack 1\n+ #else:\n+ --consensusSlack 0\n+ #end if\n+ #end if\n $adv.perTranscriptPrior\n #if $adv.vbPrior:\n --vbPrior $adv.vbPrior\n #end if\n $adv.writeUnmappedNames\n+ --sigDigits $adv.sigDigits\n #if str($adv.writeMappings):\n $adv.writeMappings > ${output_sam}\n #end if\n@@ -263,21 +272,31 @@\n <conditional name="quasi_orphans">\n <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">\n <option value="quasi" selected="True">quasi</option>\n- <option value="fmd">fmd</option>\n </param>\n <when value="quasi">\n+ <param argument="--validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False'..b'/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_gene_quant">\n+ <assert_contents>\n+ <has_text text="EffectiveLength" />\n+ <has_text text="TPM" />\n+ <has_text text="baz" />\n+ <has_text text="bar" />\n+ <has_text text="2283" />\n+ <has_text text="1640" />\n+ <has_n_columns n="5" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="single_or_paired_opts" value="paired" />\n+ <param name="input_mate1" value="reads_1.fastq" />\n+ <param name="input_mate2" value="reads_2.fastq" />\n+ <param name="TranscriptSource" value="history" />\n+ <param name="ownFile" value="transcripts.fasta" ftype="fasta" />\n+ <param name="geneMap" value="gene_map.tab" ftype="tabular" />\n+ <param name="useEM" value="True" />\n+ <output name="output_quant">\n+ <assert_contents>\n+ <has_text text="EffectiveLength" />\n+ <has_text text="TPM" />\n+ <has_text text="NM_001168316" />\n+ <has_text text="NM_174914" />\n+ <has_text text="NM_018953" />\n+ <has_text text="NR_003084" />\n+ <has_text text="NM_017410" />\n+ <has_text text="NM_153693" />\n+ <has_text text="NR_031764" />\n+ <has_n_columns n="5" />\n+ </assert_contents>\n+ </output>\n+ <output name="output_gene_quant">\n+ <assert_contents>\n+ <has_text text="EffectiveLength" />\n+ <has_text text="TPM" />\n+ <has_text text="baz" />\n+ <has_text text="bar" />\n+ <has_text text="2283" />\n+ <has_text text="1640" />\n+ <has_n_columns n="5" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="single_or_paired_opts" value="paired_collection" />\n+ <param name="input_1">\n+ <collection type="paired">\n+ <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />\n+ <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />\n+ </collection> \n+ </param> \n+ <param name="TranscriptSource" value="history" />\n+ <param name="ownFile" value="transcripts.fasta" ftype="fasta" />\n+ <param name="geneMap" value="gene_map.tab" ftype="tabular" />\n+ <param name="useEM" value="True" />\n+ <output name="output_quant">\n+ <assert_contents>\n+ <has_text text="EffectiveLength" />\n+ <has_text text="TPM" />\n+ <has_text text="NM_001168316" />\n+ <has_text text="NM_174914" />\n+ <has_text text="NM_018953" />\n+ <has_text text="NR_003084" />\n+ <has_text text="NM_017410" />\n+ <has_text text="NM_153693" />\n+ <has_text text="NR_031764" />\n+ <has_n_columns n="5" />\n+ </assert_contents>\n+ </output>\n+ <output name="output_gene_quant">\n+ <assert_contents>\n+ <has_text text="EffectiveLength" />\n+ <has_text text="TPM" />\n+ <has_text text="baz" />\n+ <has_text text="bar" />\n+ <has_text text="2283" />\n+ <has_text text="1640" />\n+ <has_n_columns n="5" />\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n \n <help><![CDATA[\n' |