| Previous changeset 4:03c74355227f (2016-09-18) Next changeset 6:5bc9cd008ceb (2017-04-13) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 03edb751808fef8bce744ebcbad5661a32373211 |
|
modified:
README.rst sailfish.xml test-data/sailfish_bias_result1.tab test-data/sailfish_quant_result1.tab |
|
added:
sailfish.tar.bz2 test-data/gene_map.tab test-data/sailfish_genMap_result1.tab |
| b |
| diff -r 03c74355227f -r 1b4ed566a41c README.rst --- a/README.rst Sun Sep 18 06:05:57 2016 -0400 +++ b/README.rst Wed Nov 02 10:30:36 2016 -0400 |
| b |
| @@ -1,11 +1,10 @@ Galaxy wrappers for sailfish ===================================== -These wrappers are copyright 2014 by Björn Grüning and additional contributors. +These wrappers are copyright 2014 by Björn Grüning, Mhd Ramez Alrawas and additional contributors. All rights reserved. See the licence text below. -Currently tested with sailfish 0.6.3. - +Currently tested with sailfish 0.10.1 Automated Installation ====================== @@ -20,7 +19,8 @@ Version Changes -------- ---------------------------------------------------------------------- v0.6.3.0 - First release - +-------- ---------------------------------------------------------------------- +v0.10.1 - Second release ======== ====================================================================== |
| b |
| diff -r 03c74355227f -r 1b4ed566a41c sailfish.tar.bz2 |
| b |
| Binary file sailfish.tar.bz2 has changed |
| b |
| diff -r 03c74355227f -r 1b4ed566a41c sailfish.xml --- a/sailfish.xml Sun Sep 18 06:05:57 2016 -0400 +++ b/sailfish.xml Wed Nov 02 10:30:36 2016 -0400 |
| [ |
| b'@@ -1,9 +1,5 @@\n-<tool id="sailfish" name="Sailfish" version="0.7.6.1">\n+<tool id="sailfish" name="Sailfish" version="0.10.1">\n <description>transcript quantification from RNA-seq data</description>\n- <requirements>\n- <requirement type="package" version="0.7.6">sailfish</requirement>\n- <requirement type="package" version="1.57.0">boost</requirement>\n- </requirements>\n <macros>\n <xml name="strandedness">\n <param name="strandedness" type="select" label="Specify the strandedness of the reads">\n@@ -13,6 +9,9 @@\n </param>\n </xml>\n </macros>\n+ <requirements>\n+ <requirement type="package" version="0.10.1">sailfish</requirement>\n+ </requirements>\n <stdio>\n <exit_code range="1:" />\n <exit_code range=":-1" />\n@@ -23,7 +22,6 @@\n <version_command>sailfish -version</version_command>\n <command>\n <![CDATA[\n-\n #if $refTranscriptSource.TranscriptSource == "history":\n sailfish index\n --transcripts $refTranscriptSource.ownFile\n@@ -34,35 +32,26 @@\n #else:\n #set $index_path = $refTranscriptSource.index.fields.path\n #end if\n-\n &&\n-\n #if $single_or_paired.single_or_paired_opts == \'single\':\n-\n #if $single_or_paired.input_singles.ext == \'fasta\':\n #set $ext = \'fasta\'\n #else:\n #set $ext = \'fastq\'\n #end if\n-\n ln -s $single_or_paired.input_singles ./single.$ext &&\n #else:\n-\n #if $single_or_paired.input_mate1.ext == \'fasta\':\n #set $ext = \'fasta\'\n #else:\n #set $ext = \'fastq\'\n #end if\n-\n ln -s $single_or_paired.input_mate1 ./mate1.$ext &&\n ln -s $single_or_paired.input_mate2 ./mate2.$ext &&\n #end if\n-\n-\n #if $geneMap:\n ln -s "$geneMap" ./geneMap.$geneMap.ext &&\n #end if\n-\n sailfish quant\n --index $index_path\n #if $single_or_paired.single_or_paired_opts == \'single\':\n@@ -73,34 +62,51 @@\n --mates2 ./mate2.$ext\n --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"\n #end if\n- --output ./\n+ --output ./results\n $biasCorrect\n+ $gcBiasCorrect\n --threads "\\${GALAXY_SLOTS:-4}"\n-\n- #if $fldMean:\n+ $dumpEq\n+ #if str($gcSizeSamp):\n+ --gcSizeSamp $gcSizeSamp\n+ #end if\n+ #if str($gcSpeedSamp):\n+ --gcSpeedSamp $gcSpeedSamp\n+ #end if\n+ #if str($fldMean):\n --fldMean $fldMean\n #end if\n-\n- #if $fldSD:\n+ #if str($fldSD):\n --fldSD $fldSD\n #end if\n-\n #if $maxReadOcc:\n --maxReadOcc $maxReadOcc\n #end if\n-\n #if $geneMap:\n --geneMap ./geneMap.${geneMap.ext}\n #end if\n-\n+ $strictIntersect\n $noEffectiveLengthCorrection\n $useVBOpt\n- $allowOrphans\n-\n+ $discardOrphans\n $unsmoothedFLD\n --maxFragLen ${maxFragLen}\n- --txpAggregationKey "${txpAggregationKey}"\n-\n+ --txpAggregationKey \'${txpAggregationKey}\'\n+ $ignoreLibCompat\n+ $enforceLibCompat\n+ $allowDovetail\n+ #if str($numBiasSamples):\n+ --numBiasSamples $numBiasSamples\n+ #end if\n+ #if str($numFragSamples):\n+ --numFragSamples $numFragSamples\n+ #end if\n+ #if str($numGibbsSamples):\n+ --numGibbsSamples $numGibbsSamples\n+ #end if\n+ #if str($numBootstraps):\n+ --numBootstraps $numBootstraps\n+ #end if\n ]]>\n </command>\n <inputs>\n@@ -118,7 +124,7 @@\n '..b'BiasSamples" type="integer" value="1000000" optional="True"\n+ label="Number of fragment mappings to use when learning the sequene-specific bias model"\n+ help=""/>\n+ <param argument="--numFragSamples" type="integer" value="10000" optional="True"\n+ label="Number of fragments from unique alignments to sample when building the fragment length distribution"\n+ help=""/>\n+ <param argument="--numGibbsSamples" type="integer" value="0" optional="True"\n+ label="Number of Gibbs sampling rounds to perform."\n+ help=""/>\n+ <param argument="--numBootstraps" type="integer" value="0" optional="True"\n+ label="Number of bootstrap samples to generate."\n+ help="This is mutually exclusive with Gibbs"/>\n+ </inputs>\n \n- </inputs>\n+\n <outputs>\n- <data name="output_quant" format="tabular" from_work_dir="quant.sf" label="${tool.name} on ${on_string} (Quantification)" />\n- <data name="output_bias_corrected_quant" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)">\n- <filter>biasCorrect is True</filter>\n- </data>\n- <data name="output_gene_quant" format="tabular" from_work_dir="quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">\n- <filter>geneMap is True</filter>\n+ <data name="output_quant" format="tabular" from_work_dir="results/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />\n+ <data name="output_gene_quant" format="tabular" from_work_dir="results/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">\n+ <filter>geneMap</filter>\n </data>\n </outputs>\n <tests>\n@@ -200,15 +268,33 @@\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="biasCorrect" value="True" />\n+ <param name="biasCorrect" value="False" />\n <param name="TranscriptSource" value="history" />\n <param name="ownFile" value="transcripts.fasta" ftype="fasta" />\n <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />\n- <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_bias_corrected_quant" />\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="biasCorrect" value="True" />\n+ <param name="TranscriptSource" value="history" />\n+ <param name="ownFile" value="transcripts.fasta" ftype="fasta" />\n+ <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" />\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="biasCorrect" value="True" />\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+ <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" />\n+ <output file="sailfish_genMap_result1.tab" ftype="tabular" name="output_gene_quant" />\n </test>\n </tests>\n- <help>\n-<![CDATA[\n+ <help><![CDATA[\n \n **What it does**\n \n@@ -336,6 +422,8 @@\n of the TopHat library types, and so there is no direct mapping for them.\n \n \n-]]>\n- </help>\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1038/nbt.2862</citation>\n+ </citations>\n </tool>\n' |
| b |
| diff -r 03c74355227f -r 1b4ed566a41c test-data/gene_map.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_map.tab Wed Nov 02 10:30:36 2016 -0400 |
| b |
| @@ -0,0 +1,3 @@ +NM_174914 foo +NM_001168316 bar +NR_003084 baz |
| b |
| diff -r 03c74355227f -r 1b4ed566a41c test-data/sailfish_bias_result1.tab --- a/test-data/sailfish_bias_result1.tab Sun Sep 18 06:05:57 2016 -0400 +++ b/test-data/sailfish_bias_result1.tab Wed Nov 02 10:30:36 2016 -0400 |
| [ |
| @@ -1,32 +1,16 @@ -# sailfish (quasi-mapping-based) v0.7.6 -# [ program ] => sailfish -# [ command ] => quant -# [ index ] => { ./index_dir } -# [ mates1 ] => { ./mate1.fastq } -# [ mates2 ] => { ./mate2.fastq } -# [ libType ] => { IU } -# [ output ] => { ./ } -# [ biasCorrect ] => { } -# [ threads ] => { 1 } -# [ fldMean ] => { 200 } -# [ fldSD ] => { 80 } -# [ maxReadOcc ] => { 200 } -# [ maxFragLen ] => { 1000 } -# [ txpAggregationKey ] => { gene_id } -# [ mapping rate ] => { 100% } -# Name Length TPM NumReads -NM_022658 2288 378838 4881 -NM_174914 2385 111257 1500.04 -NM_017410 2396 3099.5 42 -NM_018953 1612 26168.3 228 -NM_001168316 2283 12398.5 159.361 -NM_004503 1681 36198.8 330.806 -NR_003084 1640 0 0 -NM_173860 849 240218 962 -NM_006897 1541 80244.3 664 -NM_153693 2072 6430.57 74.2815 -NR_031764 1853 10254.5 104.595 -NM_014620 2300 45132.7 584.838 -NM_153633 1666 40578.4 367.074 -NM_014212 2037 4852.08 55 -NM_017409 1959 4330.19 47 +Name Length EffectiveLength TPM NumReads +NM_001168316 2283 1528.95 12702.4 158.926 +NM_174914 2385 1599.63 114719 1501.66 +NR_031764 1853 1214.33 10407.1 103.415 +NM_004503 1681 1085.83 37300.1 331.428 +NM_006897 1541 984.724 82401.9 664 +NM_014212 2037 1316.12 5106.81 55 +NM_014620 2300 1541.27 46908.6 591.628 +NM_017409 1959 1273.24 4510.99 47 +NM_017410 2396 1562.29 3285.28 42 +NM_018953 1612 1019.15 27338 227.994 +NM_022658 2288 1634.87 364846 4881 +NM_153633 1666 1082.85 40694.7 360.597 +NM_153693 2072 1374.67 6520.1 73.3448 +NM_173860 849 483.271 243258 962 +NR_003084 1640 1052.77 1.09566 0.00943897 |
| b |
| diff -r 03c74355227f -r 1b4ed566a41c test-data/sailfish_genMap_result1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish_genMap_result1.tab Wed Nov 02 10:30:36 2016 -0400 |
| b |
| @@ -0,0 +1,5 @@ +Name Length EffectiveLength TPM NumReads +baz 1640 1052.77 1.09566 0.00943897 +NR_031764 1853 1214.33 10407.1 103.415 +foo 348.949 235.269 976889 9737.65 +bar 2283 1528.95 12702.4 158.926 |
| b |
| diff -r 03c74355227f -r 1b4ed566a41c test-data/sailfish_quant_result1.tab --- a/test-data/sailfish_quant_result1.tab Sun Sep 18 06:05:57 2016 -0400 +++ b/test-data/sailfish_quant_result1.tab Wed Nov 02 10:30:36 2016 -0400 |
| [ |
| @@ -1,32 +1,16 @@ -# sailfish (quasi-mapping-based) v0.7.6 -# [ program ] => sailfish -# [ command ] => quant -# [ index ] => { ./index_dir } -# [ mates1 ] => { ./mate1.fastq } -# [ mates2 ] => { ./mate2.fastq } -# [ libType ] => { IU } -# [ output ] => { ./ } -# [ biasCorrect ] => { } -# [ threads ] => { 1 } -# [ fldMean ] => { 200 } -# [ fldSD ] => { 80 } -# [ maxReadOcc ] => { 200 } -# [ maxFragLen ] => { 1000 } -# [ txpAggregationKey ] => { gene_id } -# [ mapping rate ] => { 100% } -# Name Length TPM NumReads -NM_001168316 2283 12398.5 159.361 -NM_174914 2385 111257 1500.04 -NR_031764 1853 10254.5 104.595 -NM_004503 1681 36198.8 330.806 -NM_006897 1541 80244.3 664 -NM_014212 2037 4852.08 55 -NM_014620 2300 45132.7 584.838 -NM_017409 1959 4330.19 47 -NM_017410 2396 3099.5 42 -NM_018953 1612 26168.3 228 -NM_022658 2288 378838 4881 -NM_153633 1666 40578.4 367.074 -NM_153693 2072 6430.57 74.2815 -NM_173860 849 240218 962 -NR_003084 1640 0 0 +Name Length EffectiveLength TPM NumReads +NM_001168316 2283 2082.61 12552.5 161.366 +NM_174914 2385 2184.61 111020 1497.1 +NR_031764 1853 1652.61 10345.6 105.535 +NM_004503 1681 1480.61 36162.7 330.503 +NM_006897 1541 1340.61 80240.2 664 +NM_014212 2037 1836.61 4851.45 55 +NM_014620 2300 2099.61 45082 584.273 +NM_017409 1959 1758.61 4329.67 47 +NM_017410 2396 2195.61 3098.99 42 +NM_018953 1612 1411.61 26165.8 227.994 +NM_022658 2288 2087.61 378779 4881 +NM_153633 1666 1465.61 40626.6 367.539 +NM_153693 2072 1871.61 6464.46 74.683 +NM_173860 849 648.611 240280 962 +NR_003084 1640 1439.61 1.04309 0.00926914 |