# HG changeset patch # User iuc # Date 1430275601 14400 # Node ID 048f294031c78bcbdcb3176702d71a000c5d2b78 # Parent 361d2cb38860b709bd2cdd1c41154d6d0d86eb76 Uploaded diff -r 361d2cb38860 -r 048f294031c7 pear.xml --- a/pear.xml Wed Feb 25 22:42:34 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,160 +0,0 @@ - - Paired-End read merger - - - pear - - - - - - - - - 0: - --max-asm-length $max_assembly_length - #end if - --min-asm-length $min_assembly_length - --min-trim-length $min_trim_length - --quality-theshold $quality_threshold - --max-uncalled-base $max_uncalled_base - --test-method $test_method - --empirical-freqs $empirical_freqs - -j "\${GALAXY_SLOTS:-8}" - --score-method $score_method - --cap $cap - $nbase -]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'assembled' in outputs - - - 'forward' in outputs - - - 'reverse' in outputs - - - 'discarded' in outputs - - - - - - - - - - - - - - - - - - - 10.1093/bioinformatics/btt593 - - diff -r 361d2cb38860 -r 048f294031c7 test-data/forward.fastq --- a/test-data/forward.fastq Wed Feb 25 22:42:34 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -@EU861894-140/1 -CAACCATTCCACTCGCCTCTGCCGCACTCGAGGCCCCCAGTATGAGAGGCAGTTACGAGGTTGAACCTCAGAATCTCACCCCACACTTAAGGGCGCGCCT -+ -@#CAAF4FHFG;DIJJI?JG#GIIIDECD#4H*1IBIIIH#?IDID*DFIIF?C#HGBJICJBC#JEGEA>ECH#=7#DDF@##D#D<@C#CC@#C?D@, -@EU861894-138/1 -TCCGAGGTTGAGCCTCAGAATTTCACCCCCCACTTAACGGCCCGACTCCGCGCTCCTTACGCCCAGTAAGTTCGGACAACGCTGGCCCCCTACGTACTAC -+ -@CCFFFBFFDHFHJJJ+#C@B9DEFDD@ED#EDBD> -@EU861894-134/1 -TTGTGCAAGAGTCCTAATTGCTGCCCCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATCCGGCTGTTCGTCCCCTCAGACCATGTACCCGTAGATGCC -+ -=CCFDFFFA?#BHIJJJCIJJJJD;EEJB#@2GFIE#>A;C@FCA@##BD>AD=D#D?##A, -@EU861894-132/1 -CGGAACACCCATGGCGAAGGCAGCTCGCTGGCCTGCAACTGACCCTGAGGCGCAAAAGCCGGGGGATCAAACAGGTTTATATACCCTGGTAGTCCCGAGC -+ -CCC4FFDFFFHH#AIJDEDBC#H;#E8A(?>##D -@EU861894-130/1 -TCGTCACTAACCGAAGAACCTTACCAGGGTTTGACATCCCCGGCCAGCACGAGAGATCGGGTGGTGCCCGCAAGGGGACCGGGTGACAGGTGTTGACTAG -+ -:B@FDFDFHCA@:CDFDEDAA#DDF:-D, -@EU861894-126/1 -GGAATGGTCGGTGTAGCGGTGAAATGCGTAGATATCGATCGGAACACCCATGGCTAAGGTAGCTTGCTGGCGTGCAACAGACGCTCAGGCGCAAAAGCCG -+ -BC?#FF=FBFHHHFGIGEIJ@IJJIFI@HJI9IJ;GHBGIIJGHDC<>#9E7@CG#D(BHED#=;CD:;#>C#C?B, -@EU861894-124/1 -CTGTGCCGCAGCTAACCCAAAAAGTATTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAACGGAATTGACGGGGAACCGCACAAGCGGTGGACCAT -+ -CCCFFFFD,GBBD@8D>:BDD<###, -@EU861894-120/1 -CTGTCACCCGGTCCGCTTGCGGGGAACACCCGATCTCTCGCGCTGTCCGGGGATGTCAAACCCTGGTAATGTTCTTCCGTTAGTGACGAATTAATGCAGA -+ -@C@FAFFFAHHHFA#JJ#J:IJ?H:HJJH9IJ#9I?IG:J#*IEBIC;I?AEJDIJJHHCICCHDJJ;C##C2EF?B#C>?DD6(B+#(D@E:DCDCC#, -@EU861894-118/1 -CGAGCGCAACCCTGACCCAATGTTGGCAGCGTAAAGTCGGCAACTCTTTGGGAACTGCCCGTGGAAGCGGGAGGAAGGTGGGGATGACGTCAAATAGGCA -+ -@?;FF?EFFHHHH#HEAIGJ@J1JIJIJJGDGIF7GGH=J#JGIJJ#:GFJID#FJJ#JID4?#DBDJHEFID;EA5EDD;C?CCDCBDA>:CB>#DD#C -@EU861894-116/1 -GAGGCAGTTCCGAGGTTGAGCCTCAGAATTTCACCCCCCACTTAAGGGCCCGCCTACGCCCTATTTACGCCCATTAAATTCGGACAACGCTGGCCGCCTA -+ -C@@FFFD2GHHFFICFAGJJI3JJIIII8II#<*JJH#JJIID(EGEGJ;GE@D7IJHF#B;#C?H@GH;FCI#DD@DE6CCDCDDC<#ACD4 -@EU861894-114/1 -TTACTAGGGATTCCGGCTTCATGCAGGCGAGTTGCAGCCTGCAATCCGAACTGAGACCATATTTGTGCGATTGGCTCCTCTACGCGGCATAGCGTCGCGC -+ -@C:FFDD#BHHAAIJ(GIFGIJGHBHDI9ICHGE7JHEJI4IJBBIDIAHJIBCBFIF#J=BDFFDD8HCHJ8E:@@C#D##BA@DD5=E#A5B#D#B#F diff -r 361d2cb38860 -r 048f294031c7 test-data/pear_assembled_results1.fastq --- a/test-data/pear_assembled_results1.fastq Wed Feb 25 22:42:34 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -@EU861894-140/1 -CAACCATTCCACTCGCCTCTGCCGCACTCGAGGCCCCCAGTATGAGAGGCAGTTACGAGGTTGAGCCTCAGAATTTCTCCCCCCACTTAAGGGCCCGCCTACTCGCTCTTTACGACCAGTAAAATCGGTCAAAGCTCACCCCCTACGTATTACCGC -+ -@#CAAF4FHFG;DIJJI?JG#GIIIDECD#4H*1IBIIIH#?IDID*DFIIF?C#HjZmKE^ed@LEiedWfekA=7#iFmcD=W%Qc\g7ekeDjf_bU)G#EE=?'>:EHDG#CIHHJIH!#J:BI#JJH#IEGGGGCGJJH@*GJ;J#JJJD;EEiaAd4dFIG%ad^fciCdc6=ej_d^dlClbDAAT#7J#C>#J#F!#JDIBI(GGIIJCJHEH:JJ#IHJF=HJJHG+HIJI)kD_hQICPaCfaC`ERFfg@mAfjmeddfFPIIGI#HIG#HCI??JDIHIJBAG?F3?JJAJ*JJ!FG:?DD1HFDADF@@= -@EU861894-126/1 -GGAATGGTCGGTGTAGCGGTGAAATGCGTAGATATCGATCGGAACACCCATGGCGAAGGCAGCTCGCTGGCCTGCAACTGACGCTGAGGCGCAAAAGCCGGGGGACCAACCAGGATTAGATACTCTGGTAGTCCCGGCCGTAAACGATGAATA -+ -BC?#FF=FBFHHHFGIGEIJ@IJJIFI@HJI9IJ;GHBGIIJGE;g7adIEkLfk_gFbbC][aDfeDlYkQHFGG'(HG?#@F2JGIIEDCJG>!J3EFGEJ3EGJGJHAJHDHF?:CADF8C@ -@EU861894-124/1 -CTGTGCCGCAGCTAACCCAAAAAGTATTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATCTGCATTAATTCGTTACTAACCTAAGAACCTTAGCAGGGTTTGACATCCCCG -+ -CCCFFFFD,GBdlclfkD`kAiiCD5hZS##HGBGJFFI6HFG#IJF:JHI#FIEJFG2#HI#HJ:GL#NJJG#E@#<:J2JJCAIJEFHHJA2CH!422FF@@+ -@EU861894-120/1 -CTGTCACCCGGTCCGCTTGCGGGGAACACCCGATCTCTCGCGCTGTCCGGGGATGTCAAACCCTGGTAATTTTCTTCGGTTAGTGACGAATTAATGCACATGCTCCTCCCCTTGTGCGGGCCGCCGTCAATTCCTTTGAGTTTCAACCTTGCG -+ -@C@FAFFFAHHHFA#JJ#J:IJ?H:HJJH9IJ#9I?IG:J#*IEBIC;I?AEJJIJljHCkbbf[L^[C##jUYide=i_dheYBcSI(id^BdCll`CE7H=JGA!9G*#>E#HGC@4IF:#DEJCI#GJBAJJEJJGB4J;AJH#EF)#??BHHHHH;F=F=CC8 diff -r 361d2cb38860 -r 048f294031c7 test-data/pear_unassembled_forward_results1.fastq diff -r 361d2cb38860 -r 048f294031c7 test-data/reverse.fastq --- a/test-data/reverse.fastq Wed Feb 25 22:42:34 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -@EU861894-140/2 -GCGGTAATACGTAGGGGGTGAGCTTTGACCGATTTTACTGGTCGTAAAGAGCGAGTAGGCGGGCCCTTAAGTGGGGGGAATAATTCTGACGCTCAACCTC -+ -;BCFDF#FHHFH)GJJHI##E'?=EE#G)JCB;A#C#E@###9CD#C<##@C -@EU861894-136/2 -TACCGCATGTGGATGTGCTCTGCCCTCAGAGCTTATCCAAAGCCTTCGGGCGCTTCGGGATGGGCACGCGGTCTACCAGCTATTTGGGTGGGTAACGTCC -+ -1B@FDFF:HHHA#AHGGGEG?@J<#J;JG*@HJJGCGGGGE>IFFDJJJCC#GCBHAFEJGIDEG#J;DBG#EDC)#C(GFD#C#@2?#D8CCD53D#AA -@EU861894-134/2 -GCCTTCGGGCACTTCGGGATGGGCCCGCGGCCTTTCAGCTAGTTGGGAGGGTACTGTCACATCAAGACTTCGACGGGTAGCTGCTCTGAGGGTTCGATCA -+ -@@+?+;FDDAHCHCIJFC#J7#I#?DDICIH;DBGD=6DD#DDDDDD####>#EA@@ -@EU861894-132/2 -GCGGCACAGGGGGGGTCGCTACCCCCAGCACCTAGTATTCATCGTTTACGGCCGGGAATACCAGCGTACCTAGTCCTGTTTGCTCCCCCGTCTTTTGCGC -+ -@1@DF=F)HH2H;JGJF3!FF+EIHH+#JC#BEHJ?JGBGFE8HDIFJJF?@GH#@B#B;ECEJ#C:I#D@C#C#A=DC#DDB!5FB+##AD' -@EU861894-130/2 -CAACATTGGGTGAGGGTTGCGCTTGTTGCATGACTTAACCCAACATCTCACGATAGTAGCTGACGACAACTGTGCAACCCCTGTCGACCGGTCCCCTTGC -+ -1@:DFDFDAH#+DGGG:EGFHI;+JJ::H##IF9CAI?IJ#I#D?GJDJBHF)#H##J@GJBADEGH;JC(!=3ACE>#DDE)C#AC -@EU861894-128/2 -CAAGGCCCCCAGTATGGGAGGCAGTTCCGAGGTTGAGCCTCAGAATCTCACCCCCCACTTCAGGGCCCGCCTTCGGTCTCATAACGCCCAGTAACTTCGG -+ -=@@FDADFH1DD?:GF!JJ*JAJJ?3F?GABJIHIDJ??ICH#GIH#IGIIE#I@BJIGD#J@IF#8E=C>D#A6##:ED#D')BBC@;&F?#80D;@@C -@EU861894-126/2 -TATTCATCGTTTACGGCCGGGACTACCAGAGTATCTAATCCTGGTTGGTCCCCCGGCTTTTGCGGCTCAGCGTCAGTTTCAGACCACCGAGCCGCCTTCG -+ -@C8FDAC:?FHDHJAHJGJGE3JEGFE3J!>GJCDEIIGJ2F@#?GH('GGFHFJ;JBCIBGB:#HFFD;DEEHE#BB#C#E#D>#!>A>#D#C##?DD' -@EU861894-124/2 -CGGGGATGTCAAACCCTGCTAAGGTTCTTAGGTTAGTAACGAATTAATGCAGATGCGTCACCGTTTGTGCGGGCCCCCGTTAATTCCTCAGCGTTTCTAC -+ -=C@F#DDDHGHAHB<:JH#IH#2GFJEIF#IHJ:FJI#GFH6IFFJGBGH##H9G5##JF#F;!HGJEGB#ADHH#ECA>(CAFD##D##@6CC5@?##' -@EU861894-122/2 -GTCCGAAGATACTGGGCGTAAAGAGCGCGTACGCGGCCCCTTAAGTGGAGGGTGAAATTCTGAGGCTCAACCTCGGAACTGCCACACATACTGTGGGCTT -+ -+@@FF224!HC2AJHHFEJIACJJ2J:<#@E#GJJC!JG#II)JIIF:#EIBII;JHC.HHFI@DGFDF/D@#D>EAF#C=HF#D##BC77:D#C?D:#A -@EU861894-120/2 -CGCAAGGTTGAAACTCAAAGGAATTGACGGCGGCCCGCACAAGGGGAGGAGCATGTGCGTTAATCCGTCACTAACCGAAGAAAGGTACCAGGGGATGGGA -+ -B1BFFDDBHHHHHB#*G9!AGJ=H7:C>JI#A):EF#GIB;DBEFBG=DFD5DH#!#A5#8?@@C##CC##' -@EU861894-118/2 -CCAGTGTAGCATGTGTGAAGCCCAGGGCGTAAGGGCCATGCCGATTTGACCTCCTCCCCATCTTCCTCCCGTTTACATGGGCACTTCCCAAAGAGTCGCC -+ -@CC++DD?ABHFHA+G#I#J3D2IJGJJCJHJHEJIJGJ4IJII#I?(EA!GH#CGG8E##5JHEHCD@BE#=@H@##CDBC:&DCD>D>?#C:C###C@ -@EU861894-116/2 -AATGACCGTACCACACGAAAAAGCCCTGGATAACTACGTGCCAGCAGCCGCGATAATACGTAGGGGGCCAACGTTGTCCTAAGTGTCTGGGCGTATAAAG -+ -BBCFFD#BFHHH:G#JE@F#J+JJJ@#CJ#HIIGGF#GIGEF=HJ?ECFJBE!BDIGE#EEI=>BHHC@D#G#=A#CFA#DECD##CDBD>#CC?#@#@D -@EU861894-114/2 -CCCTTACGCCCTGGGCCTGATACATGCTACAATGGCCGTTAATCAGAGCTACGCGATGCTACGAGGCGGAGCCAATCGCACAAGTAGGGTCACAGTTCGG -+ -8CC=F=F;HHHHHB??#)FE#HJA;J4BG>BI;@#JFI):GJ#D? - - - - - diff -r 361d2cb38860 -r 048f294031c7 tool_test_output.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_test_output.html Tue Apr 28 22:46:41 2015 -0400 @@ -0,0 +1,356 @@ + + + + + + + Tool Test Results (powered by Planemo) + + + + + + + + + + + + + + +
+
+
+ + +
+
+ +

Overview

+
+
+
+

Tests

+

The remainder of this contains a description for each test executed to run these jobs.

+
+
+
+ + + + + + + diff -r 361d2cb38860 -r 048f294031c7 tool_test_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_test_output.json Tue Apr 28 22:46:41 2015 -0400 @@ -0,0 +1,1 @@ +{"tests": [{"data": {"status": "success", "inputs": {"reverse": {"src": "hda", "id": "5729865256bc2525"}, "min_overlap": "10", "outputs": ["assembled", "forward"], "cap": "0", "forward": {"src": "hda", "id": "2891970512fa2d5a"}, "min_assembly_length": "50"}, "job": {"inputs": {"forward": {"src": "hda", "id": "2891970512fa2d5a"}, "reverse": {"src": "hda", "id": "5729865256bc2525"}}, "update_time": "2015-02-11T12:50:31.576393", "tool_id": "iuc_pear", "outputs": {"unassembled_forward_reads": {"src": "hda", "id": "8155e4b4bf1581ff"}, "assembled_reads": {"src": "hda", "id": "54f2a3a23292eb07"}}, "stdout": " ____ _____ _ ____ \n| _ \\| ____| / \\ | _ \\\n| |_) | _| / _ \\ | |_) |\n| __/| |___ / ___ \\| _ <\n|_| |_____/_/ \\_\\_| \\_\\\n\nPEAR v0.9.6 [January 15, 2015]\n\nCitation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR\nZhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593\n\nForward reads file.................: /tmp/tmpSuVRNdfiles/000/dataset_1.dat\nReverse reads file.................: /tmp/tmpSuVRNdfiles/000/dataset_2.dat\nPHRED..............................: 33\nUsing empirical frequencies........: NO\nStatistical method.................: OES\nMaximum assembly length............: 999999\nMinimum assembly length............: 50\np-value............................: 0.010000\nQuality score threshold (trimming).: 0\nMinimum read size after trimming...: 1\nMaximal ratio of uncalled bases....: 1.000000\nMinimum overlap....................: 10\nScoring method.....................: Scaled score\nThreads............................: 1\n\nAllocating memory..................: 200,000,000 bytes\nAssemblying reads: 0%\rAssemblying reads: 100%\n\nAssembled reads ...................: 14 / 14 (100.000%)\nDiscarded reads ...................: 0 / 14 (0.000%)\nNot assembled reads ...............: 0 / 14 (0.000%)\nAssembled reads file...............: pear.assembled.fastq\nDiscarded reads file...............: pear.discarded.fastq\nUnassembled forward reads file.....: pear.unassembled.forward.fastq\nUnassembled reverse reads file.....: pear.unassembled.reverse.fastq\n", "command_line": "pear -f /tmp/tmpSuVRNdfiles/000/dataset_1.dat -r /tmp/tmpSuVRNdfiles/000/dataset_2.dat --output pear --p-value 0.01 --min-overlap 10 --min-asm-length 50 --min-trim-length 1 --quality-theshold 0 --max-uncalled-base 1.0 --test-method 1 --empirical-freqs -j \"${GALAXY_SLOTS:-8}\" --score-method 2 --cap 0", "exit_code": 0, "state": "ok", "create_time": "2015-02-11T12:50:27.868953", "params": {"max_uncalled_base": "\"1.0\"", "min_assembly_length": "\"50\"", "quality_threshold": "\"0\"", "empirical_freqs": "\"False\"", "nbase": "\"False\"", "outputs": "[\"assembled\", \"forward\"]", "cap": "\"0\"", "max_assembly_length": "\"0\"", "dbkey": "\"hg17\"", "min_overlap": "\"10\"", "score_method": "\"2\"", "test_method": "\"1\"", "min_trim_length": "\"1\"", "chromInfo": "\"/home/bag/projects/code/galaxy-central-1/tool-data/shared/ucsc/chrom/hg17.len\"", "pvalue": "\"0.01\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "6761", "id": "54f2a3a23292eb07", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_iuc_pear.test_tool_000000", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 0, "num_tests": 1}} \ No newline at end of file