| Next changeset 1:87983967544b (2017-01-24) |
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Commit message:
planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08 |
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added:
busco.xml test-data/arthropoda/ancestral test-data/arthropoda/clade_parameters test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm test-data/arthropoda/lengths_cutoff test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl test-data/arthropoda/scores_cutoff test-data/busco.loc test-data/genome.fa test-data/genome_results/full_table test-data/genome_results/missing_buscos_list test-data/genome_results/short_summary test-data/proteome.fa test-data/proteome_results/full_table test-data/proteome_results/missing_buscos_list test-data/proteome_results/short_summary test-data/transcriptome.fa test-data/transcriptome_results/full_table test-data/transcriptome_results/missing_buscos_list test-data/transcriptome_results/short_summary tool-data/busco.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 5e3543b1ef9f busco.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/busco.xml Thu Jan 12 15:12:47 2017 -0500 |
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| @@ -0,0 +1,86 @@ +<tool id="busco" name="Busco" version="2.0"> + <description>assess genome assembly and annotation completeness</description> + + <requirements> + <requirement type="package" version="2.0">busco</requirement> + </requirements> + + <command><![CDATA[ + BUSCO.py + --in '${input}' + --lineage '${lineage.fields.path}' + --mode '${mode}' + -o "busco_galaxy" + --cpu \${GALAXY_SLOTS:-4} + --evalue ${adv.evalue} + ${adv.long} + --limit ${adv.limit} + --species ${adv.species} + --tarzip + ]]></command> + + <inputs> + + <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" /> + + <param argument="--mode" type="select" label="Mode"> + <option value="geno">Genome</option> + <option value="tran">Transcriptome</option> + <option value="prot">Proteome</option> + </param> + + <param argument="--lineage" type="select" label="Lineage"> + <options from_data_table="busco"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + + <section name="adv" title="Advanced Options" expanded="False"> + <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/> + <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/> + <param argument="--species" type="text" value="generic" label="Name of existing Augustus species gene finding metaparameters"/> + <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/> + </section> + </inputs> + <outputs> + <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/> + <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy.tsv"/> + <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/> + </outputs> + <tests> + <test> + <param name="input" value="genome.fa"/> + <param name="lineage" value="arthropoda_2.0"/> + <param name="mode" value="geno"/> + <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/> + <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/> + <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/> + </test> + <test> + <param name="input" value="proteome.fa"/> + <param name="lineage" value="arthropoda_2.0"/> + <param name="mode" value="prot"/> + <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/> + <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/> + <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/> + </test> + <test> + <param name="input" value="transcriptome.fa"/> + <param name="lineage" value="arthropoda_2.0"/> + <param name="mode" value="tran"/> + <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/> + <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/> + <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/> + </test> + </tests> + <help> + BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs + + .. _BUSCO: http://busco.ezlab.org/ + </help> + + <citations> + <citation type="doi">doi:10.1093/bioinformatics/btv351</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 5e3543b1ef9f test-data/arthropoda/ancestral --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/ancestral Thu Jan 12 15:12:47 2017 -0500 |
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| @@ -0,0 +1,20 @@ +>BUSCOaEOG7B0HST +MAADQAQFQQLLVSLLSTDNEVRKQAEEAYNNLPVESKVTFLLGAIANGQLSEEVRQLAA +VLLRRLFSSEFLEFYKKLPAEAQAQLKEQILLAVQQEVSEQLRRKVCEVVAEVARNLIDE +DGNNQWPEFLQFLFQCANSPSPQLKESALRIFTSVPGIFGNQEAQYLDLIKQMLAKSLED +TEDAEVRLQAVRAVGAFILLHDKEKEIQKHFADLLPALLQVVAESIEKQDDDALLKVLID +LAEATPKFLRPQLETILELCLKVLSEEDVEDSWRHLALEVLVTLAETAPAMVRKRAEKYI +VALVPLVLKMMTDLEEDEDWSVADEITEDDNDSNNVVAESALDRLACGLGGKVVLPLVVE +AIPAMLSSSDWKKRHAALMAISAIGEGCHKQMEALLDQVLDGVLKYLQDPHPRVRYAACN +AIGQMSTDFAPIFEKKFHDKVIPGLLLLLDDEANPRVQAHAGAALVNFSEDCPKNILTRY +LDAIMAKLEAILTSKFKELVEKGTKLVLEQVVTTIASVADTAEEEFVAYYDRLMPCLKYI +IQNANSEELKLLRGKTIECVSLIGLAVGREKFIADASEVMDLLLKTHTEGAELPDDDPQT +SYLISAWARICKILGKQFEQYLPLVMGPVLRTASLKPEVALLDNEDLEDIEGDVDWQFVS +LGEQQNFGIRTAGLEDKASACEMLVCYARELKEGFAEYAEEVVRLMVPLLKFYFHDGVRT +AAAESLPYLLDCAKIKGPQYLEGMWAYICPELLKAIDTEPEKEVLSELLSSLAKCIETLG +AGCLSEEALKELLRILDKLLKEHFERAEKRLEKRKDEDYDEVVEEELAEEDDEDVYILSK +VADILHALFATYKEAFLPAFDQVVPHFVKLLEPERPLADRQWALCVFDDVIEFGGPACVK +YQEIFLRALLQYVSDKSAEVRQAAAYGCGVLGQFGGEQFAEACAEALPKLVEVINDPESR +ELENINATENAISAVTKILKYNKSAITNVDELLAVWLSWLPVVEDEEEAAHVYGYLCDLI +EANHPVVLGANNANLPRIVSILAEAFLREVVEAESAVAKRLLSIVKQIESNEELLQACIS +ELSAEQQQALKEALRELAA |
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| diff -r 000000000000 -r 5e3543b1ef9f test-data/arthropoda/clade_parameters --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/clade_parameters Thu Jan 12 15:12:47 2017 -0500 |
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| @@ -0,0 +1,6 @@ +#ARTHROPODA Clade parameters for BUSCOS +Z 102785 +sp1 fly +sp2 nasonia +sp3 generic +flank 5000 |
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| diff -r 000000000000 -r 5e3543b1ef9f test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm Thu Jan 12 15:12:47 2017 -0500 |
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| b'@@ -0,0 +1,3319 @@\n+HMMER3/f [3.1b1 | May 2013]\n+NAME BUSCOaEOG7B0HST\n+LENG 1099\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Apr 15 12:38:52 2014\n+NSEQ 23\n+EFFN 0.603638\n+CKSUM 3500044453\n+STATS LOCAL MSV -12.8285 0.69537\n+STATS LOCAL VITERBI -13.9416 0.69537\n+STATS LOCAL FORWARD -6.9634 0.69537\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.48078 4.06146 2.86181 2.63028 3.29447 3.05836 3.78580 2.74928 2.73520 2.31160 3.52187 3.11102 3.40692 3.07770 2.99944 2.73817 2.93658 2.56860 4.67180 3.56430\n+ 2.68613 4.42194 2.77509 2.73133 3.46348 2.40518 3.72504 3.29351 2.67743 2.69350 4.24642 2.90347 2.73745 3.18156 2.89802 2.37884 2.77522 2.98518 4.58487 3.61513\n+ 0.08969 2.57172 4.66890 1.68962 0.20406 0.00000 *\n+ 1 2.57261 4.35167 3.86119 3.40692 3.39776 3.63900 4.23782 2.41302 3.22676 2.05613 1.62924 3.68308 4.13489 3.59563 3.47552 3.02060 2.87665 2.31461 5.12383 3.92328 24 m - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 2 1.67850 4.50203 3.03694 2.37498 3.89784 3.30262 3.77719 3.19331 2.62660 2.92462 3.55380 3.06800 3.81401 2.99279 3.01679 2.53568 2.82599 2.89438 5.25006 3.96735 25 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 3 1.72593 4.51596 3.03450 2.62358 3.94870 3.02850 3.77178 3.31742 2.58759 2.83773 3.85577 3.06024 3.80166 2.49425 2.96418 2.62424 2.82773 2.99569 5.27761 3.99238 26 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 4 3.06989 5.20867 0.81737 2.38286 4.59580 3.26742 3.99737 4.20098 3.09568 3.79622 4.77615 2.94287 3.92548 3.23679 3.62179 3.02404 3.41012 3.83236 5.74996 4.45674 27 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 5 2.80194 4.77013 3.14922 2.71763 3.71311 3.52519 3.75923 3.19152 2.43092 2.26797 3.77243 3.16939 3.97062 1.69754 2.73211 2.88896 3.05024 3.01368 5.15367 3.80747 28 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 6 1.96528 5.02402 2.30355 2.05596 4.32542 3.05196 3.65086 3.77327 2.51296 3.33530 4.14888 2.71539 3.78621 2.65549 3.01420 2.66175 2.94409 3.40418 5.54285 4.15135 29 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 7 2.80616 5.09448 2.63904 2.23927 4.35587 3.37371 3.36290 3.83921 2.30093 3.36613 4.20407 2.73502 3.85607 1.67'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03105 3.88362 4.60597 0.61958 0.77255 0.54401 0.86849\n+ 1092 2.48411 4.80914 2.38269 2.16541 4.06714 3.19545 3.59049 3.47448 2.36289 3.08014 3.58530 2.86918 3.76448 2.73883 2.86648 2.59333 2.81189 2.86703 5.31779 3.97005 1199 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03105 3.88362 4.60597 0.61958 0.77255 0.54401 0.86849\n+ 1093 1.24199 4.14570 3.59318 3.27579 3.90565 3.06922 4.23995 2.85564 3.22241 2.82059 3.86698 3.41584 3.78036 3.55807 3.49165 2.52495 2.75938 2.36754 5.42950 4.19313 1200 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.06474 3.88362 3.16732 0.61958 0.77255 0.54401 0.86849\n+ 1094 2.97106 4.49154 3.93866 3.46547 2.54041 3.89976 3.77718 2.63214 3.27427 1.57888 3.33399 3.70082 4.26271 3.58207 3.49841 3.23908 3.21105 2.56656 4.22346 1.92820 1201 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03209 3.85097 4.57331 0.61958 0.77255 0.57161 0.83152\n+ 1095 2.60101 4.65512 3.08558 2.56003 3.93846 3.38076 3.35844 3.37716 2.29364 2.98880 3.84025 3.01919 3.81697 2.81258 2.11081 2.23871 2.85240 2.88090 5.19817 3.90318 1202 r - - -\n+ 2.68618 4.42210 2.77520 2.73124 3.46354 2.40513 3.72495 3.29354 2.67741 2.69355 4.24690 2.90347 2.73740 3.18147 2.89801 2.37883 2.77520 2.98519 4.58477 3.61504\n+ 0.08263 2.67392 4.57331 0.47744 0.96856 0.57161 0.83152\n+ 1096 2.18154 4.62997 2.75539 1.99629 4.09189 3.21947 3.71130 3.44588 2.55475 3.11415 3.95949 2.91659 3.75436 2.89454 2.98369 2.45299 2.43810 3.09910 5.37976 4.06153 1204 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03209 3.85097 4.57331 0.61958 0.77255 0.52453 0.89608\n+ 1097 2.46358 4.30538 3.37350 2.85594 3.45882 3.46342 3.46832 2.79047 2.73797 1.87351 3.43484 3.24873 3.57204 3.10968 3.06502 2.75631 2.66774 2.52856 4.91799 3.66813 1205 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.06381 3.88362 3.18837 0.61958 0.77255 0.54401 0.86849\n+ 1098 1.76981 4.22446 3.25481 2.84716 3.91324 3.07102 3.91525 3.24756 2.83205 2.73784 3.84439 3.15656 3.31202 3.16923 3.18419 1.97191 2.69401 2.87700 5.28803 4.03807 1206 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.17726 3.85187 1.95758 0.61958 0.77255 0.57087 0.83249\n+ 1099 2.12671 4.27681 2.94823 2.62386 4.02260 3.00213 3.81075 3.41128 2.69615 3.08313 3.92445 2.61229 3.24401 3.03239 3.07499 2.18871 2.34694 2.99753 5.34368 4.07427 1207 a - - -\n+ 2.68560 4.42236 2.77531 2.73135 3.46365 2.40517 3.72506 3.29361 2.67747 2.69366 4.24701 2.90355 2.73729 3.18150 2.89812 2.37889 2.77501 2.98510 4.58488 3.61514\n+ 0.29451 1.36610 * 1.25311 0.33633 0.00000 *\n+//\n' |
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| diff -r 000000000000 -r 5e3543b1ef9f test-data/arthropoda/lengths_cutoff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/lengths_cutoff Thu Jan 12 15:12:47 2017 -0500 |
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| @@ -0,0 +1,1 @@ +BUSCOaEOG7B0HST 1099 16.763712248907 1099.28947368421 |
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| diff -r 000000000000 -r 5e3543b1ef9f test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl Thu Jan 12 15:12:47 2017 -0500 |
| [ |
| b'@@ -0,0 +1,1179 @@\n+[name]\n+unknown\n+\n+[dist]\n+# distance from previous block\n+# <min> <max>\n+2\t136\n+\n+[block]\n+# block no. 0 follows, 38 sequences, length 19\n+# corresponding to MSA columns:\n+# 159-177\n+name=unknown_A\n+#\n+# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n+#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n+0\t0.00849\t0.00611\t0.00840\t0.00857\t0.00923\t0.00669\t0.00611\t0.00985\t0.00961\t0.01343\t0.01902\t0.11988\t0.02008\t0.26734\t0.45119\t0.00764\t0.01148\t0.00842\t0.00363\t0.00479\n+1\t0.04698\t0.19994\t0.01897\t0.01402\t0.05388\t0.40529\t0.01057\t0.01996\t0.01473\t0.02840\t0.01285\t0.12269\t0.01254\t0.00774\t0.00537\t0.00165\t0.00826\t0.00573\t0.00343\t0.00702\n+2\t0.10059\t0.05592\t0.04037\t0.12369\t0.03571\t0.33917\t0.01177\t0.05040\t0.04291\t0.12639\t0.01235\t0.01357\t0.00924\t0.00633\t0.00543\t0.00172\t0.00824\t0.00453\t0.00392\t0.00774\n+3\t0.00726\t0.00551\t0.00670\t0.00765\t0.00853\t0.00495\t0.00526\t0.00846\t0.01222\t0.01564\t0.04202\t0.55279\t0.26594\t0.01769\t0.00750\t0.00231\t0.00335\t0.01570\t0.00558\t0.00495\n+4\t0.01515\t0.01282\t0.01932\t0.01411\t0.01942\t0.01141\t0.20122\t0.08029\t0.06461\t0.07934\t0.01338\t0.01496\t0.01020\t0.00535\t0.00554\t0.00143\t0.00624\t0.00509\t0.00412\t0.41602\n+5\t0.01058\t0.00786\t0.01056\t0.13305\t0.01554\t0.00789\t0.00807\t0.01432\t0.07133\t0.05518\t0.29599\t0.18162\t0.03460\t0.01123\t0.00661\t0.00194\t0.00427\t0.02125\t0.02469\t0.08341\n+6\t0.05178\t0.16631\t0.50028\t0.01491\t0.02246\t0.01521\t0.03686\t0.01844\t0.01252\t0.01860\t0.01027\t0.01208\t0.00775\t0.00547\t0.00520\t0.00170\t0.00786\t0.00415\t0.00271\t0.08546\n+7\t0.01705\t0.01432\t0.01620\t0.01348\t0.01711\t0.07518\t0.07737\t0.22677\t0.26217\t0.05482\t0.04993\t0.11213\t0.01834\t0.00888\t0.00635\t0.00197\t0.00608\t0.00758\t0.00556\t0.00869\n+8\t0.01317\t0.01251\t0.02070\t0.15609\t0.52474\t0.01281\t0.01616\t0.01652\t0.01342\t0.01844\t0.01838\t0.02129\t0.11604\t0.00690\t0.00613\t0.00186\t0.00670\t0.00642\t0.00330\t0.00841\n+9\t0.01162\t0.00686\t0.00910\t0.00862\t0.01050\t0.00629\t0.00674\t0.01414\t0.01595\t0.14470\t0.42875\t0.11434\t0.07208\t0.01284\t0.00715\t0.00207\t0.00368\t0.11180\t0.00647\t0.00632\n+10\t0.01274\t0.01372\t0.12068\t0.01259\t0.01636\t0.01187\t0.04762\t0.04955\t0.31522\t0.02196\t0.05626\t0.13802\t0.02193\t0.00996\t0.00649\t0.00206\t0.00548\t0.07423\t0.00517\t0.05810\n+11\t0.00985\t0.00796\t0.01067\t0.01037\t0.01075\t0.00947\t0.00786\t0.01102\t0.01014\t0.01418\t0.01964\t0.14789\t0.02183\t0.26045\t0.10775\t0.00446\t0.21652\t0.11018\t0.00389\t0.00511\n+12\t0.00789\t0.00529\t0.00678\t0.00798\t0.00848\t0.00499\t0.00539\t0.00919\t0.01168\t0.01638\t0.03120\t0.67455\t0.03627\t0.01714\t0.00718\t0.00229\t0.00339\t0.01544\t0.12352\t0.00499\n+13\t0.00773\t0.00552\t0.00742\t0.00873\t0.00928\t0.00522\t0.00618\t0.00911\t0.01211\t0.01615\t0.06621\t0.64670\t0.03983\t0.01822\t0.00774\t0.00246\t0.00376\t0.11699\t0.00563\t0.00502\n+14\t0.23475\t0.01397\t0.01501\t0.05417\t0.12272\t0.06638\t0.01071\t0.11816\t0.17197\t0.11209\t0.01510\t0.01554\t0.01116\t0.00661\t0.00538\t0.00187\t0.00596\t0.00510\t0.00478\t0.00858\n+15\t0.01774\t0.01310\t0.01239\t0.01066\t0.01380\t0.13284\t0.00829\t0.12299\t0.12073\t0.17836\t0.04824\t0.03777\t0.12169\t0.04898\t0.00726\t0.00202\t0.00564\t0.00710\t0.08255\t0.00785\n+16\t0.00774\t0.00594\t0.00698\t0.00734\t0.00855\t0.00550\t0.00526\t0.00913\t0.01231\t0.01568\t0.07962\t0.21341\t0.34318\t0.13048\t0.08206\t0.00342\t0.00490\t0.04842\t0.00514\t0.00491\n+17\t0.01499\t0.01157\t0.01661\t0.08113\t0.01840\t0.01286\t0.11905\t0.12120\t0.08357\t0.07287\t0.05034\t0.01918\t0.01402\t0.00762\t0.00806\t0.00193\t0.13253\t0.00612\t0.20034\t0.00760\n+18\t0.02074\t0.06499\t0.01691\t0.01445\t0.01751\t0.60356\t0.01097\t0.07075\t0.01705\t0.01634\t0.01185\t0.08393\t0.01094\t0.00741\t0.00560\t0.00164\t0.00964\t0.00519\t0.00351\t0.00704\n+\n+[dist]\n+# distance from previous block\n+# <min> <max>\n+0\t1\n+\n+[block]\n+# block no. 1 follows, 38 sequences, length 22\n+# corresponding to MSA columns:\n+# 179-200\n+name=unknown_B\n+#\n+# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n+#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n+0\t0.08270\t0.19710\t0.02137\t0.01349\t0.01801\t0.06215\t0.13254\t0.04863\t0.19656\t0.08108\t0.01574\t0.01622\t0.02523\t0.00640\t0.00542\t0.00172\t0.00649\t0.00534\t0.00432\t0.05948\n+1\t0.01139\t0.00879\t0.01512\t0.01313\t0.01560\t0.00826\t0.17794\t0.01415\t0.01395\t0.08259\t0.12369\t0.26603\t0.03144\t0.01318\t0.00747\t0.00230\t0.00560\t0.17772\t0.0'..b'01399\t0.02763\t0.59409\t0.01622\t0.02410\t0.01459\t0.01966\t0.15312\t0.01578\t0.02277\t0.03493\t0.01405\t0.00968\t0.00621\t0.00582\t0.00189\t0.00827\t0.00483\t0.00333\t0.00904\n+17\t0.01558\t0.61804\t0.05875\t0.01338\t0.01885\t0.02182\t0.14636\t0.01829\t0.01261\t0.01530\t0.00917\t0.01100\t0.00798\t0.00515\t0.00454\t0.00145\t0.00722\t0.00399\t0.00266\t0.00784\n+18\t0.03107\t0.12435\t0.21748\t0.02929\t0.04145\t0.01280\t0.01239\t0.04101\t0.05280\t0.01971\t0.03883\t0.03793\t0.01160\t0.00601\t0.00512\t0.00147\t0.00610\t0.00477\t0.00351\t0.30232\n+19\t0.01371\t0.36393\t0.29683\t0.15693\t0.02425\t0.01821\t0.01591\t0.01790\t0.01236\t0.01619\t0.00970\t0.01198\t0.00774\t0.00552\t0.00495\t0.00165\t0.00764\t0.00407\t0.00258\t0.00796\n+20\t0.16658\t0.02744\t0.61619\t0.01540\t0.02332\t0.01388\t0.01926\t0.01879\t0.01224\t0.02055\t0.01034\t0.01215\t0.00741\t0.00569\t0.00534\t0.00190\t0.00809\t0.00422\t0.00276\t0.00844\n+21\t0.02417\t0.01022\t0.01334\t0.01041\t0.01471\t0.00913\t0.00853\t0.08055\t0.01774\t0.60573\t0.05239\t0.02435\t0.08388\t0.00832\t0.00618\t0.00187\t0.00496\t0.00679\t0.00713\t0.00960\n+22\t0.01677\t0.01205\t0.08140\t0.01031\t0.01522\t0.00893\t0.00905\t0.02045\t0.05274\t0.25615\t0.06649\t0.04544\t0.01557\t0.00678\t0.00547\t0.00148\t0.00495\t0.00560\t0.00513\t0.36003\n+23\t0.16683\t0.01180\t0.01496\t0.01290\t0.01423\t0.01516\t0.01064\t0.01467\t0.00977\t0.01725\t0.00928\t0.01378\t0.00863\t0.01340\t0.10939\t0.00321\t0.46410\t0.00488\t0.00300\t0.08213\n+\n+[dist]\n+# distance from previous block\n+# <min> <max>\n+7\t16\n+\n+[block]\n+# block no. 22 follows, 38 sequences, length 6\n+# corresponding to MSA columns:\n+# 1247-1252\n+name=unknown_W\n+#\n+# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n+#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n+0\t0.00733\t0.00524\t0.00698\t0.00838\t0.00873\t0.00489\t0.00558\t0.00838\t0.01152\t0.01536\t0.03316\t0.78466\t0.03979\t0.01885\t0.00768\t0.00244\t0.00349\t0.01710\t0.00558\t0.00489\n+1\t0.01041\t0.00709\t0.00808\t0.00738\t0.00993\t0.00599\t0.00575\t0.01235\t0.01441\t0.11123\t0.12398\t0.04824\t0.47386\t0.01304\t0.00680\t0.00193\t0.00356\t0.05072\t0.00575\t0.07949\n+2\t0.01430\t0.02608\t0.54722\t0.01765\t0.02555\t0.01352\t0.13402\t0.02039\t0.01351\t0.11246\t0.01266\t0.01425\t0.00878\t0.00583\t0.00598\t0.00192\t0.00861\t0.00507\t0.00324\t0.00894\n+3\t0.26692\t0.01203\t0.01543\t0.01222\t0.01656\t0.01225\t0.10707\t0.07068\t0.07963\t0.29248\t0.01726\t0.01826\t0.01233\t0.00696\t0.00558\t0.00193\t0.00575\t0.03264\t0.00543\t0.00857\n+4\t0.19703\t0.02395\t0.01536\t0.01387\t0.01690\t0.55243\t0.01062\t0.02202\t0.01505\t0.01736\t0.00901\t0.01077\t0.00749\t0.00635\t0.00600\t0.00169\t0.06019\t0.00383\t0.00320\t0.00685\n+5\t0.01450\t0.01539\t0.01823\t0.01575\t0.01620\t0.12585\t0.01294\t0.01585\t0.01034\t0.01451\t0.00810\t0.01283\t0.00788\t0.00991\t0.01768\t0.00248\t0.66716\t0.00506\t0.00270\t0.00664\n+\n+[dist]\n+# distance from previous block\n+# <min> <max>\n+0\t1\n+\n+[block]\n+# block no. 23 follows, 38 sequences, length 6\n+# corresponding to MSA columns:\n+# 1254-1259\n+name=unknown_X\n+#\n+# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n+#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n+0\t0.01343\t0.01028\t0.01283\t0.00977\t0.01415\t0.00866\t0.03490\t0.04640\t0.05049\t0.08028\t0.16725\t0.02064\t0.01996\t0.00666\t0.00539\t0.00132\t0.00449\t0.00567\t0.00472\t0.48271\n+1\t0.04265\t0.10015\t0.01305\t0.00922\t0.01226\t0.00970\t0.00754\t0.01866\t0.03805\t0.26240\t0.27072\t0.05409\t0.09335\t0.00992\t0.00664\t0.00187\t0.02797\t0.00820\t0.00606\t0.00751\n+2\t0.00774\t0.00584\t0.00715\t0.00741\t0.00866\t0.00525\t0.00533\t0.00963\t0.01433\t0.01908\t0.32409\t0.28450\t0.24864\t0.01522\t0.00729\t0.00211\t0.00311\t0.01338\t0.00600\t0.00525\n+3\t0.01099\t0.00669\t0.00941\t0.09845\t0.01363\t0.00652\t0.00742\t0.01259\t0.01250\t0.13528\t0.02900\t0.57076\t0.03203\t0.01550\t0.00722\t0.00230\t0.00428\t0.01393\t0.00554\t0.00596\n+4\t0.69880\t0.01184\t0.00961\t0.00861\t0.01228\t0.01373\t0.00700\t0.02000\t0.12855\t0.02669\t0.01099\t0.01183\t0.00844\t0.00600\t0.00411\t0.00189\t0.00467\t0.00383\t0.00411\t0.00700\n+5\t0.01499\t0.01161\t0.03484\t0.10038\t0.03814\t0.03077\t0.00958\t0.01979\t0.11229\t0.14220\t0.06861\t0.04057\t0.01539\t0.00673\t0.00552\t0.00153\t0.00526\t0.00563\t0.00467\t0.33149\n+\n+[dist]\n+# distance from previous block\n+# <min> <max>\n+12\t79\n+\n+# created by:\n+# /software/SequenceAnalysis/GenePrediction/augustus/3.0.1/scripts/msa2prfl.pl ./aligns/BUSCOaEOG7B0HST.fas\n' |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/arthropoda/scores_cutoff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/scores_cutoff Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +BUSCOaEOG7B0HST 996.48 |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/busco.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busco.loc Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +arthropoda_2.0 arthropoda_2.0 Arthropoda (v2) ${__HERE__}/arthropoda/ |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/genome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fa Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,14 @@ +>sample +TGCATCGGTTATTTGCATTGGCTGGCATTTAATTTATGCACAAACACACACGCTGGAACACATTAGTCATACGCAACGTTGCACAAATATTTATTAGCTATTGCAAGTCAGTGCGGGGCAAATAGCACCGTGAAATGCAAACGAAAGCATTGAGTGTGCTGGCATCATCGATTTAGCAGCCATAAATACTGCTCAACACTAAATCAATCATACGCAATGTGGTGCTAATTGATTGAGCAAACATTGCCAAGATGCAATTGCCATGATCAAGG +GGCGAAGGTTTCTTTGGGCCAAACAGAAGAGTGGTTTCGCCACTTAACTAGAGGTTAATTATTAGATTGTATTAGCCAGCTAGCTGCGTACGAGCATATTGAGCTACTAATGATACCACAAGTTCGCAGTTATCGCCCCAGTGGAACCCTTGAGCTTAATCCCAGTGCCCCATTAAATACTTAAGCGCGGACCCTCCAGCGCTACTCCACTCGAGCGGTTCAACGAACTGGCCAGCACTCGAAACTAAAGCCCTACCATGATTCAATATCAA +GTTGGCAACTCGAAACCCACTTGGCATTAAGTATGACTGACCTGCAGGCGACTCAACCTCAACCTGAAGCTCAACCTGAAGCTCAACCGGCGCATTCAGCTCCAGCGTTTTGCATTTAGCATTCAGCCGTGTCCAATGCTAAGATCAATGCCACTCCACGCTGGCTGTGCCAACTTCCTGTTGCAGCAACCACTACTACCCTATATGGACACAATGTGCCACGCCACGAGTATAGTGTATCGTACCTACACGAGTATCTGGCCAGTCCGCAG +TCCTAGTTCTTCCCTGCTCCTTTTTATTTAAACACTTCCTCATTTCGCTTTGTGCCCTGGCATTTGGCAGCTATTCTGTGTCAATTCCCGGTGAGTGTCATTCGAACTGGTGAACCGGAGAATGGAGCAGTCGCCAGCCGAGGATTCAGAGCCAGAACCCCAAACCCAGAACCCAGAAGGCCAGGTGAATGGGATCGGGATTCACCCAGTCCTCGCTCGCCTGGCTGAGTGCCAAGTGTAGTGCAATAAACTTGCCGTCCTGAATGGCTGGC +AATCAAAGATCTGAATGCAAGATACGATGACATTTACTCGCACATTCAATTGCGCTTTTGATTTGAATATTTACATGCTTTCTGGTCGTAGTCCCAGTTCCGCAGACTCGAGTCCCTCGGGCTGCCATTCTTTCATGTCCTTTCGTTCTATTGACATAGTCAAATTGGCTTTGCTGCACAGCGAGAAAATGTACTTAACTTCCACACAATCCTGGCTATTTGCTGCTATGACTGTAAGCATAATTTATTTTAGGGTAAATGGGTGAGTGACC +AAAAGGCATGCCGTGCAGTTCATTTTATCAAAGCACCATGACTAACTGGTACAACCATTTTTTCTGCGTGCCTTTCGGGTCAACCGAATCAGGCCCTAATTGATTTTCAAATGTTTCCACAGCGTCTTAAAGTCCAGTCCTTATTTAAACAACTTACTAAGTATTGCAGAGCCTTGGCATACTTAGCTGCAGTTATGCATTTCAAGCATAAACAACTAATTTGACTAATTGATAAGCCATGCAAAGGCAAAGGCATCTCGAGATGTCTTGAG +TCGACTTCACTGCACTTCTGGCCGGCTTGTCTCGGCCTGGTTGGTTGCGTTTCTGTATCTTTGGCTCCGGCTGTTTGCTTTGTCCATCAACATCTTTTGAGCGGAGGCACTCAGGCGCAAACTGTTGCACTTCAGACCAGTCTGGAGAGCAGTGTTCACTAGGATACGAGTATATACATAGGCTCATGTGGAGCCGGGATCAAGCCACCCCAAACCCCAAACCCCATTAATTGCAATCAATTTCGCTGTCAACACACACTCCAAATAACTGC +GGGATATTTATTTATGGGCTGCGCTTCCCTTCAGCAACCTTTTGCAACTGAATAATTGCCTTATGACACATTATCATTATTATTAAGGCTGCCACGGGTCGGCAAAGTAATCATTACCTCCTGCCCATATCATCCTGCCCCTGGGCCATGAACCTGGGAATTAGGGAGTCAGCATTGCAGTGCCCACAGCTCCTCTATGCTCATAAATATATTTCCAGCTGGCAACATTATATAATTATTTTGCCATGGATTGCATTGAACTTAGTCCGAGT +GCGTCGATGTTGCTCGTTTGCTGTTTGCTGTTTGCTATTTCTGTTTGCACTTCTTGCCGCAGGCGCGCAACTCTTCATGTGGCTTCTTCTCGTTTTTAGGCCAGAATCCAGAAGGCAGCGTTCAGAACCCAGAATCCAGAATCCATGTGATGCCTTTGCGTGAATTTCATTTTAAAGTGCAAATATTTGCGGCCTGGCCCGGCCAGTTGCTTAAATGGAAAACTGGGCGAGAAAAAAGAATGCACTGGTAGCTCACAAACAGCCCACACAGA +AACCAGTAATGAAATTGTGCGGCACTCGTCATTGCGGCACTGGCCTTACATATAAATTATATAAAATATATACACATTTGTTTGGCATTGACCGGCCTACAAAGGAACTGCAGCCAGGGATGCAGCATGGGTATGATTTCCCTATAGTCGTGGCAAATACCTTTAACACGAGTAAGTACAAGTAATGCCCAACTGAGGGCCTTCAAGTAATATTAAGAGAAGATATTTTTAAACATCTATCTTTTTTAAGGACACACATTCTAACTTTATTT +ACGAGAGACACTGGCACCCTCATACAAAATTCTAGAAAGCTAGTCAGTAAACTAGAACTGCAGTTCTCCCCTGCTTATGACAATAACAGCAATTTGTATTTAAATTTAGGAATGACCAGGGCTCTTCCGCTCCACCCTGGCCAGTATAATTTGTGCATCTCTAGCCAATACAAACTTATTATATACTTGCAAAAGTTGTGCACTGTAAATATTTGCGGCGACCACCCGCACTTTCGCCATGACTACAAAATGGGTGGCATGAAATGGGGGCT +TTTGGGGGGCAACCGCAGAGAATGCTTGACTTTGGCCGGTAAAAAACTACGCAGACCACCCACCACCCAACCCGGTTTTTCTCTCTTGGCCACGTTTATTGATGGCGGCGGGAAGTGCTTTAATGGAAATTTAAGTATCATCGTTTAAAATGAAGCAGAAAAGCGCAAGCGAACGAAAGACCCTGGAAAATTGCGAGTTGCGACTGGTATTGCGACCCTTGAGCTTTGGTCATTGCGTTGGCAACGCAAATTATTATTTTTATTATTATTGC +AGGTTTTCGGTGCACATTTATTTCATGCAACTTTACAGCGCTGCACATAGAAATTATGTACAGGCCGCGTGGGCCATAATGCAGATTGCCAACCCGAGAAGGGTAACTCGGAGTGAAATGGCGGGAATTAGGCAAGCAAACAGGCAACTAAAATATGCAACGCAGGCAGTGGGGAAATTTGATGGGCGCCAGAAAAGGCCGTGAAAAGGCCGTAAAACTGGGCCAAGTAATGAGCTACGGCGGCCACACATTAAATATGCAACAATTAAAAG |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/genome_results/full_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results/full_table Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +# BUSCO version is: 2.0 +# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# To reproduce this run: python /tmp/tmpeQaU9k/job_working_directory/000/2/conda-env/bin/BUSCO.py -i /tmp/tmpeQaU9k/files/000/dataset_1.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m genome -c 1 -sp generic -e 0.01 -z +# +# Busco id Status Contig Start End Score Length +BUSCOaEOG7B0HST Missing |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/genome_results/missing_buscos_list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results/missing_buscos_list Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,5 @@ +# BUSCO version is: 2.0 +# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# To reproduce this run: python /tmp/tmpeQaU9k/job_working_directory/000/2/conda-env/bin/BUSCO.py -i /tmp/tmpeQaU9k/files/000/dataset_1.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m genome -c 1 -sp generic -e 0.01 -z +# +BUSCOaEOG7B0HST |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/genome_results/short_summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results/short_summary Thu Jan 12 15:12:47 2017 -0500 |
| [ |
| @@ -0,0 +1,15 @@ +# BUSCO version is: 2.0 +# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# To reproduce this run: python /tmp/tmpeQaU9k/job_working_directory/000/2/conda-env/bin/BUSCO.py -i /tmp/tmpeQaU9k/files/000/dataset_1.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m genome -c 1 -sp generic -e 0.01 -z +# +# Summarized benchmarking in BUSCO notation for file /tmp/tmpeQaU9k/files/000/dataset_1.dat +# BUSCO was run in mode: genome + + C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:1 + + 0 Complete BUSCOs (C) + 0 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 0 Fragmented BUSCOs (F) + 1 Missing BUSCOs (M) + 1 Total BUSCO groups searched |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/proteome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteome.fa Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,16 @@ +>BUSCOaEOG7B0HST +MAADQAQFQQLLVSLLSTDNEVRKQAEEAYNNLPVESKVTFLLGAIANGQLSEEVRQLAA +VLLRRLFSSEFLEFYKKLPAEAQAQLKEQILLAVQQEVSEQLRRKVCEVVAEVARNLIDE +DGNNQWPEFLQFLFQCANSPSPQLKESALRIFTSVPGIFGNQEAQYLDLIKQMLAKSLED +TEDAEVRLQAVRAVGAFILLHDKEKEIQKHFADLLPALLQVVAESIEKQDDDALLKVLID +LAEATPKFLRPQLETILELCLKVLSEEDVEDSWRHLALEVLVTLAETAPAMVRKRAEKYI +VALVPLVLKMMTDLEEDEDWSVADEITEDDNDSNNVVAESALDRLACGLGGKVVLPLVVE +AIPAMLSSSDWKKRHAALMAISAIGEGCHKQMEALLDQVLDGVLKYLQDPHPRVRYAACN +AIGQMSTDFAPIFEKKFHDKVIPGLLLLLDDEANPRVQAHAGAALVNFSEDCPKNILTRY +LDAIMAKLEAILTSKFKELVEKGTKLVLEQVVTTIASVADTAEEEFVAYYDRLMPCLKYI +IQNANSEELKLLRGKTIECVSLIGLAVGREKFIADASEVMDLLLKTHTEGAELPDDDPQT +SYLISAWARICKILGKQFEQYLPLVMGPVLRTASLKPEVALLDNEDLEDIEGDVDWQFVS +LGEQQNFGIRTAGLEDKASACEMLVCYARELKEGFAEYAEEVVRLMVPLLKFYFHDGVRT +AAAESLPYLLDCAKIKGPQYLEGMWAYICPELLKAIDTEPEKEVLSELLSSLAKCIETLG +AGCLSEEALKELLRILDKLLKEHFERAEKRLEKRKDEDYDEVVEEELAEEDDEDVYILSK +VADILHALFATYKEAFLPAFDQVVPHFVKLLEPERPLADRQWALCVFDDVIEFGGPACVK |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/proteome_results/full_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteome_results/full_table Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +# BUSCO version is: 2.0 +# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/4/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_5.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m proteins -c 1 -sp generic -e 0.01 -z +# +# Busco id Status Sequence Score Length +BUSCOaEOG7B0HST Fragmented BUSCOaEOG7B0HST 1877.5 899 |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/proteome_results/missing_buscos_list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteome_results/missing_buscos_list Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,4 @@ +# BUSCO version is: 2.0 +# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/4/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_5.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m proteins -c 1 -sp generic -e 0.01 -z +# |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/proteome_results/short_summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteome_results/short_summary Thu Jan 12 15:12:47 2017 -0500 |
| [ |
| @@ -0,0 +1,15 @@ +# BUSCO version is: 2.0 +# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/4/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_5.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m proteins -c 1 -sp generic -e 0.01 -z +# +# Summarized benchmarking in BUSCO notation for file /tmp/tmpCgx5rU/files/000/dataset_5.dat +# BUSCO was run in mode: proteins + + C:0.0%[S:0.0%,D:0.0%],F:100.0%,M:0.0%,n:1 + + 0 Complete BUSCOs (C) + 0 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 1 Fragmented BUSCOs (F) + 0 Missing BUSCOs (M) + 1 Total BUSCO groups searched |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/transcriptome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptome.fa Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,46 @@ +>BUSCOaEOG7B0HST +atggcggcggatcaggcgcagtttcagcagctgctggtgagcctgctgagcaccgataac +gaagtgcgcaaacaggcggaagaagcgtataacaacctgccggtggaaagcaaagtgacc +tttctgctgggcgcgattgcgaacggccagctgagcgaagaagtgcgccagctggcggcg +gtgctgctgcgccgcctgtttagcagcgaatttctggaattttataaaaaactgccggcg +gaagcgcaggcgcagctgaaagaacagattctgctggcggtgcagcaggaagtgagcgaa +cagctgcgccgcaaagtgtgcgaagtggtggcggaagtggcgcgcaacctgattgatgaa +gatggcaacaaccagtggccggaatttctgcagtttctgtttcagtgcgcgaacagcccg +agcccgcagctgaaagaaagcgcgctgcgcatttttaccagcgtgccgggcatttttggc +aaccaggaagcgcagtatctggatctgattaaacagatgctggcgaaaagcctggaagat +accgaagatgcggaagtgcgcctgcaggcggtgcgcgcggtgggcgcgtttattctgctg +catgataaagaaaaagaaattcagaaacattttgcggatctgctgccggcgctgctgcag +gtggtggcggaaagcattgaaaaacaggatgatgatgcgctgctgaaagtgctgattgat +ctggcggaagcgaccccgaaatttctgcgcccgcagctggaaaccattctggaactgtgc +ctgaaagtgctgagcgaagaagatgtggaagatagctggcgccatctggcgctggaagtg +ctggtgaccctggcggaaaccgcgccggcgatggtgcgcaaacgcgcggaaaaatatatt +gtggcgctggtgccgctggtgctgaaaatgatgaccgatctggaagaagatgaagattgg +agcgtggcggatgaaattaccgaagatgataacgatagcaacaacgtggtggcggaaagc +gcgctggatcgcctggcgtgcggcctgggcggcaaagtggtgctgccgctggtggtggaa +gcgattccggcgatgctgagcagcagcgattggaaaaaacgccatgcggcgctgatggcg +attagcgcgattggcgaaggctgccataaacagatggaagcgctgctggatcaggtgctg +gatggcgtgctgaaatatctgcaggatccgcatccgcgcgtgcgctatgcggcgtgcaac +gcgattggccagatgagcaccgattttgcgccgatttttgaaaaaaaatttcatgataaa +gtgattccgggcctgctgctgctgctggatgatgaagcgaacccgcgcgtgcaggcgcat +gcgggcgcggcgctggtgaactttagcgaagattgcccgaaaaacattctgacccgctat +ctggatgcgattatggcgaaactggaagcgattctgaccagcaaatttaaagaactggtg +gaaaaaggcaccaaactggtgctggaacaggtggtgaccaccattgcgagcgtggcggat +accgcggaagaagaatttgtggcgtattatgatcgcctgatgccgtgcctgaaatatatt +attcagaacgcgaacagcgaagaactgaaactgctgcgcggcaaaaccattgaatgcgtg +agcctgattggcctggcggtgggccgcgaaaaatttattgcggatgcgagcgaagtgatg +gatctgctgctgaaaacccataccgaaggcgcggaactgccggatgatgatccgcagacc +agctatctgattagcgcgtgggcgcgcatttgcaaaattctgggcaaacagtttgaacag +tatctgccgctggtgatgggcccggtgctgcgcaccgcgagcctgaaaccggaagtggcg +ctgctggataacgaagatctggaagatattgaaggcgatgtggattggcagtttgtgagc +ctgggcgaacagcagaactttggcattcgcaccgcgggcctggaagataaagcgagcgcg +tgcgaaatgctggtgtgctatgcgcgcgaactgaaagaaggctttgcggaatatgcggaa +gaagtggtgcgcctgatggtgccgctgctgaaattttattttcatgatggcgtgcgcacc +gcggcggcggaaagcctgccgtatctgctggattgcgcgaaaattaaaggcccgcagtat +ctggaaggcatgtgggcgtatatttgcccggaactgctgaaagcgattgataccgaaccg +gaaaaagaagtgctgagcgaactgctgagcagcctggcgaaatgcattgaaaccctgggc +gcgggctgcctgagcgaagaagcgctgaaagaactgctgcgcattctggataaactgctg +aaagaacattttgaacgcgcggaaaaacgcctggaaaaacgcaaagatgaagattatgat +gaagtggtggaagaagaactggcggaagaagatgatgaagatgtgtatattctgagcaaa +gtggcggatattctgcatgcgctgtttgcgacctataaagaagcgtttctgccggcgttt +gatcaggtggtgccgcattttgtgaaactgctggaaccggaacgcccgctggcggatcgc +cagtgggcgctgtgcgtgtttgatgatgtgattgaatttggcggcccggcgtgcgtgaaa |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/transcriptome_results/full_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptome_results/full_table Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +# BUSCO version is: 2.0 +# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/6/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_9.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m tran -c 1 -sp generic -e 0.01 -z +# +# Busco id Status Sequence Score Length +BUSCOaEOG7B0HST Missing |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/transcriptome_results/missing_buscos_list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptome_results/missing_buscos_list Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,5 @@ +# BUSCO version is: 2.0 +# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/6/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_9.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m tran -c 1 -sp generic -e 0.01 -z +# +BUSCOaEOG7B0HST |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f test-data/transcriptome_results/short_summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptome_results/short_summary Thu Jan 12 15:12:47 2017 -0500 |
| [ |
| @@ -0,0 +1,15 @@ +# BUSCO version is: 2.0 +# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/6/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_9.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m tran -c 1 -sp generic -e 0.01 -z +# +# Summarized benchmarking in BUSCO notation for file /tmp/tmpCgx5rU/files/000/dataset_9.dat +# BUSCO was run in mode: tran + + C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:1 + + 0 Complete BUSCOs (C) + 0 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 0 Fragmented BUSCOs (F) + 1 Missing BUSCOs (M) + 1 Total BUSCO groups searched |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f tool-data/busco.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/busco.loc.sample Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,13 @@ +# This is a sample file distributed with Galaxy that is used to define a +# list of busco datasets, using four columns tab separated: +# +# <unique_build_id> <dbkey> <display_name> <genome_fasta_file_path> +# +# Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html +# +# "/some/path/arthropoda/" would be the last column in the line +# If this were for the mm10 mouse genome, the resulting entry would look like: +# +#arthropoda_2.0 arthropoda_2.0 Arthropoda (v2) /some/path/arthropoda/ +# +# |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="busco" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/busco.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 5e3543b1ef9f tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Jan 12 15:12:47 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="busco" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/busco.loc" /> + </table> +</tables> |