| Previous changeset 1:1e881a00d8ff (2017-09-26) Next changeset 3:b49e453e6f97 (2017-10-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5 |
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modified:
crossmap_bed.xml macros.xml test-data/test_bam_01_output_a.bam |
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added:
test-data/cached_locally/aToB.over.chain test-data/cached_locally/liftOver.loc test-data/test_bed_01_output_a__only_fails.bed test-data/test_bed_02_output_a__only_fails.bed tool_data_table_conf.xml.test |
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removed:
test-data/test_bam_01_output_a.unmap.bam |
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| diff -r 1e881a00d8ff -r 79f9e32b380b crossmap_bed.xml --- a/crossmap_bed.xml Tue Sep 26 06:05:09 2017 -0400 +++ b/crossmap_bed.xml Fri Oct 20 02:48:24 2017 -0400 |
| [ |
| b'@@ -7,84 +7,96 @@\n <expand macro="stdio"/>\n <expand macro="version_command"/>\n \n- <command><![CDATA[\n- #set $input_file = str($seq_source.input)\n-\n- CrossMap.py bed\n- \'${chain_source.input_chain}\'\n+<!--\n+1. CrossMap bed x.chain in.bed > out.bed\n+stdout/out.bed: valid and invalid combined\n \n- \'${input_file}\'\n+2. CrossMap bed x.chain in.bed out.bed\n+out.bed: valid only\n+out.bed.unmap: invalid only\n+-->\n+ <command><![CDATA[\n+CrossMap.py bed\n+\'${chain_source.input_chain}\'\n \n- #if str($include_fails) == "True"\n- >\n- #end if\n+\'${input}\'\n \n- \'${output}\'\n+#if $merge_unmapped_entries:\n+ > \'${output_combined}\'\n+#else:\n+ \'${output_valid}\'\n+ && mv \'${output_valid}.unmap\' \'${output_failed}\'\n+#end if\n+\n ]]></command>\n \n \n <inputs>\n- <conditional name="seq_source">\n- <expand macro="source" />\n+ <param name="input" type="data" format="bed" label="BED file"\n+ help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>\n \n- <when value="cached">\n- <param format="bed" name="input" type="data" label="BED file"\n- help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.">\n- <validator type="unspecified_build"/>\n- <!-- Gives error in tests\n- <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>\n- -->\n- </param>\n- </when>\n- <when value="history">\n- <param type="data" format="bed" name="input" label="BED file"\n- help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns."/>\n- </when>\n- </conditional>\n <expand macro="chain" />\n \n- <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers"\n- help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked \'fail\')"/>\n+ <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>\n </inputs>\n \n <outputs>\n- <data format="bed" name="output" label="${tool.name} on ${on_string}" />\n- <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}" />\n+ <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}">\n+ <filter>merge_unmapped_entries is False</filter>\n+ </data>\n+ <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}">\n+ <filter>merge_unmapped_entries is False</filter>\n+ </data>\n+\n+ <data name="output_combined" format="bed" label="${tool.name} on ${on_string}">\n+ <filter>merge_unmapped_entries is True</filter>\n+ </data>\n </outputs>\n \n <tests>\n- <!-- BED -->\n- <test>\n+ <test><!-- this test only contains perfect entries that do get liftOvered (separate output) -->\n+ <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>\n <param name="index_source" value="history"/>\n- <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>\n <param name="input_chain" value="aToB.over.chain" ftype="csv"/>\n- <param name="include_fails" value="False"/>\n+ <param name="merge_unmapped_entries" value="false" />\n \n- <output name="output" file="test_bed_01_output_a__only-matches.bed"/>\n+ <output name="output_valid" file="test_bed_01_output_a__only-match'..b' <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>\n+ <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>\n </test>\n </tests>\n <help><![CDATA[\n@@ -96,36 +108,35 @@\n BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.\n BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1\n \n- A BED (Browser Extensible Data) file is a tab-delimited text file\n- describing genome regions or gene annotations. It is the standard file\n- format used by UCSC. It consists of one line per feature, each containing\n- 3-12 columns. CrossMap converts BED files with less than 12 columns to a\n- different assembly by updating the chromosome and genome coordinates only;\n- all other columns remain unchanged. Regions from old assembly mapping to\n- multiple locations to the new assembly will be split. For 12-columns BED\n- files, all columns will be updated accordingly except the 4th column (name\n- of bed line), 5th column (score value) and 9th column (RGB value describing\n- the display color). 12-column BED files usually define multiple blocks (eg.\n- exon); if any of the exons fails to map to a new assembly, the whole BED\n- line is skipped.\n+A BED (Browser Extensible Data) file is a tab-delimited text file\n+describing genome regions or gene annotations. It is the standard file\n+format used by UCSC. It consists of one line per feature, each containing\n+3-12 columns. CrossMap converts BED files with less than 12 columns to a\n+different assembly by updating the chromosome and genome coordinates only;\n+all other columns remain unchanged. Regions from old assembly mapping to\n+multiple locations to the new assembly will be split. For 12-columns BED\n+files, all columns will be updated accordingly except the 4th column (name\n+of bed line), 5th column (score value) and 9th column (RGB value describing\n+the display color). 12-column BED files usually define multiple blocks (eg.\n+exon); if any of the exons fails to map to a new assembly, the whole BED\n+line is skipped.\n \n- NOTE:\n+Notes:\n \n- 1. For BED-like formats mentioned above, CrossMap only updates \xe2\x80\x9cchrom (1st\n- column)\xe2\x80\x9d, \xe2\x80\x9cstart (2nd column) \xe2\x80\x9d, \xe2\x80\x9cend (3rd column) \xe2\x80\x9d and \xe2\x80\x9cstrand\xe2\x80\x9d (if\n- any). All other columns will keep AS-IS.\n- 2. Lines starting with \xe2\x80\x98#\xe2\x80\x99, \xe2\x80\x98browser\xe2\x80\x99, \xe2\x80\x98track\xe2\x80\x99 will be skipped.\n- 3. Lines will less than 3 columns will be skipped.\n- 4. 2nd-column and 3-column must be integer, otherwise skipped.\n- 5. \xe2\x80\x9c+\xe2\x80\x9d strand is assumed if no strand information was found.\n- 6. For standard BED format (12 columns). If any of the defined exon blocks\n- cannot be uniquely mapped to target assembly, the whole entry will be\n- skipped.\n- 7. If input region cannot be consecutively mapped target assembly, it will be split.\n- 8. *.unmap file contains regions that cannot be unambiguously converted.\n+1. For BED-like formats mentioned above, CrossMap only updates \xe2\x80\x9cchrom (1st\n+ column)\xe2\x80\x9d, \xe2\x80\x9cstart (2nd column) \xe2\x80\x9d, \xe2\x80\x9cend (3rd column) \xe2\x80\x9d and \xe2\x80\x9cstrand\xe2\x80\x9d (if\n+ any). All other columns will keep AS-IS.\n+2. Lines starting with \xe2\x80\x98#\xe2\x80\x99, \xe2\x80\x98browser\xe2\x80\x99, \xe2\x80\x98track\xe2\x80\x99 will be skipped.\n+3. Lines will less than 3 columns will be skipped.\n+4. 2nd-column and 3-column must be integer, otherwise skipped.\n+5. \xe2\x80\x9c+\xe2\x80\x9d strand is assumed if no strand information was found.\n+6. For standard BED format (12 columns). If any of the defined exon blocks\n+ cannot be uniquely mapped to target assembly, the whole entry will be\n+ skipped.\n+7. If input region cannot be consecutively mapped target assembly, it will be split.\n+8. \\*.unmap file contains regions that cannot be unambiguously converted.\n \n-Please see `the manual <http://crossmap.sourceforge.net/#convert-bed-format-files>`__ for more details.\n-]]></help>\n+ ]]></help>\n \n <citations>\n <citation type="doi">10.1093/bioinformatics/btt730</citation>\n' |
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| diff -r 1e881a00d8ff -r 79f9e32b380b macros.xml --- a/macros.xml Tue Sep 26 06:05:09 2017 -0400 +++ b/macros.xml Fri Oct 20 02:48:24 2017 -0400 |
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| @@ -2,12 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="324">ucsc-wigtobigwig</requirement> - <requirement type="package" version="0.2.2">crossmap</requirement> + <requirement type="package" version="0.2.5">crossmap</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">0.2.2</token> + <token name="@WRAPPER_VERSION@">0.2.5</token> <xml name="stdio"> <stdio> <regex match="Aborted (core dumped)" source="stdout" level="fatal"/> @@ -16,7 +15,9 @@ </stdio> </xml> <xml name="version_command"> - <version_command>CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> + <version_command><![CDATA[ +CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' + ]]></version_command> </xml> <xml name="chain"> <conditional name="chain_source"> @@ -26,25 +27,18 @@ </param> <when value="cached"> <param name="input_chain" type="select" label="Lift Over To"> - <options from_file="liftOver.loc"> - <column name="dbkey" index="0"/><!-- species/build 'from' --> - <column name="name" index="1"/><!-- species/build 'to' --> - <column name="value" index="2"/><!-- path of chain file --> - <filter type="data_meta" ref="input" key="dbkey"/> + <options from_data_table="liftOver"> + <!-- + <filter type="data_meta" ref="input" key="dbkey" column="0"/> + --> </options> </param> </when> <when value="history"> - <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/> + <param name="input_chain" type="data" format="csv" label="LiftOver chain file"/> </when> </conditional> </xml> - <xml name="source"> - <param name="index_source" type="select" label="Source for Input Data"> - <option value="cached">Local data (in galaxy)</option> - <option value="history">From History</option> - </param> - </xml> <token name="@HELP_GENERAL@"> CrossMap -------- |
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| diff -r 1e881a00d8ff -r 79f9e32b380b test-data/cached_locally/aToB.over.chain --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/aToB.over.chain Fri Oct 20 02:48:24 2017 -0400 |
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| @@ -0,0 +1,498 @@ +chain 21270171362 chr1 249250621 + 10000 249233096 chr1 247249719 + 0 247199719 2 +619 137 0 +166661 50000 50000 +40302 50000 50000 +153649 50000 50000 +1098479 1 1 +47 1 1 +73 117 114 +773 1 1 +43 1 1 +864369 2 2 +51 3 0 +104 13694 13694 +104 0 3 +51 2 2 +134936 50000 50000 +1161048 150000 60000 +1440092 27273 50000 +7590365 50000 50000 +116914 100000 50000 +237250 50000 50000 +3518496 50000 50000 +12702424 150000 50000 +16145012 0 1 +7772 1 0 +4705841 0 1 +52977198 50000 50000 +157344 21065 50000 +16604841 50000 50000 +189539 150000 50000 +398739 21050000 20290000 +195588 50000 50000 +186739 150000 50000 +175055 50000 50000 +201709 100000 50000 +126477 130183 50000 +381 0 3 +315 0 2 +62 1 1 +45 1 0 +19 0 1 +8 1 1 +1158 1 0 +314 12 13 +2849 3 0 +5615 1 1 +37 1 1 +3172 6 4 +190 1 1 +34 1 1 +380 0 1 +2099 3 0 +765 2 2 +366 0 4 +1186 1 0 +460 0 1 +1242 28 28 +574 1 1 +21 1 1 +1460 1 1 +105 1 1 +701 3 0 +239 0 1 +970 11 11 +2365 1 1 +21 1 1 +384 8 8 +996 2 0 +10383 2 0 +713 0 1 +5188 1 1 +30 1 1 +1233 1 0 +132 1 1 +44 1 1 +1123 22 22 +1810 1 0 +512 1 1 +39 1 1 +1096 0 16 +743 1 0 +9028 0 1 +2506 0 6 +8446 2 0 +5505 0 3 +7541 1 0 +109864 50000 50000 +78698 50000 50000 +127263 50000 50000 +170669 50000 50000 +38311 100000 100000 +1022394 50000 50000 +281532 289973 50000 +1648 1539 0 +76 3225 3 +1018 34 34 +1716 2 0 +159 4 0 +1600 0 6 +1385 1 0 +2066 1 1 +32 1 3 +1556908 150000 50000 +185320 150000 50000 +172789 50000 50000 +220313 50000 50000 +455185 50000 50000 +22047237 1 0 +34365824 150000 50000 +259514 150000 50000 +17265625 50000 50000 +11394365 50000 50000 +13665999 150000 50000 +174886 + +chain 22466185064 chr2 243199373 + 10000 243102476 chr2 242951149 + 0 242751149 1 +1201236 0 1 +2057 1 1 +26 1 1 +4043 22 0 +82 7 101 +33 84 0 +26 1 23 +67 48 0 +176 318 0 +40 92 0 +33 0 74 +62 0 6 +22 0 118 +387 2446 0 +843 2450 0 +167 2304 0 +21342 1 1 +50 4 0 +2040 0 4 +9053 2 0 +88 3 53 +1078 0 1 +4122 1 0 +1608 28 1 +4029 0 9 +967 4547 1000 +420 27 0 +2237126 0 1 +2458 17 17 +4595 4 0 +3531 14 14 +3954 51129 50000 +1426129 160449 100025 +11087286 0 3 +773 103977 50000 +1576 0 1 +240 0 1 +318 2 0 +255 0 16 +2851 10 10 +1404 1 1 +27 1 1 +703 13 0 +375 0 1 +4783388 35000 25000 +848 0 2 +1225 0 2 +391 1 0 +3653 1 1 +28 1 1 +49 0 4 +4514 0 9 +9628 1 9 +1483 7 7 +1990 0 1 +1949 1 0 +2716230 1 0 +7799848 851 851 +38932068 5 9 +9477928 0 3 +7529698 72396 0 +1891551 294073 150000 +17672 1 0 +5792 1 0 +9017 0 266 +2944 0 1 +9388 2 0 +37828 4 0 +23436 0 4 +290931 1273578 1000000 +731068 3000000 3000000 +2558421 0 1 +1197 10 0 +685 42 46 +2309 0 1 +1332 22 23 +344 0 1 +1645 4 4 +4093 25 25 +2446 1 0 +6329 1 0 +769 0 1 +873 7 0 +1299 0 1 +8250 15 15 +4291 10626 12548 +1063 103 0 +75 0 218 +5897 1 1 +33 1 1 +9905 51 37 +1711 1 1 +45 1 1 +1597 4 4 +61 1 1 +869 13 0 +1633 15 15 +1179 3 0 +2819 0 2 +156 88 465 +100 0 25 +4753 0 8 +4903 6 6 +3847 0 2 +108126 0 145 +3542 1 0 +10276 0 1 +402 1 1 +47 1 1 +63 2 0 +583 1 1 +34 1 1 +8974 0 46 +379 1 1 +70 1 1 +2474 0 102 +1756 0 1 +8426 0 1 +11986570 151150 142000 +14207 1 1 +49 1 1 +1781 0 12 +409 1 0 +1874 1 1 +33 1 1 +4795 2 0 +3686 1 1 +15 1 1 +164 2 0 +7287 5 5 +702023 72796 150000 +69 1 0 +1598 0 1 +1340 0 1 +1030 0 4 +1166 10 10 +6406 1 1 +34 1 1 +3283 2 4 +496 1 23 +25 10 0 +40 1 1 +21282 2 1 +1406 0 44 +937 17 0 +18255 1 0 +172366 0 281526 +40517 0 406 +58864 1 2 +1843 0 2 +14994 0 1 +12992 2 0 +2571146 1 0 +35688061 108224 100000 +29671719 1 0 +39665349 1 0 +14876089 64197 20000 +401 0 3 +1831 1 1 +61 1 1 +654 11 1 +127 0 28 +116 25 29 +74 9 9 +3247 2 0 +1355 1 0 +816 1 0 +21 3 0 +526 1 1 +60 1 1 +773 1 0 +1494 1 0 +1683 1 0 +21 1 1 +596 1 0 +1582 1 0 +425 0 3 +1139 0 8 +138 144 813 +71 1 0 +385638 1 1 +219 1 1 +51 7 7 +54 15205 15205 +54 7 7 +51 1 1 +110 1 1 +5198249 0 1 +115 80 0 +60 40 0 +80 100 20 +442 1 1 +35 1 1 +119 9 129 +14 0 40 +61 1 1 +85 0 40 +1331 0 1 +1194 12 14 +1773 0 5 +1623 1 1 +25 1 1 +2422 21 22 +2315 0 1 +31 1 1 +1508 0 3 +50 0 4 +970 6 6 +7234 4 0 +1228 1 0 +1233 8 1 +4207 1 1 +41 1 1 +1715 50 50 +1532 0 2 +1714 2 0 +2299 2 0 +2143 1 1 +18 1 1 +917 1 0 +1082 1 1 +49 1 1 +9098 0 4 +5529 0 1 +3266 0 8 +894 6 0 +1440 1 1 +2095 2 0 +4179 18 13 +1785 0 1 +1674 0 6 +1217 32348 33000 +287 17 23 +40 173 0 +20 161 0 +13 66 0 +12 71 1 +12548 30000 30000 +952154 41011 25000 +1914 1 0 +225 1 1 +57 1 1 +2910 0 1 +471 1 0 +1956 1 1 +43 1 1 +991 0 92 +2863 3 0 +1838 306 0 +1006 30 0 +206 1 1 +27 0 3 +221 17 17 +1525 8 0 +413 1 1 +32 2 2 +1573 12 12 +2258676 + +chain 18404394637 chr3 198022430 + 60000 197962430 chr3 199501827 + 35000 199446827 3 +13552792 0 1 +585083 0 1 +2092 1 2 +71 0 1 +31067262 0 1 +90 1 0 +5628461 0 15 +788 1 0 +3676 0 2 +35 1 1 +4682 1 0 +1295 0 5 +437 53 42 +326 0 2 +3309 1 1 +40 1 1 +998 0 3 +3584 5 0 +930 5 7 +845 1 1 +28 2 1 +303 0 1 +507 0 5 +5088 1 0 +2185 10046 10048 +949 4 4 +35 1 1 +2874 0 1 +6717 0 1 +2823 1 0 +703 0 4 +5143 1 0 +2490 10 10 +162 7 7 +6308 0 15 +15177535 152352 260003 +2532 1 0 +1633 2 2 +24207544 3000000 4400000 +60453436 0 4 +40076813 20999 20000 +8195 1 1 +44 1 1 +1408 1 1 +33 1 1 +172 3 4 +25 1 1 +538 13 13 +173 1 1 +27 1 1 +636 1 1 +28 1 1 +470 3 3 +112 1 1 +375 1 1 +26 26 0 +115 78 0 +52 23 0 +104 26 0 +15 231 0 +56 1 1 +20 1 1 +815 16 16 +484 1 1 +49 18 0 +509 4 3 +23 1 1 +391 1 1 +44 1 1 +1278 0 4 +32 1 1 +263 4 0 +27 1 1 +2416 0 2 +3184 43 43 +1150 13 13 +736 1 1 +47 1 1 +1416 1 1 +20 1 1 +1020 1 1 +25 1 1 +482 5 0 +716 1 0 +1697 1 1 +29 1 1 +1270261 23108 27000 +40930 1 0 +17455 1 1 +28 4 4 +43 0 491 +1679 1 1 +33 7 5 +29 1 3 +54863 53 16 +7653 2 2 +29 2 2 +15 0 30 +180 0 75 +215 45 0 +360 915 0 +6188 96 0 +17 288 0 +1388 1 1 +37 1 1 +7956 0 1 +374 0 1 +2442058 + +chain 310844 chr4 191154276 + 9241835 9252105 chr4 191273063 + 8941714 8947231 850 +2726 14 14 +243 9 9 +78 4 4 +157 213 211 +265 85 85 +524 4751 0 +379 283 283 +539 + +chain 9105 chr4 191154276 + 8982741 8983189 chr10 135374737 - 120304868 120305301 22041837 +59 380 365 +9 |
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| diff -r 1e881a00d8ff -r 79f9e32b380b test-data/cached_locally/liftOver.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/liftOver.loc Fri Oct 20 02:48:24 2017 -0400 |
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| @@ -0,0 +1,32 @@ +#This is a sample file distributed with Galaxy that is used by the +#liftOver tools. The liftOver.loc file has this format (white space +#characters are TAB characters): +# +#<FromSpecies> <ToSpecies> <PathToChainFile> +# +#So, for example, if you had the chain file to convert from anoCar1 to galGal3 +#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, +#then the liftOver.loc entry would look like this: +# +#<FromSpecies> <ToSpecies> <PathToChainFile> +#<dbkey> <name> <value> +# +#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain +# +#and your /depot/data2/galaxy/anoCar1/liftOver directory would +#contain all of your "chain" files (e.g.): +# +#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain +#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain +#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain +#...etc... +# +#Your liftOver.loc file should include an entry per line for each build you can +#convert. For example: +# +#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain +#anoCar1 gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain +#anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain +#...etc... + +A B ${__HERE__}/aToB.over.chain |
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| diff -r 1e881a00d8ff -r 79f9e32b380b test-data/test_bam_01_output_a.bam |
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| Binary file test-data/test_bam_01_output_a.bam has changed |
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| diff -r 1e881a00d8ff -r 79f9e32b380b test-data/test_bam_01_output_a.unmap.bam |
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| Binary file test-data/test_bam_01_output_a.unmap.bam has changed |
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| diff -r 1e881a00d8ff -r 79f9e32b380b test-data/test_bed_02_output_a__only_fails.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_02_output_a__only_fails.bed Fri Oct 20 02:48:24 2017 -0400 |
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| @@ -0,0 +1,5 @@ +chr1 100 10000 +chr2 100 10000 +chr3 100 10000 +chr4 8941700 8947200 +chr5 1 100000000 |
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| diff -r 1e881a00d8ff -r 79f9e32b380b tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Oct 20 02:48:24 2017 -0400 |
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| @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" /> + </table> + <!-- Locations of all liftOver files --> + <table name="liftOver" comment_char="#"> + <columns>dbkey, name, value</columns> + <file path="${__HERE__}/test-data/cached_locally/liftOver.loc" /> + </table> +</tables> |