| Previous changeset 8:0b5a01448cb5 (2017-01-13) Next changeset 10:4a978cf8cf92 (2017-02-24) |
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Commit message:
planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit 87e9dfebf772b1403f8b09af1e995d354879f761 |
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modified:
hifive_macros.xml |
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added:
test-data/hic.raw test-data/temp.fends test-data/temp.hcd test-data/temp.hcp test-data/temp.txt test-data/test.txt test-data/test_fend.bed test-data/test_frag.bed |
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removed:
tool_dependencies.xml |
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| diff -r 0b5a01448cb5 -r fb53ebc92f14 hifive_macros.xml --- a/hifive_macros.xml Fri Jan 13 13:57:11 2017 -0500 +++ b/hifive_macros.xml Fri Jan 13 15:43:34 2017 -0500 |
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| @@ -3,10 +3,6 @@ <xml name="requirements"> <requirements> <requirement type='package' version="1.3">hifive</requirement> - <requirement type='package' version='0.12'>scipy</requirement> - <requirement type='package' version='0.20.1'>cython</requirement> - <requirement type='package' version='2.5.0'>h5py</requirement> - <requirement type='package' version='1.7.1'>numpy</requirement> <yield/> </requirements> </xml> |
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| diff -r 0b5a01448cb5 -r fb53ebc92f14 test-data/hic.raw --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hic.raw Fri Jan 13 15:43:34 2017 -0500 |
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| b'@@ -0,0 +1,400 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| diff -r 0b5a01448cb5 -r fb53ebc92f14 test-data/temp.fends |
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| Binary file test-data/temp.fends has changed |
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| diff -r 0b5a01448cb5 -r fb53ebc92f14 test-data/temp.hcd |
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| Binary file test-data/temp.hcd has changed |
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| diff -r 0b5a01448cb5 -r fb53ebc92f14 test-data/temp.hcp |
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| Binary file test-data/temp.hcp has changed |
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| diff -r 0b5a01448cb5 -r fb53ebc92f14 test-data/temp.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/temp.txt Fri Jan 13 15:43:34 2017 -0500 |
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| @@ -0,0 +1,1 @@ +chr1 20000 30000 chr1 30000 40000 0.303682 |
| b |
| diff -r 0b5a01448cb5 -r fb53ebc92f14 test-data/test.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.txt Fri Jan 13 15:43:34 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +hifive hic-complete express --bed test_fend.bed -R hic.raw -i 600 -f 3 -j 1000 -n 10 -d -P temp +hifive hic-interval -c 1 -s 20000 -e 40000 -b 10000 -d enrichment temp.hcp temp.txt |
| b |
| diff -r 0b5a01448cb5 -r fb53ebc92f14 test-data/test_fend.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_fend.bed Fri Jan 13 15:43:34 2017 -0500 |
| b |
| @@ -0,0 +1,50 @@ +chr1 16007 16013 HindIII 0 . +chr1 24571 24577 HindIII 0 . +chr1 27981 27987 HindIII 0 . +chr1 30429 30435 HindIII 0 . +chr1 32153 32159 HindIII 0 . +chr1 32774 32780 HindIII 0 . +chr1 37752 37758 HindIII 0 . +chr1 38369 38375 HindIII 0 . +chr1 38791 38797 HindIII 0 . +chr1 39255 39261 HindIII 0 . +chr1 43602 43608 HindIII 0 . +chr1 46455 46461 HindIII 0 . +chr1 52419 52425 HindIII 0 . +chr1 56815 56821 HindIII 0 . +chr1 58747 58753 HindIII 0 . +chr1 58954 58960 HindIII 0 . +chr1 59356 59362 HindIII 0 . +chr1 75365 75371 HindIII 0 . +chr1 83359 83365 HindIII 0 . +chr1 84049 84055 HindIII 0 . +chr1 90742 90748 HindIII 0 . +chr1 91319 91325 HindIII 0 . +chr1 91586 91592 HindIII 0 . +chr1 92457 92463 HindIII 0 . +chr1 97923 97929 HindIII 0 . +chr2 15298 15304 HindIII 0 . +chr2 16049 16055 HindIII 0 . +chr2 18132 18138 HindIII 0 . +chr2 24992 24998 HindIII 0 . +chr2 28070 28076 HindIII 0 . +chr2 28179 28185 HindIII 0 . +chr2 36363 36369 HindIII 0 . +chr2 39160 39166 HindIII 0 . +chr2 39794 39800 HindIII 0 . +chr2 40429 40435 HindIII 0 . +chr2 51587 51593 HindIII 0 . +chr2 51663 51669 HindIII 0 . +chr2 52608 52614 HindIII 0 . +chr2 55288 55294 HindIII 0 . +chr2 57768 57774 HindIII 0 . +chr2 58355 58361 HindIII 0 . +chr2 62941 62947 HindIII 0 . +chr2 63723 63729 HindIII 0 . +chr2 65095 65101 HindIII 0 . +chr2 71813 71819 HindIII 0 . +chr2 74696 74702 HindIII 0 . +chr2 85327 85333 HindIII 0 . +chr2 93076 93082 HindIII 0 . +chr2 95210 95216 HindIII 0 . +chr2 97029 97035 HindIII 0 . |
| b |
| diff -r 0b5a01448cb5 -r fb53ebc92f14 test-data/test_frag.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_frag.bed Fri Jan 13 15:43:34 2017 -0500 |
| b |
| @@ -0,0 +1,202 @@ +chr1 16010 24574 Primer_00_For 0 + +chr1 24574 27984 Primer_01_Rev 0 - +chr1 27984 30432 Primer_02_For 0 + +chr1 30432 32156 Primer_03_Rev 0 - +chr1 32156 32777 Primer_04_For 0 + +chr1 32777 37755 Primer_05_Rev 0 - +chr1 37755 38372 Primer_06_For 0 + +chr1 38372 38794 Primer_07_Rev 0 - +chr1 38794 39258 Primer_08_For 0 + +chr1 39258 43605 Primer_09_Rev 0 - +chr1 43605 46458 Primer_10_For 0 + +chr1 46458 52422 Primer_11_Rev 0 - +chr1 52422 56818 Primer_12_For 0 + +chr1 56818 58750 Primer_13_Rev 0 - +chr1 58750 58957 Primer_14_For 0 + +chr1 58957 59359 Primer_15_Rev 0 - +chr1 59359 75368 Primer_16_For 0 + +chr1 75368 83362 Primer_17_Rev 0 - +chr1 83362 84052 Primer_18_For 0 + +chr1 84052 90745 Primer_19_Rev 0 - +chr1 90745 91322 Primer_20_For 0 + +chr1 91322 91589 Primer_21_Rev 0 - +chr1 91589 92460 Primer_22_For 0 + +chr1 92460 97926 Primer_23_Rev 0 - +chr1 97926 101019 Primer_24_For 0 + +chr1 101019 102675 Primer_25_Rev 0 - +chr1 102675 105560 Primer_26_For 0 + +chr1 105560 106653 Primer_27_Rev 0 - +chr1 106653 107961 Primer_28_For 0 + +chr1 107961 108199 Primer_29_Rev 0 - +chr1 108199 109520 Primer_30_For 0 + +chr1 109520 114996 Primer_31_Rev 0 - +chr1 114996 115430 Primer_32_For 0 + +chr1 115430 116794 Primer_33_Rev 0 - +chr1 116794 117062 Primer_34_For 0 + +chr1 117062 118302 Primer_35_Rev 0 - +chr1 118302 121958 Primer_36_For 0 + +chr1 121958 124939 Primer_37_Rev 0 - +chr1 124939 130395 Primer_38_For 0 + +chr1 130395 130462 Primer_39_Rev 0 - +chr1 130462 139819 Primer_40_For 0 + +chr1 139819 140043 Primer_41_Rev 0 - +chr1 140043 142853 Primer_42_For 0 + +chr1 142853 155675 Primer_43_Rev 0 - +chr1 155675 157488 Primer_44_For 0 + +chr1 157488 157623 Primer_45_Rev 0 - +chr1 157623 159127 Primer_46_For 0 + +chr1 159127 159862 Primer_47_Rev 0 - +chr1 159862 161091 Primer_48_For 0 + +chr1 161091 173282 Primer_49_Rev 0 - +chr1 173282 174260 Primer_50_For 0 + +chr1 174260 175546 Primer_51_Rev 0 - +chr1 175546 228207 Primer_52_For 0 + +chr1 228207 228568 Primer_53_Rev 0 - +chr1 228568 231797 Primer_54_For 0 + +chr1 231797 237073 Primer_55_Rev 0 - +chr1 237073 237652 Primer_56_For 0 + +chr1 237652 237915 Primer_57_Rev 0 - +chr1 237915 238787 Primer_58_For 0 + +chr1 238787 244261 Primer_59_Rev 0 - +chr1 244261 247336 Primer_60_For 0 + +chr1 247336 248991 Primer_61_Rev 0 - +chr1 248991 251875 Primer_62_For 0 + +chr1 251875 252968 Primer_63_Rev 0 - +chr1 252968 254276 Primer_64_For 0 + +chr1 254276 254514 Primer_65_Rev 0 - +chr1 254514 255841 Primer_66_For 0 + +chr1 255841 261311 Primer_67_Rev 0 - +chr1 261311 261745 Primer_68_For 0 + +chr1 261745 263111 Primer_69_Rev 0 - +chr1 263111 263379 Primer_70_For 0 + +chr1 263379 264619 Primer_71_Rev 0 - +chr1 264619 317876 Primer_72_For 0 + +chr1 317876 320686 Primer_73_Rev 0 - +chr1 320686 320910 Primer_74_For 0 + +chr1 320910 324093 Primer_75_Rev 0 - +chr1 324093 324317 Primer_76_For 0 + +chr1 324317 332889 Primer_77_Rev 0 - +chr1 332889 332956 Primer_78_For 0 + +chr1 332956 338410 Primer_79_Rev 0 - +chr1 338410 341367 Primer_80_For 0 + +chr1 341367 345029 Primer_81_Rev 0 - +chr1 345029 346269 Primer_82_For 0 + +chr1 346269 346537 Primer_83_Rev 0 - +chr1 346537 347902 Primer_84_For 0 + +chr1 347902 348336 Primer_85_Rev 0 - +chr1 348336 352886 Primer_86_For 0 + +chr1 352886 354735 Primer_87_Rev 0 - +chr1 354735 355945 Primer_88_For 0 + +chr1 355945 369333 Primer_89_Rev 0 - +chr1 369333 370804 Primer_90_For 0 + +chr1 370804 371769 Primer_91_Rev 0 - +chr1 371769 374307 Primer_92_For 0 + +chr1 374307 376188 Primer_93_Rev 0 - +chr1 376188 378553 Primer_94_For 0 + +chr1 378553 382213 Primer_95_Rev 0 - +chr1 382213 390650 Primer_96_For 0 + +chr1 390650 395284 Primer_97_Rev 0 - +chr1 395284 396271 Primer_98_For 0 + +chr1 396271 401276 Primer_99_Rev 0 - +chr2 16010 16052 Primer_100_For 0 + +chr2 24574 18135 Primer_101_Rev 0 - +chr2 27984 24995 Primer_102_For 0 + +chr2 30432 28073 Primer_103_Rev 0 - +chr2 32156 28182 Primer_104_For 0 + +chr2 32777 36366 Primer_105_Rev 0 - +chr2 37755 39163 Primer_106_For 0 + +chr2 38372 39797 Primer_107_Rev 0 - +chr2 38794 40432 Primer_108_For 0 + +chr2 39258 51590 Primer_109_Rev 0 - +chr2 43605 51666 Primer_110_For 0 + +chr2 46458 52611 Primer_111_Rev 0 - +chr2 52422 55291 Primer_112_For 0 + +chr2 56818 57771 Primer_113_Rev 0 - +chr2 58750 58358 Primer_114_For 0 + +chr2 58957 62944 Primer_115_Rev 0 - +chr2 59359 63726 Primer_116_For 0 + +chr2 75368 65098 Primer_117_Rev 0 - +chr2 83362 71816 Primer_118_For 0 + +chr2 84052 74699 Primer_119_Rev 0 - +chr2 90745 85330 Primer_120_For 0 + +chr2 91322 93079 Primer_121_Rev 0 - +chr2 91589 95213 Primer_122_For 0 + +chr2 92460 97032 Primer_123_Rev 0 - +chr2 97926 109082 Primer_124_For 0 + +chr2 101019 111682 Primer_125_Rev 0 - +chr2 102675 111896 Primer_126_For 0 + +chr2 105560 112076 Primer_127_Rev 0 - +chr2 106653 113602 Primer_128_For 0 + +chr2 107961 116730 Primer_129_Rev 0 - +chr2 108199 118064 Primer_130_For 0 + +chr2 109520 118670 Primer_131_Rev 0 - +chr2 114996 120123 Primer_132_For 0 + +chr2 115430 124293 Primer_133_Rev 0 - +chr2 116794 130563 Primer_134_For 0 + +chr2 117062 130766 Primer_135_Rev 0 - +chr2 118302 135969 Primer_136_For 0 + +chr2 121958 137384 Primer_137_Rev 0 - +chr2 124939 137513 Primer_138_For 0 + +chr2 130395 138953 Primer_139_Rev 0 - +chr2 130462 139055 Primer_140_For 0 + +chr2 139819 143191 Primer_141_Rev 0 - +chr2 140043 150160 Primer_142_For 0 + +chr2 142853 151998 Primer_143_Rev 0 - +chr2 155675 152598 Primer_144_For 0 + +chr2 157488 155847 Primer_145_Rev 0 - +chr2 157623 158493 Primer_146_For 0 + +chr2 159127 163026 Primer_147_Rev 0 - +chr2 159862 164088 Primer_148_For 0 + +chr2 161091 165947 Primer_149_Rev 0 - +chr2 173282 168787 Primer_150_For 0 + +chr2 174260 173095 Primer_151_Rev 0 - +chr2 175546 173128 Primer_152_For 0 + +chr2 228207 175550 Primer_153_Rev 0 - +chr2 228568 176745 Primer_154_For 0 + +chr2 231797 183924 Primer_155_Rev 0 - +chr2 237073 185645 Primer_156_For 0 + +chr2 237652 186944 Primer_157_Rev 0 - +chr2 237915 188303 Primer_158_For 0 + +chr2 238787 188400 Primer_159_Rev 0 - +chr2 244261 188957 Primer_160_For 0 + +chr2 247336 192256 Primer_161_Rev 0 - +chr2 248991 193266 Primer_162_For 0 + +chr2 251875 194546 Primer_163_Rev 0 - +chr2 252968 196809 Primer_164_For 0 + +chr2 254276 199072 Primer_165_Rev 0 - +chr2 254514 199559 Primer_166_For 0 + +chr2 255841 203683 Primer_167_Rev 0 - +chr2 261311 211898 Primer_168_For 0 + +chr2 261745 212927 Primer_169_Rev 0 - +chr2 263111 221159 Primer_170_For 0 + +chr2 263379 222594 Primer_171_Rev 0 - +chr2 264619 224468 Primer_172_For 0 + +chr2 317876 233839 Primer_173_Rev 0 - +chr2 320686 233884 Primer_174_For 0 + +chr2 320910 234227 Primer_175_Rev 0 - +chr2 324093 238333 Primer_176_For 0 + +chr2 324317 239004 Primer_177_Rev 0 - +chr2 332889 239505 Primer_178_For 0 + +chr2 332956 240406 Primer_179_Rev 0 - +chr2 338410 246696 Primer_180_For 0 + +chr2 341367 250702 Primer_181_Rev 0 - +chr2 345029 254585 Primer_182_For 0 + +chr2 346269 258819 Primer_183_Rev 0 - +chr2 346537 261894 Primer_184_For 0 + +chr2 347902 262250 Primer_185_Rev 0 - +chr2 348336 262408 Primer_186_For 0 + +chr2 352886 274458 Primer_187_Rev 0 - +chr2 354735 281363 Primer_188_For 0 + +chr2 355945 283106 Primer_189_Rev 0 - +chr2 369333 287295 Primer_190_For 0 + +chr2 370804 291827 Primer_191_Rev 0 - +chr2 371769 296242 Primer_192_For 0 + +chr2 374307 301841 Primer_193_Rev 0 - +chr2 376188 302409 Primer_194_For 0 + +chr2 378553 311206 Primer_195_Rev 0 - +chr2 382213 315861 Primer_196_For 0 + +chr2 390650 318418 Primer_197_Rev 0 - +chr2 395284 324520 Primer_198_For 0 + +chr2 396271 327297 Primer_199_Rev 0 - +chr3 16010 63687 Primer_200_For 0 + +chr3 24574 64310 Primer_201_Rev 0 - \ No newline at end of file |
| b |
| diff -r 0b5a01448cb5 -r fb53ebc92f14 tool_dependencies.xml --- a/tool_dependencies.xml Fri Jan 13 13:57:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,18 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="scipy" version="0.12.0"> - <repository changeset_revision="cfbbe183f8a7" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="numpy" version="1.7.1"> - <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="cython" version="0.20.1"> - <repository changeset_revision="bf766623094e" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="h5py" version="2.5.0"> - <repository changeset_revision="cc1a2aae5057" name="package_h5py_2_5_0" owner="sauria" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="hifive" version="1.3"> - <repository changeset_revision="a1a962713395" name="package_hifive_1_3" owner="sauria" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |