| Previous changeset 1:c43f4b80f5a9 (2020-06-08) Next changeset 3:b833eff63b10 (2020-07-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32" |
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modified:
NanocomporeDB_process.py macros.xml sampcomp.xml test-data/GMM_logit_pvalue.bedgraph test-data/KS_dwell_pvalue.bedgraph test-data/KS_intensity_pvalue.bedgraph |
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added:
test-data/GMM_logit_pvalue.bed test-data/KS_dwell_pvalue.bed test-data/KS_intensity_pvalue.bed |
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| diff -r c43f4b80f5a9 -r 25abc2c72ff9 NanocomporeDB_process.py --- a/NanocomporeDB_process.py Mon Jun 08 14:36:18 2020 -0400 +++ b/NanocomporeDB_process.py Wed Jun 17 13:28:27 2020 -0400 |
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| @@ -38,7 +38,7 @@ parser.add_argument('--pvalue-types', type=str, default='GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue', help='path to the annotations') - parser.add_argument('--bedgraph', default=False, + parser.add_argument('--bedgraph', action="store_true", help='write output in BEDGRAPH format instead of BED') parser.add_argument('--pvalue-threshold', default=1.0, help='Maximum reported p-value.') |
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| diff -r c43f4b80f5a9 -r 25abc2c72ff9 macros.xml --- a/macros.xml Mon Jun 08 14:36:18 2020 -0400 +++ b/macros.xml Wed Jun 17 13:28:27 2020 -0400 |
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| @@ -1,7 +1,6 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.0.0rc3.post2</token> - <token name="@WRAPPER_VERSION@">galaxy0</token> <token name="@DESCRIPTION@"></token> <xml name="requirements"> <requirements> @@ -29,4 +28,4 @@ <token name="@REFERENCES@"><![CDATA[ More information are available on the `project website <https://nanocompore.rna.rocks/>`_ and `github <https://github.com/tleonardi/nanocompore>`_. ]]></token> -</macros> \ No newline at end of file +</macros> |
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| diff -r c43f4b80f5a9 -r 25abc2c72ff9 sampcomp.xml --- a/sampcomp.xml Mon Jun 08 14:36:18 2020 -0400 +++ b/sampcomp.xml Wed Jun 17 13:28:27 2020 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> +<tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+galaxy0"> <description>to compare Nanopolished datasets</description> <macros> <import>macros.xml</import> @@ -217,4 +217,4 @@ @REFERENCES@ ]]></help> <expand macro="citations"/> -</tool> \ No newline at end of file +</tool> |
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| diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/GMM_logit_pvalue.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GMM_logit_pvalue.bed Wed Jun 17 13:28:27 2020 -0400 |
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| @@ -0,0 +1,2 @@ +chr 22102 22107 chr_AGGAA 0 + +chr 22103 22108 chr_GGAAA 1.0472150418546853 + |
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| diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/GMM_logit_pvalue.bedgraph --- a/test-data/GMM_logit_pvalue.bedgraph Mon Jun 08 14:36:18 2020 -0400 +++ b/test-data/GMM_logit_pvalue.bedgraph Wed Jun 17 13:28:27 2020 -0400 |
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| @@ -1,2 +1,2 @@ -chr 22102 22107 chr_AGGAA 0 + -chr 22103 22108 chr_GGAAA 1.0472150418546853 + +chr 22104 22105 0 +chr 22105 22106 1.0472150418546853 |
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| diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/KS_dwell_pvalue.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/KS_dwell_pvalue.bed Wed Jun 17 13:28:27 2020 -0400 |
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| @@ -0,0 +1,2 @@ +chr 22102 22107 chr_AGGAA 0.037294307603991536 + +chr 22103 22108 chr_GGAAA 0.037294307603991536 + |
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| diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/KS_dwell_pvalue.bedgraph --- a/test-data/KS_dwell_pvalue.bedgraph Mon Jun 08 14:36:18 2020 -0400 +++ b/test-data/KS_dwell_pvalue.bedgraph Wed Jun 17 13:28:27 2020 -0400 |
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| @@ -1,2 +1,2 @@ -chr 22102 22107 chr_AGGAA 0.037294307603991536 + -chr 22103 22108 chr_GGAAA 0.037294307603991536 + +chr 22104 22105 0.037294307603991536 +chr 22105 22106 0.037294307603991536 |
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| diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/KS_intensity_pvalue.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/KS_intensity_pvalue.bed Wed Jun 17 13:28:27 2020 -0400 |
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| @@ -0,0 +1,2 @@ +chr 22102 22107 chr_AGGAA 0.5940708247528699 + +chr 22103 22108 chr_GGAAA 0.5940708247528699 + |
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| diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/KS_intensity_pvalue.bedgraph --- a/test-data/KS_intensity_pvalue.bedgraph Mon Jun 08 14:36:18 2020 -0400 +++ b/test-data/KS_intensity_pvalue.bedgraph Wed Jun 17 13:28:27 2020 -0400 |
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| @@ -1,2 +1,2 @@ -chr 22102 22107 chr_AGGAA 0.5940708247528699 + -chr 22103 22108 chr_GGAAA 0.5940708247528699 + +chr 22104 22105 0.5940708247528699 +chr 22105 22106 0.5940708247528699 |