Mercurial > repos > iuc > nanocompore_sampcomp
changeset 2:25abc2c72ff9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"
| author | iuc |
|---|---|
| date | Wed, 17 Jun 2020 13:28:27 -0400 |
| parents | c43f4b80f5a9 |
| children | b833eff63b10 |
| files | NanocomporeDB_process.py macros.xml sampcomp.xml test-data/GMM_logit_pvalue.bed test-data/GMM_logit_pvalue.bedgraph test-data/KS_dwell_pvalue.bed test-data/KS_dwell_pvalue.bedgraph test-data/KS_intensity_pvalue.bed test-data/KS_intensity_pvalue.bedgraph |
| diffstat | 9 files changed, 16 insertions(+), 11 deletions(-) [+] |
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--- a/NanocomporeDB_process.py Mon Jun 08 14:36:18 2020 -0400 +++ b/NanocomporeDB_process.py Wed Jun 17 13:28:27 2020 -0400 @@ -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.')
--- a/macros.xml Mon Jun 08 14:36:18 2020 -0400 +++ b/macros.xml Wed Jun 17 13:28:27 2020 -0400 @@ -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>
--- a/sampcomp.xml Mon Jun 08 14:36:18 2020 -0400 +++ b/sampcomp.xml Wed Jun 17 13:28:27 2020 -0400 @@ -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>
--- /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 @@ -0,0 +1,2 @@ +chr 22102 22107 chr_AGGAA 0 + +chr 22103 22108 chr_GGAAA 1.0472150418546853 +
--- 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 @@ -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
--- /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 @@ -0,0 +1,2 @@ +chr 22102 22107 chr_AGGAA 0.037294307603991536 + +chr 22103 22108 chr_GGAAA 0.037294307603991536 +
--- 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 @@ -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
--- /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 @@ -0,0 +1,2 @@ +chr 22102 22107 chr_AGGAA 0.5940708247528699 + +chr 22103 22108 chr_GGAAA 0.5940708247528699 +
--- 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 @@ -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