| Previous changeset 100:666c07b60cd2 (2024-06-21) Next changeset 102:099370690407 (2024-06-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty |
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modified:
__pycache__/jbrowse2.cpython-312.pyc jbrowse2.py jbrowse2.xml macros.xml |
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| diff -r 666c07b60cd2 -r e4ba5f1da6ef __pycache__/jbrowse2.cpython-312.pyc |
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| Binary file __pycache__/jbrowse2.cpython-312.pyc has changed |
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| diff -r 666c07b60cd2 -r e4ba5f1da6ef jbrowse2.py --- a/jbrowse2.py Fri Jun 21 23:49:10 2024 +0000 +++ b/jbrowse2.py Sat Jun 22 03:52:09 2024 +0000 |
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| @@ -403,6 +403,7 @@ class JbrowseConnector(object): def __init__(self, outdir, jbrowse2path): + self.bpPerPx = 50 self.trackCounter = 0 # to avoid name clashes self.assemblies = [] # these require more than a few line diff. self.assmeta = {} @@ -1319,7 +1320,7 @@ https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py """ # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708 - bpPerPx = 50 # this is tricky since browser window width is unknown - this seems a compromise that sort of works.... + bpPerPx = self.bpPerPx # Browser window width is unknown and apparently cannot be figured out in JB2 code so could be 200-2000+ pixels. track_types = {} with open(self.config_json_file, "r") as config_file: config_json = json.load(config_file) @@ -1669,6 +1670,7 @@ track_conf["category"] = track.attrib["cat"] track_conf["format"] = track.attrib["format"] track_conf["conf"] = etree_to_dict(track.find("options")) + logging keys = jc.process_annotations(track_conf) if keys: for key in keys: @@ -1702,6 +1704,7 @@ ).text logging.debug("default_session=%s" % (json.dumps(default_session_data, indent=2))) jc.zipOut = root.find("metadata/general/zipOut").text == "true" + jc.bpPerPx = root.find("metadata/general/bpPerPx").text general_data = { "analytics": root.find("metadata/general/analytics").text, "primary_color": root.find("metadata/general/primary_color").text, |
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| diff -r 666c07b60cd2 -r e4ba5f1da6ef jbrowse2.xml --- a/jbrowse2.xml Fri Jun 21 23:49:10 2024 +0000 +++ b/jbrowse2.xml Sat Jun 22 03:52:09 2024 +0000 |
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| @@ -75,6 +75,7 @@ <general> <defaultLocation>${jbgen.defaultLocation}</defaultLocation> <zipOut>${jbgen.zipOut}</zipOut> + <bpPerPx>${jbgen.bpPerPx}</bpPerPx> <analytics>${jbgen.enableAnalytics}</analytics> <primary_color>${jbgen.primary_color}</primary_color> <secondary_color>${jbgen.secondary_color}</secondary_color> |
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| diff -r 666c07b60cd2 -r e4ba5f1da6ef macros.xml --- a/macros.xml Fri Jun 21 23:49:10 2024 +0000 +++ b/macros.xml Sat Jun 22 03:52:09 2024 +0000 |
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| @@ -94,7 +94,7 @@ </param> </xml> <xml name="general_options"> - <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> + <section name="jbgen" title="Advanced JBrowse Options: collections, locations, colours, font size and default bp per pixel" expanded="false"> <conditional name="ucol"> <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form" help="A collection of bam/vcf and other track types will be converted into a JBrowse2 automatically"> <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option> @@ -108,6 +108,7 @@ <param name="zipOut" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create a zip archive for downloading rather than viewing" help="Default is to make an interactive browser appear when the 'eye' icon is activated"/> <param name="defaultLocation" type="text" value="" label="Subset to display to new users" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678"/> <param name="session_name" type="text" value="New JBrowse2 session" label="Session name" help="Displayed at the top of the window"/> + <param name="bpPerPx" type="integer" value="50" label="Base pairs per display pixel for default view" help="Make the default window show more or less BP of sequence. For some reason not automatable in JB2, sorry"/> <param name="enableAnalytics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166"/> <param name="primary_color" type="color" value="#0D233F" label="Primary color"> <sanitizer> |