| Previous changeset 11:4cbceec1d6b4 (2016-12-14) Next changeset 13:69c5e9c0add0 (2017-02-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 |
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modified:
blastxml_to_gapped_gff3.py jbrowse.py jbrowse.xml |
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| diff -r 4cbceec1d6b4 -r db5fe5a3176a blastxml_to_gapped_gff3.py --- a/blastxml_to_gapped_gff3.py Wed Dec 14 09:19:48 2016 -0500 +++ b/blastxml_to_gapped_gff3.py Mon Feb 06 12:52:09 2017 -0500 |
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| @@ -253,7 +253,7 @@ if __name__ == '__main__': parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='') - parser.add_argument('blastxml', type=file, help='Blast XML Output') + parser.add_argument('blastxml', type=open, help='Blast XML Output') parser.add_argument('--min_gap', type=int, help='Maximum gap size before generating a new match_part', default=3) parser.add_argument('--trim', action='store_true', help='Trim blast hits to be only as long as the parent feature') parser.add_argument('--trim_end', action='store_true', help='Cut blast results off at end of gene') |
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| diff -r 4cbceec1d6b4 -r db5fe5a3176a jbrowse.py --- a/jbrowse.py Wed Dec 14 09:19:48 2016 -0500 +++ b/jbrowse.py Mon Feb 06 12:52:09 2017 -0500 |
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| @@ -158,7 +158,7 @@ return r, g, b def parse_menus(self, track): - trackConfig = {'menuTemplate': [{}, {}, {}]} + trackConfig = {'menuTemplate': [{}, {}, {}, {}]} if 'menu' in track['menus']: menu_list = [track['menus']['menu']] @@ -435,8 +435,9 @@ cmd = ['ln', data, dest] self.subprocess_check_call(cmd) + url = os.path.join('raw', trackData['label'] + '.bw') trackData.update({ - "urlTemplate": os.path.join('..', dest), + "urlTemplate": url, "storeClass": "JBrowse/Store/SeqFeature/BigWig", "type": "JBrowse/View/Track/Wiggle/Density", }) @@ -460,8 +461,9 @@ cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai'] self.subprocess_check_call(cmd) + url = os.path.join('raw', trackData['label'] + '.bam') trackData.update({ - "urlTemplate": os.path.join('..', dest), + "urlTemplate": url, "type": "JBrowse/View/Track/Alignments2", "storeClass": "JBrowse/Store/SeqFeature/BAM", }) @@ -487,8 +489,9 @@ cmd = ['tabix', '-p', 'vcf', dest + '.gz'] self.subprocess_check_call(cmd) + url = os.path.join('raw', trackData['label'] + '.vcf') trackData.update({ - "urlTemplate": os.path.join('..', dest + '.gz'), + "urlTemplate": url, "type": "JBrowse/View/Track/HTMLVariants", "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", }) @@ -564,8 +567,9 @@ else: outputTrackConfig[key] = colourOptions[key] - menus = self.cs.parse_menus(track['conf']['options']) - outputTrackConfig.update(menus) + if 'menus' in track['conf']['options']: + menus = self.cs.parse_menus(track['conf']['options']) + outputTrackConfig.update(menus) # import pprint; pprint.pprint(track) # import sys; sys.exit() |
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| diff -r 4cbceec1d6b4 -r db5fe5a3176a jbrowse.xml --- a/jbrowse.xml Wed Dec 14 09:19:48 2016 -0500 +++ b/jbrowse.xml Mon Feb 06 12:52:09 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@"> +<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.1"> <description>genome browser</description> <macros> <import>macros.xml</import> |