| Previous changeset 6:a39471bf7d13 (2019-03-08) Next changeset 8:7708da43aefb (2019-03-11) |
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Commit message:
Bug fixes |
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modified:
galaxy/tools/config_builder/config_builder galaxy/tools/config_builder/config_builder.xml |
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| diff -r a39471bf7d13 -r 4bfb3a8dd955 galaxy/tools/config_builder/config_builder --- a/galaxy/tools/config_builder/config_builder Fri Mar 08 18:42:31 2019 -0500 +++ b/galaxy/tools/config_builder/config_builder Sun Mar 10 00:07:09 2019 -0500 |
| [ |
| @@ -3,7 +3,11 @@ import sys import yaml import argparse as ap -import subprocess +import urllib.request as urllib + +# Version of PathOGiST +MAJOR_VERSION = 0 +MINOR_VERSION = 3 parser = ap.ArgumentParser(prog='config_builder', conflict_handler='resolve', description="Builds the config file for PathOGiST") @@ -73,7 +77,8 @@ args = parser.parse_args() -print(subprocess.check_output(['PATHOGIST', 'all', 'blank_config.yaml', '--new_config'])) +urllib.urlretrieve("https://github.com/WGS-TB/PathOGiST/releases/download/v{0}.{1}/blank_config.yaml" + .format(MAJOR_VERSION, MINOR_VERSION), 'blank_config.yaml') with open('blank_config.yaml') as f: list_doc = yaml.load(f) |
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| diff -r a39471bf7d13 -r 4bfb3a8dd955 galaxy/tools/config_builder/config_builder.xml --- a/galaxy/tools/config_builder/config_builder.xml Fri Mar 08 18:42:31 2019 -0500 +++ b/galaxy/tools/config_builder/config_builder.xml Sun Mar 10 00:07:09 2019 -0500 |
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| @@ -113,7 +113,8 @@ variant evidence"/> </when> </conditional> - <param name="snp_fine" type="boolean" label="Consider SNP as a fine datatype"/> + <param name="snp_fine" type="boolean" checked="true" falsevalue="" truevalue="--fine_snp" + label="Consider SNP as a fine datatype"/> <param name="snp_threshold" type="integer" value="2500" min="0" label="Correlation clustering threshold for MLST"/> </when> @@ -164,7 +165,8 @@ kmer is seen to be considered present in the sample"/> </when> </conditional> - <param name="mlst_fine" type="boolean" label="Consider MLST as a fine datatype"/> + <param name="mlst_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_mlst" + label="Consider MLST as a fine datatype"/> <param name="mlst_threshold" type="integer" value="300" min="0" label="Correlation clustering threshold for MLST"/> </when> @@ -173,7 +175,8 @@ <conditional name="prince"> <param name="prince_checkbox" type="boolean" label="Run PRINCE"/> <when value="true"> - <param name="cnv_fine" type="boolean" label="Consider CNV as a fine datatype"/> + <param name="cnv_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_cnv" + label="Consider CNV as a fine datatype"/> <param name="cnv_threshold" type="integer" value="100" min="0" label="Correlation clustering threshold for CNV"/> </when> @@ -192,7 +195,8 @@ of unique kmers in the input set"/> </when> </conditional> - <param name="kwip_fine" type="boolean" label="Consider kWIP as a fine datatype"/> + <param name="kwip_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_kwip" + label="Consider kWIP as a fine datatype"/> <param name="kwip_threshold" type="float" value="0.4" min="0" label="Correlation clustering threshold for kWIP"/> </when> @@ -201,7 +205,8 @@ <conditional name="spotyping"> <param name="spotyping_checkbox" type="boolean" label="Run SpoTyping"/> <when value="true"> - <param name="spoligo_fine" type="boolean" label="Consider spoligotype as a fine datatype"/> + <param name="spoligo_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_spoligo" + label="Consider spoligotype as a fine datatype"/> <param name="spoligo_threshold" type="integer" value="8" min="0" label="Correlation clustering threshold for Spoligotyping"/> </when> |