| Previous changeset 5:343bce47219b (2019-03-05) Next changeset 7:4bfb3a8dd955 (2019-03-10) |
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Commit message:
Update to pathogist0.3 |
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modified:
galaxy/tools/concatenator/concatenator.xml galaxy/tools/config_builder/config_builder galaxy/tools/config_builder/config_builder.xml galaxy/tools/consensus_clustering/consensus_clustering.xml galaxy/tools/correlation_clustering/correlation_clustering.xml galaxy/tools/distance/distance.xml galaxy/tools/visualization/visualization.xml |
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| diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/concatenator/concatenator.xml --- a/galaxy/tools/concatenator/concatenator.xml Tue Mar 05 03:59:00 2019 -0500 +++ b/galaxy/tools/concatenator/concatenator.xml Fri Mar 08 18:42:31 2019 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="concatenator" name="Concatenator" version="1.0.0"> <description>creates a list of accessions and the associated path to their variant calls</description> <requirements> - <requirement type="package" version="0.2.3">pathogist</requirement> + <requirement type="package" version="0.3">pathogist</requirement> </requirements> <command><![CDATA[ |
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| diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/config_builder/config_builder --- a/galaxy/tools/config_builder/config_builder Tue Mar 05 03:59:00 2019 -0500 +++ b/galaxy/tools/config_builder/config_builder Fri Mar 08 18:42:31 2019 -0500 |
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| @@ -3,11 +3,11 @@ import sys import yaml import argparse as ap +import subprocess parser = ap.ArgumentParser(prog='config_builder', conflict_handler='resolve', description="Builds the config file for PathOGiST") -parser.add_argument('yaml', help="Blank config file") parser.add_argument('forward', help="File to list of forward reads") parser.add_argument('reverse', help="File to list of reverse reads") parser.add_argument('output', help="Output prefix for final consensus clustering and visualization") @@ -73,7 +73,9 @@ args = parser.parse_args() -with open(args.yaml) as f: +print(subprocess.check_output(['PATHOGIST', 'all', 'blank_config.yaml', '--new_config'])) + +with open('blank_config.yaml') as f: list_doc = yaml.load(f) for line in list_doc: |
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| diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/config_builder/config_builder.xml --- a/galaxy/tools/config_builder/config_builder.xml Tue Mar 05 03:59:00 2019 -0500 +++ b/galaxy/tools/config_builder/config_builder.xml Fri Mar 08 18:42:31 2019 -0500 |
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| @@ -1,12 +1,10 @@ <tool id="config_builder" name="PathOGiST - Config Builder" version="1.0.0"> <description>: Creates and populates the config file to run PathOGiST</description> <requirements> - <requirement type="package" version="0.2.3">pathogist</requirement> + <requirement type="package" version="0.3">pathogist</requirement> </requirements> <command><![CDATA[ - PATHOGIST all blank_config.yaml --new_config - $__tool_directory__/config_builder #if $snippy.snippy_checkbox @@ -88,7 +86,6 @@ $adv_clustering.visualize #end if - blank_config.yaml $forward $reverse config.yaml |
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| diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/consensus_clustering/consensus_clustering.xml --- a/galaxy/tools/consensus_clustering/consensus_clustering.xml Tue Mar 05 03:59:00 2019 -0500 +++ b/galaxy/tools/consensus_clustering/consensus_clustering.xml Fri Mar 08 18:42:31 2019 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="consensus_clustering" name="PathOGiST - Consensus Clustering" version="1.0.0"> <description>: Performs consensus clustering on multiple clusterings</description> <requirements> - <requirement type="package" version="0.2.3">pathogist</requirement> + <requirement type="package" version="0.3">pathogist</requirement> </requirements> <command><![CDATA[ |
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| diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/correlation_clustering/correlation_clustering.xml --- a/galaxy/tools/correlation_clustering/correlation_clustering.xml Tue Mar 05 03:59:00 2019 -0500 +++ b/galaxy/tools/correlation_clustering/correlation_clustering.xml Fri Mar 08 18:42:31 2019 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="correlation_clustering" name="PathOGiST - Correlation Clustering" version="1.0.0"> <description>: Runs correlation clustering on a distance matrix file</description> <requirements> - <requirement type="package" version="0.2.3">pathogist</requirement> + <requirement type="package" version="0.3">pathogist</requirement> </requirements> <command><![CDATA[ |
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| diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/distance/distance.xml --- a/galaxy/tools/distance/distance.xml Tue Mar 05 03:59:00 2019 -0500 +++ b/galaxy/tools/distance/distance.xml Fri Mar 08 18:42:31 2019 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="distance" name="PathOGiST - Distance" version="1.0.0"> <description>: Construct distance matrix from genotyping data</description> <requirements> - <requirement type="package" version="0.2.3">pathogist</requirement> + <requirement type="package" version="0.3">pathogist</requirement> </requirements> <command><![CDATA[ |
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| diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/visualization/visualization.xml --- a/galaxy/tools/visualization/visualization.xml Tue Mar 05 03:59:00 2019 -0500 +++ b/galaxy/tools/visualization/visualization.xml Fri Mar 08 18:42:31 2019 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="visualization" name="PathOGiST - Visualization" version="1.0.0"> <description>: Visualize distance matrix</description> <requirements> - <requirement type="package" version="0.2.3">pathogist</requirement> + <requirement type="package" version="0.3">pathogist</requirement> </requirements> <command><![CDATA[ |