Mercurial > repos > iuc > data_manager_snpsift_dbnsfp
changeset 6:0a68ef0303c5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
| author | iuc |
|---|---|
| date | Thu, 28 Nov 2019 20:32:17 +0000 |
| parents | 2cd22c2881e3 |
| children | 8636c3740779 |
| files | data_manager/data_manager_snpsift_dbnsfp.py data_manager/data_manager_snpsift_dbnsfp.xml test-data/test_nsfp.data_manager_json tool_dependencies.xml |
| diffstat | 4 files changed, 9 insertions(+), 8 deletions(-) [+] |
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--- a/data_manager/data_manager_snpsift_dbnsfp.py Tue Oct 30 18:44:24 2018 -0400 +++ b/data_manager/data_manager_snpsift_dbnsfp.py Thu Nov 28 20:32:17 2019 +0000 @@ -195,7 +195,7 @@ data_manager_dict['data_tables'][data_table].append(data_table_entry) # save info to json file - open(filename, 'wb').write(json.dumps(data_manager_dict)) + open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True)) if __name__ == "__main__":
--- a/data_manager/data_manager_snpsift_dbnsfp.xml Tue Oct 30 18:44:24 2018 -0400 +++ b/data_manager/data_manager_snpsift_dbnsfp.xml Thu Nov 28 20:32:17 2019 +0000 @@ -1,15 +1,16 @@ -<tool id="data_manager_snpsift_dbnsfp" name="SnpSift dbNSFP" version="4.1.0" tool_type="manage_data"> +<tool id="data_manager_snpsift_dbnsfp" name="SnpSift dbNSFP" version="4.1.1" tool_type="manage_data" profile="19.05"> <description>Install a dbNSFP variant annotation database</description> <requirements> <requirement type="package" version="0.8.3">pysam</requirement> + <requirement type="package" version="2.7">python</requirement> </requirements> <stdio> <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command interpreter="python"> + <command> #import re - data_manager_snpsift_dbnsfp.py + python '$__tool_directory__/data_manager_snpsift_dbnsfp.py' #if $db.src == 'softgenetics': --softgenetics "$db.softgenetics_name" #elif $db.src == 'history':
--- a/test-data/test_nsfp.data_manager_json Tue Oct 30 18:44:24 2018 -0400 +++ b/test-data/test_nsfp.data_manager_json Thu Nov 28 20:32:17 2019 +0000 @@ -1,1 +1,1 @@ -{"data_tables": {"snpsift_dbnsfp": [{"value": "test_nsfp_tsv.txt.gz", "name": "? test_nsfp_tsv", "build": "?", "dbkey": "?_test_nsfp_tsv", "annotations": "hg18_pos(1-coor), genename, SIFT_score, SIFT_pred, Polyphen2_HDIV_score"}]}} \ No newline at end of file +{"data_tables": {"snpsift_dbnsfps": [{"annotations": "hg18_pos(1-coor),genename,SIFT_score,SIFT_pred,Polyphen2_HDIV_score", "build": "hg19", "key": "hg19_test_nsfp_tsv", "name": "hg19 test_nsfp_tsv", "value": "test_nsfp_tsv.txt.gz"}]}} \ No newline at end of file
--- a/tool_dependencies.xml Tue Oct 30 18:44:24 2018 -0400 +++ b/tool_dependencies.xml Thu Nov 28 20:32:17 2019 +0000 @@ -1,6 +1,6 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <tool_dependency> <package name="pysam" version="0.8.3"> - <repository changeset_revision="7ac80143c68d" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="7ac80143c68d" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"/> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file