Mercurial > repos > iuc > data_manager_snpsift_dbnsfp

changeset 6:e57f0b0bc73b draft

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"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 15:48:39 -0500
parents 09f9bfb2b33b
children fe8a9ab8daf9
files data_manager/data_manager_snpsift_dbnsfp.py data_manager/data_manager_snpsift_dbnsfp.xml test-data/test_nsfp.data_manager_json
diffstat 3 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_snpsift_dbnsfp.py	Tue Oct 30 18:44:43 2018 -0400
+++ b/data_manager/data_manager_snpsift_dbnsfp.py	Thu Nov 28 15:48:39 2019 -0500
@@ -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 18:44:43 2018 -0400
+++ b/data_manager/data_manager_snpsift_dbnsfp.xml	Thu Nov 28 15:48:39 2019 -0500
@@ -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 18:44:43 2018 -0400
+++ b/test-data/test_nsfp.data_manager_json	Thu Nov 28 15:48:39 2019 -0500
@@ -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