opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 00:12:08 +08:00
Code Issues Packages Projects Releases Wiki Activity

Cleaned up codebase for attempting adding api additions to the galaxy main branch

Browse Source
This commit is contained in:
Richard Park
2012-08-03 02:09:05 -04:00
parent 1ce82abc84
commit 6839829211
2 changed files with 17 additions and 27 deletions
Download Patch File Download Diff File Expand all files Collapse all files
scripts/api/workflow_delete_workflow_rpark.py → scripts/api/workflow_delete.py
+7 -2
View File
@@ -1,7 +1,12 @@
#!/usr/bin/env python
"""
# Author: RPARK
API script for deleting workflows
# ---------------------------------------------- #
# PARKLAB, Author: RPARK
API example script for deleting workflows
# ---------------------------------------------- #
Example calls:
python workflow_delete.py <api_key> <galaxy_url>/api/workflows/<workflow id> True
"""
import os, sys
scripts/api/workflow_execute_parameters.py
+10 -25
View File
@@ -1,23 +1,13 @@
#!/usr/bin/env python
"""
# ---------------------------------------------- #
# PARKLAB, Author: RPARK
# ---------------------------------------------- #
Execute workflows from the command line.
Example calls:
python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'Test API History' '38=ldda=0qr350234d2d192f'
python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'hist_id=a912e9e5d84530d4' '38=hda=03501d7626bd192f'
"""
"""
python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'hist_id=a912e9e5d84530d4' '38=hda=03501d7626bd192f' 'param=tool=name=value'
'param=tool=name=value'
Example
python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=bwa'
python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=arachne' 'param=bowtie_wrapper=suppressHeader=True'
python workflow_execute_parameters.py 35a24ae2643785ff3d046c98ea362c7f http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=bowtie' 'param=bowtie_wrapper=suppressHeader=True' 'param=peakcalling_spp=window_size=1000'
python workflow_execute.py <api_key> <galaxy_url>/api/workflows <workflow_id> 'hist_id=<history_id>' '38=hda=<file_id>' 'param=tool=name=value'
python workflow_execute_parameters.py <api_key> http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=bowtie' 'param=bowtie_wrapper=suppressHeader=True' 'param=peakcalling_spp=window_size=1000'
"""
import os, sys
@@ -34,7 +24,6 @@ def main():
data['ds_map'] = {}
#########################################################
### MY EDITS ############################################
### Trying to pass in parameter for my own dictionary ###
data['parameters'] = {};
@@ -51,14 +40,10 @@ def main():
except ValueError:
print("VALUE ERROR:");
wtype, wtool, wparam, wvalue = v.split('=');
data['parameters'][wtool] = {'param':wparam, 'value':wvalue}
#########################################################
### MY EDITS ############################################
### Trying to pass in parameter for my own dictionary ###
#data['parameters']['bowtie'] = {'param':'stepSize', 'value':100}
#data['parameters']['sam_to_bam'] = {'param':'genome', 'value':'hg18'}
try:
data['parameters'][wtool] = {'param':wparam, 'value':wvalue}
except ValueError:
print("TOOL ID ERROR:");
except IndexError:
print 'usage: %s key url workflow_id history step=src=dataset_id' % os.path.basename(sys.argv[0])