| Previous changeset 28:501f39987c9b (2019-08-02) Next changeset 30:0ad6fda90f41 (2019-08-29) |
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Commit message:
planemo upload commit c56eddc745b70354680c2a2b605840ed72bb98ef |
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modified:
README.md rpviz.xml toolRPViz.py |
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removed:
rpVisualizer.xml toolVisualizer.py |
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| diff -r 501f39987c9b -r d854b21ada0c README.md --- a/README.md Fri Aug 02 05:27:32 2019 -0400 +++ b/README.md Wed Aug 07 05:13:27 2019 -0400 |
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| @@ -36,4 +36,13 @@ - [x] Use planemo in order to create a repository in the toolshed. - [x] Register in the toolshed. - [x] Install in the Galaxy container from the toolshed. -- [ ] Write documentiation about the design specifications sheet. \ No newline at end of file +- [ ] Write documentiation about the design specifications sheet. + +## galaxy_RPViz + +A tool to visualize pathways by querying an RPViz server. + +`RPViz` returns an interactive HTML file that requires javascript. The `RPViz` tool has to be included in the [Galaxy whitelist](https://docs.galaxyproject.org/en/latest/admin/config.html). + + + |
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| diff -r 501f39987c9b -r d854b21ada0c rpVisualizer.xml --- a/rpVisualizer.xml Fri Aug 02 05:27:32 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,25 +0,0 @@ -<tool id="rpviz2" name="rpVisualizer" version="0.1.0" python_template_version="3.5"> - <description>Pathway visualizer</description> - <requirements> - <requirement type="package">python-libsbml</requirement> - <requirement type="package">networkx</requirement> - <requirement type="package">beautifulsoup4</requirement> - <requirement type="package">rdkit</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - git clone https://github.com/pablocarb/rpviz.git $__tool_directory__/rpviz; - cd $__tool_directory__/rpviz; git pull; cd ..; - cd $__tool_directory__; - echo `which python` > $__tool_directory__/info.log; - PYTHONPATH="$__tool_directory__" python $__tool_directory__/toolVisualizer.py $input1 $output1 - ]]></command> - <inputs> - <param type="data" name="input1" format="xml" /> - </inputs> - <outputs> - <data name="output1" format="html" from_work_dir="out.html" /> - </outputs> - <help><![CDATA[ - python3 toolVisualizer.py inputfile outputfile - ]]></help> -</tool> |
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| diff -r 501f39987c9b -r d854b21ada0c rpviz.xml --- a/rpviz.xml Fri Aug 02 05:27:32 2019 -0400 +++ b/rpviz.xml Wed Aug 07 05:13:27 2019 -0400 |
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| @@ -4,7 +4,7 @@ <requirement type="package">requests</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - python $__tool_directory__/toolRPViz.py $input1 $output1 -server $server + python $__tool_directory__/toolRPViz.py $input1 $output1 -server $server --input_format $input2 --selenzyme_table $input3 --outfolder $output1.extra_files_path ]]></command> <inputs> <param type="data" name="input1" format="tar" label="Input pathways"/> @@ -19,6 +19,6 @@ <data name="output1" format="html" from_work_dir="out.html" /> </outputs> <help><![CDATA[ - python3 toolRPViz.py [server SERVER] inputfile outputfile --input_format $input2 --selenzyme_table --outfolder $outputfile.extra_files_path + RPViz tool. ]]></help> </tool> |
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| diff -r 501f39987c9b -r d854b21ada0c toolRPViz.py --- a/toolRPViz.py Fri Aug 02 05:27:32 2019 -0400 +++ b/toolRPViz.py Wed Aug 07 05:13:27 2019 -0400 |
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| @@ -13,6 +13,7 @@ import os import json import tarfile +import shutil def arguments(): parser = argparse.ArgumentParser(description='toolRPViz: Pathway visualizer. Pablo Carbonell, SYNBIOCHEM, 2019') @@ -39,13 +40,13 @@ print( res ) def pathwayUpload( arg ): - files = { 'file': open(arg.infile, 'rb' ) } + # Post request data = {'selenzyme_table': arg.selenzyme_table, 'input_format': arg.input_format} + files = { 'file': open(arg.infile, 'rb' ), 'data': ('data.json', json.dumps(data)) } print('Sending query to '+arg.server) - r=requests.post( arg.server+'/Query',files=files,data=data ) - if arg.outfolder is None: - arg.outfolder = os.path.dirname( arg.outfile ) - if not os.path.exists(outfolder): + r=requests.post(arg.server+'/Query',files=files) + # Read response + if not os.path.exists(arg.outfolder): os.mkdir(arg.outfolder) outtar = os.path.join( arg.outfolder, 'out.tar' ) open(outtar,'wb').write( r.content ) @@ -53,7 +54,7 @@ tar = tarfile.open(outtar) tar.extractall(path=arg.outfolder) html = os.path.join( arg.outfolder, 'index.html' ) - shutil.cp( html, arg.outfile ) + shutil.copy( html, arg.outfile ) print( 'Files extracted' ) |
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| diff -r 501f39987c9b -r d854b21ada0c toolVisualizer.py --- a/toolVisualizer.py Fri Aug 02 05:27:32 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,31 +0,0 @@ -#!/usr/bin/env python3 -# -*- coding: utf-8 -*- -""" -Created on Mar 19 - -@author: Pablo Carbonell -@description: Pathway visualizer. - -""" -import argparse -import os -from rpviz.main import run - -def arguments(): - parser = argparse.ArgumentParser(description='toolVisualizer: Pathway visualizer. Pablo Carbonell, SYNBIOCHEM, 2019') - parser.add_argument('infile', - help='Input SBML pathway file.') - parser.add_argument('outfile', - help='Output HTML file.') - return parser - -def runVisualizer( infile, outfile ): - run(infile,outfile) - - - -if __name__ == "__main__": - parser = arguments() - arg = parser.parse_args() - assert os.path.exists(arg.infile) - runVisualizer( arg.infile, arg.outfile ) |