Mercurial > repos > mvdbeek > docker_scriptrunner
changeset 11:8571d1c719ee draft
planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ccb01d548a42beeacc01313218bff8c563da6fa9
| author | mvdbeek |
|---|---|
| date | Sat, 09 Jul 2016 07:41:09 -0400 |
| parents | ed7cf3f35799 |
| children | 81f85bafcc7c |
| files | scriptrunner.xml test-data/tf2_test.html test-data/tf2_test_in.xls test-data/tf2_test_out.xls test-data/tf2_test_runme.py |
| diffstat | 4 files changed, 68 insertions(+), 8 deletions(-) [+] |
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--- a/scriptrunner.xml Sat Jul 09 07:12:40 2016 -0400 +++ b/scriptrunner.xml Sat Jul 09 07:41:09 2016 -0400 @@ -1,5 +1,5 @@ -<tool id="docker_scriptrunner" name="Docker Scriptrunner" version="0.1.6"> - <description>Makes scripts into tools using Docker</description> +<tool id="docker_scriptrunner" name="docker scriptrunner" version="0.1.6"> + <description>Runs scripts using docker</description> <macros> <import>macros.xml</import> </macros> @@ -46,13 +46,8 @@ </configfiles> <inputs> <repeat name="input_files" title="Select input files"> - <param name="input" type="data" label="Select an input file from your history" optional="true" size="120" + <param name="input" format="data" type="data" label="Select an input file from your history" optional="true" size="120" help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/> - <param name="in_format" type="select" optional="true" multiple="true" label="Optional: Select the allowed input datatype(s) for your tool/script"> - <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> - <column name="value" index="0"/> - </options> - </param> </repeat> <repeat name="additional_parameters" title="Set additional parameters"> <param name="param_name" type="text" value="parameter_name" label="Choose a parameter name" size="20"> @@ -120,6 +115,18 @@ <filter>make_HTML == "yes"</filter> </data> </outputs> +<tests> + <test> + <param name='input_tab' value='tf2_test_in.xls' ftype='tabular' /> + <param name="make_TAB" value="yes" /> + <param name="make_HTML" value="yes" /> + <param name="out_format" value="tabular" /> + <param name="interpreter" value='python' /> + <param name="runme" value="tf2_test_runme.py"/> + <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/> + <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/> + </test> +</tests> <expand macro="help_macro" /> <expand macro="test_data_macro" /> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tf2_test.html Sat Jul 09 07:41:09 2016 -0400 @@ -0,0 +1,25 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy scriptrunner.py tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="toolFormBody"> + +<div class="infomessage">Galaxy Tool "script" run at 09/07/2016 11:37:54</div><br/> +<div class="toolFormTitle">script log output</div> +script_error.log is empty<br/> +<div class="toolFormTitle">Other log output</div> +/tmp/tmpG7m9zp/job_working_directory/000/1/dataset_2_files/script_runner.log is empty<br/> +<div class="toolFormTitle">All output files available for downloading</div> + +<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> + +<tr><td><a href="script.python">script.python</a></td><td>0 B</td></tr> +<tr class="odd_row"><td><a href="script_error.log">script_error.log</a></td><td>0 B</td></tr> +<tr><td><a href="script_runner.log">script_runner.log</a></td><td>100 B</td></tr> +</table></div><br/> +</div></body></html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tf2_test_in.xls Sat Jul 09 07:41:09 2016 -0400 @@ -0,0 +1,3 @@ +col1 col2 col3 +r11 r12 r13 +r21 r22 r23
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tf2_test_runme.py Sat Jul 09 07:41:09 2016 -0400 @@ -0,0 +1,25 @@ +# bog standard argparse for 3 possible comma separated lists +# followed by some silly reverse each row code provided as an example +# you're supposed to replace it with your great code.. +import argparse +import copy + +argp = argparse.ArgumentParser() +argp.add_argument('--INNAMES', default=None) +argp.add_argument('--INPATHS', default=None) +argp.add_argument('--OUTPATH', default=None) +argp.add_argument('--additional_parameters', default=[], action="append") +argp.add_argument('otherargs', nargs=argparse.REMAINDER) +args = argp.parse_args() +fout = open(args.OUTPATH, 'w') +sins = open(args.INPATHS.split(',')[0]).readlines() +for i, sin in enumerate(sins): + row = sin.strip().split('\t') + rrow = copy.copy(row) + lrow = len(row) + if (lrow > 1): + for j in range(lrow): + rrow[j] = row[lrow - j - 1] + fout.write('\t'.join(rrow)) + fout.write('\n') +fout.close()