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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
author mvdbeek
date Sun, 22 Jul 2018 13:38:01 -0400
parents 315a7e9ed6eb
children
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1:315a7e9ed6eb 2:495946ffc2d6
1 <tool id="docker_scriptrunner" name="docker scriptrunner" version="1.1.6"> 1 <tool id="docker_scriptrunner" name="docker scriptrunner" version="0.1.7">
2 <description>Runs scripts using docker</description> 2 <description>Runs scripts using docker</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.8.1">docker-py</requirement> 7 <requirement type="package" version="3.4.1">docker-py</requirement>
8 </requirements> 8 </requirements>
9 <command> 9 <command detect_errors="exit_code">
10 python "$__tool_directory__/scriptrunner.py" 10 python '$__tool_directory__/scriptrunner.py'
11 --script_path "$runme" 11 --script_path '$runme'
12 --interpreter "$interpreter" 12 --interpreter '$interpreter'
13 --user_email "$__user_email__" 13 --user_email '$__user_email__'
14 #if $generate_simple_output.make_TAB=="yes": 14 #if $generate_simple_output.make_file=="yes":
15 --output_tab "$tab_file" 15 --output_file "$output_file"
16 #end if 16 #end if
17 #if $make_HTML.value=="yes": 17 #if $make_HTML.value=="yes":
18 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" 18 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
19 #else: 19 #else:
20 --output_dir "." 20 --output_dir "."
21 #end if 21 #end if
22 #if $additional_parameters != 'None': 22 #if $additional_parameters != 'None':
23 #for i in $additional_parameters: 23 #for i in $additional_parameters:
24 --additional_parameters 24 --additional_parameters
25 "$i.param_name, $i.param_value" 25 "$i.param_name, $i.param_value"
26 #end for 26 #end for
27 #end if 27 #end if
28 #if $input_files != 'None': 28 #if $input_files != 'None':
29 --input_tab 29 --input_file
30 #for i in $input_files: 30 #for i in $input_files:
31 $i.input 31 $i.input
32 #end for 32 #end for
33 #for i in $input_files: 33 #for i in $input_files:
34 --input_format "Any" 34 --input_format "Any"
35 #end for 35 #end for
36 #end if 36 #end if
37 --docker_image "$docker_image" 37 --docker_image "$docker_image"
38 </command> 38 </command>
39 <configfiles> 39 <configfiles>
40 <configfile name="runme">$dynScript</configfile> 40 <configfile name="runme">$dynScript</configfile>
41 </configfiles> 41 </configfiles>
42 <inputs> 42 <inputs>
62 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output"> 62 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
63 <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option> 63 <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
64 <option value="" selected="true">No, no HTML output file thanks</option> 64 <option value="" selected="true">No, no HTML output file thanks</option>
65 </param> 65 </param>
66 <conditional name="generate_simple_output"> 66 <conditional name="generate_simple_output">
67 <param name="make_TAB" type="select" label="Create a new history output alongside the HTML file specified above" 67 <param name="make_file" type="select" label="Create a new history output alongside the HTML file specified above"
68 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes"> 68 help="This is useful if your script creates a single new file that you want to appear in the history after the tool executes">
69 <option value="yes" selected="true">My script writes to a new history output</option> 69 <option value="yes" selected="true">My script writes to a new history output</option>
70 <option value="">I do not want a new history output file</option> 70 <option value="">I do not want a new history output file</option>
71 </param> 71 </param>
72 <when value="yes"> 72 <when value="yes">
73 <param name="out_format" type="select" label="Select the datatype that your tool/script produces" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml"> 73 <param name="out_format" type="select" label="Select the datatype that your tool/script produces" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
87 </param> 87 </param>
88 <param help="The script you are pasting will be run in this image. Make sure it contains the necessary tools" label="Select a docker image" name="docker_image" type="select"> 88 <param help="The script you are pasting will be run in this image. Make sure it contains the necessary tools" label="Select a docker image" name="docker_image" type="select">
89 <options from_data_table="docker_scriptrunner_images"/> 89 <options from_data_table="docker_scriptrunner_images"/>
90 </param> 90 </param>
91 <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True" size="8x120" 91 <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True" size="8x120"
92 help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None')."> 92 help="Script must deal with two command line parameters: Path to input file path (or 'None' if none selected) and path to output tabular history file (or 'None').">
93 <sanitizer> 93 <sanitizer>
94 <valid initial="string.printable"> 94 <valid initial="string.printable">
95 </valid> 95 </valid>
96 <mapping initial="none"/> 96 <mapping initial="none"/>
97 </sanitizer> 97 </sanitizer>
98 </param> 98 </param>
99 </inputs> 99 </inputs>
100 <outputs> 100 <outputs>
101 <data format_source="input" name="tab_file"> 101 <data format_source="input" name="output_file">
102 <filter>generate_simple_output['make_TAB'] == "yes"</filter> 102 <filter>generate_simple_output['make_file'] == "yes"</filter>
103 <actions> 103 <actions>
104 <action type="format"> 104 <action type="format">
105 <option type="from_param" name="generate_simple_output.out_format" /> 105 <option type="from_param" name="generate_simple_output.out_format" />
106 </action> 106 </action>
107 </actions> 107 </actions>
110 <filter>make_HTML == "yes"</filter> 110 <filter>make_HTML == "yes"</filter>
111 </data> 111 </data>
112 </outputs> 112 </outputs>
113 <tests> 113 <tests>
114 <test> 114 <test>
115 <param name='input_tab' value='tf2_test_in.xls' ftype='tabular' /> 115 <param name="input_file" value="tf2_test_in.xls" ftype="tabular"/>
116 <param name="make_TAB" value="yes" /> 116 <param name="make_file" value="yes"/>
117 <param name="make_HTML" value="yes" /> 117 <param name="make_HTML" value="yes"/>
118 <param name="out_format" value="tabular" /> 118 <param name="out_format" value="tabular"/>
119 <param name="interpreter" value='python' /> 119 <param name="interpreter" value="python"/>
120 <param name="runme" value="tf2_test_runme.py"/> 120 <param name="runme" value="tf2_test_runme.py"/>
121 <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/> 121 <output name="output_file" file="tf2_test_out.xls" compare="diff" lines_diff="10"/>
122 <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/> 122 <output name="html_file" file="tf2_test.html" compare="diff" lines_diff="10"/>
123 </test> 123 </test>
124 </tests> 124 </tests>
125 <expand macro="help_macro" /> 125 <expand macro="help_macro" />
126 <expand macro="test_data_macro" /> 126 <expand macro="test_data_macro" />
127 </tool> 127 </tool>