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comparison scriptrunner.xml @ 0:21d312776891 draft

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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
author mvdbeek
date Sat, 09 Jul 2016 16:57:13 -0400
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-1:000000000000 0:21d312776891
1 <tool id="docker_scriptrunner" name="docker scriptrunner" version="0.1.6">
2 <description>Runs scripts using docker</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="0.4.0">docker-py</requirement>
8 </requirements>
9 <command>
10 python "$__tool_directory__/scriptrunner.py"
11 --script_path "$runme"
12 --interpreter "$interpreter"
13 --user_email "$__user_email__"
14 #if $generate_simple_output.make_TAB=="yes":
15 --output_tab "$tab_file"
16 #end if
17 #if $make_HTML.value=="yes":
18 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
19 #else:
20 --output_dir "."
21 #end if
22 #if $additional_parameters != 'None':
23 #for i in $additional_parameters:
24 --additional_parameters
25 "$i.param_name, $i.param_value"
26 #end for
27 #end if
28 #if $input_files != 'None':
29 --input_tab
30 #for i in $input_files:
31 $i.input
32 #end for
33 #for i in $input_files:
34 --input_format "Any"
35 #end for
36 #end if
37 --docker_image "$docker_image"
38 </command>
39 <configfiles>
40 <configfile name="runme">$dynScript</configfile>
41 </configfiles>
42 <inputs>
43 <repeat name="input_files" title="Select input files">
44 <param name="input" format="data" type="data" label="Select an input file from your history" optional="true" size="120"
45 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
46 </repeat>
47 <repeat name="additional_parameters" title="Set additional parameters">
48 <param name="param_name" type="text" value="parameter_name" label="Choose a parameter name" size="20">
49 <sanitizer invalid_char="">
50 <valid initial="string.letters,string.digits"><add value="@_."/></valid>>
51 </sanitizer>
52 </param>
53 <param name="param_value" type="text" value="parameter_value" label="Enter a parameter value" size="50">
54 <sanitizer>
55 <valid initial="string.printable">
56 </valid>
57 <mapping initial="none"/>
58 </sanitizer>
59 </param>
60 </repeat>
61 <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
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>
64 <option value="" selected="true">No, no HTML output file thanks</option>
65 </param>
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"
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">
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>
71 </param>
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">
74 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
75 <column name="value" index="0"/>
76 </options>
77 </param>
78 </when>
79 <when value="">
80 </when>
81 </conditional>
82 <param name="interpreter" type="select" label="Select the interpreter for your code">
83 <option value="Rscript" selected="true">Rscript</option>
84 <option value="python">python</option>
85 <option value="perl">perl</option>
86 <option value="sh">sh</option>
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">
89 <options from_data_table="docker_scriptrunner_images"/>
90 </param>
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').">
93 <sanitizer>
94 <valid initial="string.printable">
95 </valid>
96 <mapping initial="none"/>
97 </sanitizer>
98 </param>
99 </inputs>
100 <outputs>
101 <data format_source="input" name="tab_file">
102 <filter>generate_simple_output['make_TAB'] == "yes"</filter>
103 <actions>
104 <action type="format">
105 <option type="from_param" name="generate_simple_output.out_format" />
106 </action>
107 </actions>
108 </data>
109 <data format="html" name="html_file" >
110 <filter>make_HTML == "yes"</filter>
111 </data>
112 </outputs>
113 <tests>
114 <test>
115 <param name='input_tab' value='tf2_test_in.xls' ftype='tabular' />
116 <param name="make_TAB" value="yes" />
117 <param name="make_HTML" value="yes" />
118 <param name="out_format" value="tabular" />
119 <param name="interpreter" value='python' />
120 <param name="runme" value="tf2_test_runme.py"/>
121 <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/>
122 <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/>
123 </test>
124 </tests>
125 <expand macro="help_macro" />
126 <expand macro="test_data_macro" />
127 </tool>