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comparison scriptrunner.xml @ 0:b6211faea403 draft

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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
author mvdbeek
date Fri, 08 Jul 2016 15:09:10 -0400
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-1:000000000000 0:b6211faea403
1 <tool id="docker_scriptrunner" name="Docker Scriptrunner" version="0.1.6">
2 <description>Makes scripts into tools 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 $input_files:
34 --input_format
35 #if str($i.in_format) == "None":
36 "Any"
37 #else
38 "$i.in_format"
39 #end if
40 #end for
41 #end if
42 --docker_image "$docker_image"
43 </command>
44 <configfiles>
45 <configfile name="runme">$dynScript</configfile>
46 </configfiles>
47 <inputs>
48 <repeat name="input_files" title="Select input files">
49 <param name="input" type="data" label="Select an input file from your history" optional="true" size="120"
50 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
51 <param name="in_format" type="select" optional="true" multiple="true" label="Optional: Select the allowed input datatype(s) for your tool/script">
52 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
53 <column name="value" index="0"/>
54 </options>
55 </param>
56 </repeat>
57 <repeat name="additional_parameters" title="Set additional parameters">
58 <param name="param_name" type="text" value="parameter_name" label="Choose a parameter name" size="20">
59 <sanitizer invalid_char="">
60 <valid initial="string.letters,string.digits"><add value="@_."/></valid>>
61 </sanitizer>
62 </param>
63 <param name="param_value" type="text" value="parameter_value" label="Enter a parameter value" size="50">
64 <sanitizer>
65 <valid initial="string.printable">
66 </valid>
67 <mapping initial="none"/>
68 </sanitizer>
69 </param>
70 </repeat>
71 <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"
72 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
73 <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
74 <option value="" selected="true">No, no HTML output file thanks</option>
75 </param>
76 <conditional name="generate_simple_output">
77 <param name="make_TAB" type="select" label="Create a new history output alongside the HTML file specified above"
78 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
79 <option value="yes" selected="true">My script writes to a new history output</option>
80 <option value="">I do not want a new history output file</option>
81 </param>
82 <when value="yes">
83 <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">
84 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
85 <column name="value" index="0"/>
86 </options>
87 </param>
88 </when>
89 <when value="">
90 </when>
91 </conditional>
92 <param name="interpreter" type="select" label="Select the interpreter for your code">
93 <option value="Rscript" selected="true">Rscript</option>
94 <option value="python">python</option>
95 <option value="perl">perl</option>
96 <option value="sh">sh</option>
97 </param>
98 <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">
99 <options from_data_table="docker_scriptrunner_images"/>
100 </param>
101 <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True" size="8x120"
102 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').">
103 <sanitizer>
104 <valid initial="string.printable">
105 </valid>
106 <mapping initial="none"/>
107 </sanitizer>
108 </param>
109 </inputs>
110 <outputs>
111 <data format_source="input" name="tab_file">
112 <filter>generate_simple_output['make_TAB'] == "yes"</filter>
113 <actions>
114 <action type="format">
115 <option type="from_param" name="generate_simple_output.out_format" />
116 </action>
117 </actions>
118 </data>
119 <data format="html" name="html_file" >
120 <filter>make_HTML == "yes"</filter>
121 </data>
122 </outputs>
123 <expand macro="help_macro" />
124 <expand macro="test_data_macro" />
125 </tool>