Mercurial > repos > mvdbeek > docker_scriptrunner

annotate scriptrunner.xml @ 0:b6211faea403 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
author mvdbeek
date Fri, 08 Jul 2016 15:09:10 -0400
parents
children 8571d1c719ee
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
1 <tool id="docker_scriptrunner" name="Docker Scriptrunner" version="0.1.6">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
2 <description>Makes scripts into tools using Docker</description>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
3 <macros>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
4 <import>macros.xml</import>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
5 </macros>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
6 <requirements>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
7 <requirement type="package" version="0.4.0">docker-py</requirement>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
8 </requirements>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
9 <command>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
10 python "$__tool_directory__/scriptrunner.py"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
11 --script_path "$runme"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
12 --interpreter "$interpreter"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
13 --user_email "$__user_email__"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
14 #if $generate_simple_output.make_TAB=="yes":
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
15 --output_tab "$tab_file"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
16 #end if
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
17 #if $make_HTML.value=="yes":
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
18 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
19 #else:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
20 --output_dir "."
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
21 #end if
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
22 #if $additional_parameters != 'None':
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
23 #for i in $additional_parameters:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
24 --additional_parameters
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
25 "$i.param_name, $i.param_value"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
26 #end for
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
27 #end if
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
28 #if $input_files != 'None':
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
29 --input_tab
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
30 #for i in $input_files:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
31 $i.input
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
32 #end for
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
33 #for i in $input_files:
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
34 --input_format
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
35 #if str($i.in_format) == "None":
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
36 "Any"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
37 #else
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
38 "$i.in_format"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
39 #end if
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
40 #end for
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
41 #end if
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
42 --docker_image "$docker_image"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
43 </command>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
44 <configfiles>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
45 <configfile name="runme">$dynScript</configfile>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
46 </configfiles>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
47 <inputs>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
48 <repeat name="input_files" title="Select input files">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
49 <param name="input" type="data" label="Select an input file from your history" optional="true" size="120"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
50 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
51 <param name="in_format" type="select" optional="true" multiple="true" label="Optional: Select the allowed input datatype(s) for your tool/script">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
52 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
53 <column name="value" index="0"/>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
54 </options>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
55 </param>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
56 </repeat>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
57 <repeat name="additional_parameters" title="Set additional parameters">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
58 <param name="param_name" type="text" value="parameter_name" label="Choose a parameter name" size="20">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
59 <sanitizer invalid_char="">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
60 <valid initial="string.letters,string.digits"><add value="@_."/></valid>>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
61 </sanitizer>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
62 </param>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
63 <param name="param_value" type="text" value="parameter_value" label="Enter a parameter value" size="50">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
64 <sanitizer>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
65 <valid initial="string.printable">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
66 </valid>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
67 <mapping initial="none"/>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
68 </sanitizer>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
69 </param>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
70 </repeat>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
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"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
72 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
73 <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
74 <option value="" selected="true">No, no HTML output file thanks</option>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
75 </param>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
76 <conditional name="generate_simple_output">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
77 <param name="make_TAB" type="select" label="Create a new history output alongside the HTML file specified above"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
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">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
79 <option value="yes" selected="true">My script writes to a new history output</option>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
80 <option value="">I do not want a new history output file</option>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
81 </param>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
82 <when value="yes">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
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">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
84 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
85 <column name="value" index="0"/>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
86 </options>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
87 </param>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
88 </when>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
89 <when value="">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
90 </when>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
91 </conditional>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
92 <param name="interpreter" type="select" label="Select the interpreter for your code">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
93 <option value="Rscript" selected="true">Rscript</option>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
94 <option value="python">python</option>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
95 <option value="perl">perl</option>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
96 <option value="sh">sh</option>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
97 </param>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
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">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
99 <options from_data_table="docker_scriptrunner_images"/>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
100 </param>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
101 <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True" size="8x120"
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
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').">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
103 <sanitizer>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
104 <valid initial="string.printable">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
105 </valid>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
106 <mapping initial="none"/>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
107 </sanitizer>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
108 </param>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
109 </inputs>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
110 <outputs>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
111 <data format_source="input" name="tab_file">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
112 <filter>generate_simple_output['make_TAB'] == "yes"</filter>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
113 <actions>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
114 <action type="format">
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
115 <option type="from_param" name="generate_simple_output.out_format" />
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
116 </action>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
117 </actions>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
118 </data>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
119 <data format="html" name="html_file" >
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
120 <filter>make_HTML == "yes"</filter>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
121 </data>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
122 </outputs>
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
123 <expand macro="help_macro" />
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
124 <expand macro="test_data_macro" />
b6211faea403 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
mvdbeek
parents:
diff changeset
125 </tool>