Mercurial > repos > mvdbeek > docker_toolfactory

annotate DockerToolFactory.xml @ 2:fccbc118bb5b draft default tip

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planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
author mvdbeek
date Sat, 03 Oct 2015 08:59:09 -0400
parents f1efc9a69a40
children
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
1
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2 <tool id="rgTF" name="docker_tool_factory" version="0.1.4">
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3 <description>Makes scripts into tools using Docker</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="9.10">ghostscript</requirement>
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9 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
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10 <requirement type="package" version="1.3.1">docker-py</requirement>
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11 </requirements>
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12 <command interpreter="python"><![CDATA[
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13 DockerToolFactory.py --script_path "$runme" --interpreter "$interpreter"
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14 --tool_name "$tool_name" --user_email "$__user_email__"
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15 #if $generate_simple_output.make_TAB=="yes":
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16 --output_tab "$tab_file"
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17 #end if
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18 #if $makeMode.make_Tool=="yes":
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19 #if generate_simple_output.make_TAB=="yes":
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20 --output_format "$out_format"
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21 #end if
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22 --make_Tool "$makeMode.make_Tool"
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23 --tool_desc "$makeMode.tool_desc"
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24 --tool_version "$makeMode.tool_version"
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25 --new_tool "$new_tool"
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26 --help_text "$helpme"
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27 #if $make_HTML.value=="yes":
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28 --include_dependencies "${makeMode.include_deps}"
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29 #end if
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30 #end if
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31 #if $make_HTML.value=="yes":
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32 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
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33 #else:
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34 --output_dir "."
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35 #end if
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36 #if $additional_parameters != 'None':
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37 #for i in $additional_parameters:
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38 --additional_parameters
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39 "$i.param_name, $i.param_value"
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40 #end for
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41 #end if
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42 #if $input_files != 'None':
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43 --input_tab
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44 #for i in $input_files:
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45 $i.input
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46 #end for
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47 #for i in $input_files:
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48 --input_format
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49 #if str($i.in_format) == "None":
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50 "Any"
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51 #else
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52 "$i.in_format"
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53 #end if
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54 #end for
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55 #end if
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56 ]]>
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57 </command>
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58 <configfiles>
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59 <configfile name="runme">$dynScript</configfile>
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60 <configfile name="helpme">
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61 #if $makeMode.make_Tool == "yes":
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62 ${makeMode.help_text}
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63 #end if
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64 </configfile>
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65 </configfiles>
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66 <inputs>
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67 <repeat name="input_files" title="Select input files">
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68 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
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69 <param name="in_format" type="select" optional="true" multiple="true"
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70 label="Optional: Select the allowed input datatype(s) for your tool/script">
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71 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
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72 <column name="value" index="0"/>
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73 </options>
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74 </param>
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75 </repeat>
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76 <repeat name="additional_parameters" title="Set additional parameters">
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77 <param name="param_name" type="text" value="parameter_name" label="Choose a parameter name" size="20">
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78 <sanitizer invalid_char="">
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79 <valid initial="string.letters,string.digits">
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80 <add value="@_."/>
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81 </valid>
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82 >
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83 </sanitizer>
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84 </param>
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85 <param name="param_value" type="text" value="parameter_value" label="Enter a parameter value" size="50">
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86 <sanitizer>
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87 <valid initial="string.printable">
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88 </valid>
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89 <mapping initial="none"/>
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90 </sanitizer>
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91 </param>
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92 </repeat>
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93 <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs"
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94 size="60"
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95 help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
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96 <sanitizer invalid_char="">
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97 <valid initial="string.printable"/>
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98 </sanitizer>
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99 </param>
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100 <conditional name="makeMode">
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101 <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry"
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102 help="Ready to deploy securely!" size="60">
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103 <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
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104 <option value="" selected="true">No. Just run the script please</option>
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105 </param>
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106 <when value="yes">
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107 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses"
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108 type="text" value="0.01"
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109 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
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110 <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
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111 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)"/>
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112 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
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113 size="8x120" value="**What it Does**"
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114 help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html">
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115 <sanitizer>
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116 <valid initial="string.printable">
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117 </valid>
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118 <mapping initial="none"/>
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119 </sanitizer>
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120 </param>
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121 <param name="include_deps" type="select"
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122 label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
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123 help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
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124 <option value="">Rely on system ghostscript and graphicsmagick rather than include these as
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125 dependencies
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126 </option>
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127 <option value="yes" selected="true">Include dependencies so target installations will always work if
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128 HTML is being generated
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129 </option>
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130 </param>
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131
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132 </when>
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133 <when value="">
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134 </when>
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135 </conditional>
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136 <param name="out_format" type="text" value="txt" hidden="True"/>
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137 <param name="make_HTML" type="select"
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138 label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
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139 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
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140 <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
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141 <option value="" selected="true">No, no HTML output file thanks</option>
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142 </param>
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143 <conditional name="generate_simple_output">
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144 <param name="make_TAB" type="select"
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145 label="Create a new history output alongside the HTML file specified above"
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146 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
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147 <option value="yes" selected="true">My script writes to a new history output</option>
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148 <option value="no">I do not want a new history output file</option>
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149 </param>
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150 <when value="yes">
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151 <param name="out_format" type="select" label="Select the datatype that your tool/script produces"
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152 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" optional="True">
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153 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
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154 <column name="value" index="0"/>
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155 </options>
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156 </param>
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157 </when>
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158 <when value="no">
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159 <param name="out_format" type="text" value="txt" optional="True" hidden="True"/>
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160 </when>
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161 </conditional>
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162 <param name="interpreter" type="select" label="Select the interpreter for your code">
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163 <option value="Rscript" selected="true">Rscript</option>
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164 <option value="python">python</option>
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165 <option value="perl">perl</option>
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166 <option value="sh">sh</option>
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167 </param>
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168 <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True"
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169 size="8x120"
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170 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').">
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171 <sanitizer>
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172 <valid initial="string.printable">
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173 </valid>
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174 <mapping initial="none"/>
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175 </sanitizer>
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176 </param>
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177 </inputs>
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178 <outputs>
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179 <!-- <data format_source="input" name="tab_file" label="${tool_name}.${out_format}"> -->
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180 <data format_source="input" name="tab_file">
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181 <filter>generate_simple_output['make_TAB'] == "yes"</filter>
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182 <actions>
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183 <action type="format">
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184 <option type="from_param" name="out_format"/>
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185 </action>
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186 </actions>
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187 </data>
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188 <data format="html" name="html_file" label="${tool_name}.html">
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189 <filter>make_HTML == "yes"</filter>
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190 </data>
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191 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
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192 <filter>makeMode['make_Tool'] == "yes"</filter>
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193 </data>
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194 </outputs>
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195 <tests>
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196 <test>
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197 <param name="interpreter" value="Rscript"/>
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198 <param name="make_HTML" value="yes"/>
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199 <param name="generate_simple_output|makeTAB" value="no"/>
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200 <param name="out_format" value="txt"/>
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201 <param name="dynScript" value="for (i in 1:10) {; foo = runif(100); bar = rnorm(100); bar = foo + bar; pdf(&quot;anotherplot.pdf&quot;); plot(1,2); dev.off();}"/>
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202 <output name="html_file" file="html_output/My_dynamic_script_html.html" compare="diff"/>
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203 </test>
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204 </tests>
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205 <expand macro="help_macro"/>
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206 </tool>