annotate env/lib/python3.9/site-packages/galaxy/tool_util/xsd/galaxy.xsd @ 0:4f3585e2f14b draft default tip

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date Mon, 22 Mar 2021 18:12:50 +0000
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <xs:schema
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3 xmlns:xs="http://www.w3.org/2001/XMLSchema"
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4 xmlns:gxdocs="http://galaxyproject.org/xml/1.0"
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5 elementFormDefault="qualified"
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6 attributeFormDefault="unqualified"
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7 >
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8 <xs:annotation>
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9 <xs:appinfo>Galaxy Schema</xs:appinfo>
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10 <xs:documentation xml:lang="en">A Galaxy XML tool wrapper</xs:documentation>
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11 </xs:annotation>
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12
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13 <xs:element name="tool">
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14 <xs:annotation gxdocs:best_practices="tools">
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15 <xs:documentation xml:lang="en"><![CDATA[
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16 The outer-most tag set of tool XML files. Attributes on this tag apply to the
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17 tool as a whole.
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18
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19 ### Examples
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20
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21 A normal tool:
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22
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23 ```xml
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24 <tool id="seqtk_seq"
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25 name="Convert FASTQ to FASTA"
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26 version="1.0.0"
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27 profile="16.04"
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28 >
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29 ```
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30
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31 A ``data_source`` tool contains a few more relevant attributes.
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32
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33 ```xml
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34 <tool id="ucsc_table_direct1"
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35 name="UCSC Main"
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36 version="1.0.0"
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37 hidden="false"
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38 profile="16.01"
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39 tool_type="data_source"
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40 URL_method="post">
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41 ```
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42 ]]></xs:documentation>
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43 </xs:annotation>
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44 <xs:complexType>
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45 <xs:all>
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46 <!-- TODO: Move the anyType further into macros def... -->
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47 <xs:element name="macros" type="Macros" minOccurs="0"/>
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48 <xs:element name="edam_topics" type="EdamTopics" minOccurs="0"/>
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49 <xs:element name="edam_operations" type="EdamOperations" minOccurs="0"/>
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50 <xs:element name="xrefs" type="xrefs" minOccurs="0" />
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51 <xs:element name="creator" type="Creator" minOccurs="0" />
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52 <xs:element name="requirements" type="Requirements" minOccurs="0"/>
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53 <xs:element name="entry_points" type="EntryPoints" minOccurs="0" maxOccurs="1" />
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54 <xs:element name="description" type="xs:string" minOccurs="0">
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55 <xs:annotation gxdocs:best_practices="tool-descriptions">
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56 <xs:documentation xml:lang="en"><![CDATA[The value is displayed in
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57 the tool menu immediately following the hyperlink for the tool (based on the
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58 ``name`` attribute of the ``<tool>`` tag set described above).
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59
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60 ### Example
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61
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62 ```xml
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63 <description>table browser</description>
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64 ```
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65 ]]></xs:documentation>
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66 </xs:annotation>
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67 </xs:element>
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68 <xs:element name="parallelism" type="Parallelism" minOccurs="0"/>
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69 <xs:element name="version_command" type="VersionCommand" minOccurs="0">
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70 </xs:element>
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71 <xs:element name="action" type="ToolAction" minOccurs="0" maxOccurs="1" />
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72 <xs:element name="environment_variables" type="EnvironmentVariables" minOccurs="0" maxOccurs="1"/>
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73 <xs:element name="command" type="Command" minOccurs="0" maxOccurs="1"/>
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74 <xs:element name="expression" type="Expression" minOccurs="0" maxOccurs="1"/>
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75 <xs:element name="request_param_translation" type="RequestParameterTranslation" minOccurs="0"/>
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76 <xs:element name="configfiles" type="ConfigFiles" minOccurs="0"/>
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77 <xs:element name="outputs" type="Outputs" minOccurs="0"/>
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78 <xs:element name="inputs" type="Inputs" minOccurs="0"/>
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79 <xs:element name="tests" type="Tests" minOccurs="0"/>
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80 <xs:element name="stdio" type="Stdio" minOccurs="0"/>
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81 <xs:element name="help" type="xs:string" minOccurs="0">
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82 <xs:annotation gxdocs:best_practices="help-tag">
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83 <xs:documentation xml:lang="en"><![CDATA[This tag set includes all of the necessary details of how to use the tool. This tag set should be included as the next to the last tag set, before citations, in the tool config. Tool help is written in reStructuredText. Included here is only an overview of a subset of features. For more information see [here](https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html).
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84
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85 tag | details
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86 --- | -------
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87 ``.. class:: warningmark`` | a yellow warning symbol
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88 ``.. class:: infomark`` | a blue information symbol
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89 ``.. image:: path-of-the-file.png :height: 500 :width: 600`` | insert a png file of height 500 and width 600 at this position |
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90 ``**bold**`` | bold
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91 ``*italic*`` | italic
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92 ``*`` | list
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93 ``-`` | list
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94 ``::`` | paragraph
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95 ``-----`` | a horizontal line
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96
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97 ### Examples
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98
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99 Show a warning sign to remind users that this tool accept fasta format files only, followed by an example of the query sequence and a figure.
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100
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101 ```xml
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102 <help>
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103
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104 .. class:: warningmark
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105
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106 '''TIP''' This tool requires *fasta* format.
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107
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108 ----
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109
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110 '''Example'''
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111
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112 Query sequence::
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113 >seq1
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114 ATCG...
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115
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116 .. image:: my_figure.png
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117 :height: 500
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118 :width: 600
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119
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120 </help>
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121 ```
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122
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123 ]]></xs:documentation>
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124 </xs:annotation>
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125 </xs:element>
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126 <xs:element name="code" type="Code" minOccurs="0"/>
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127 <xs:element name="uihints" type="UIhints" minOccurs="0"/>
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128 <xs:element name="options" type="Options" minOccurs="0"/>
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129 <xs:element name="trackster_conf" type="TracksterConf" minOccurs="0"/>
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130 <xs:element name="citations" type="Citations" minOccurs="0"/>
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131 </xs:all>
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132 <xs:attribute name="id" type="xs:string" use="required">
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133 <xs:annotation gxdocs:best_practices="tool-ids">
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134 <xs:documentation xml:lang="en">Must be unique across all tools;
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135 should be lowercase and contain only letters, numbers, and underscores.
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136 It allows for tool versioning and metrics of the number of times a tool is used,
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137 among other things.</xs:documentation>
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138 </xs:annotation>
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139 </xs:attribute>
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140 <xs:attribute name="name" type="xs:string" use="required">
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141 <xs:annotation gxdocs:best_practices="tool-names">
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142 <xs:documentation xml:lang="en">This string is what is displayed as a
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143 hyperlink in the tool menu.</xs:documentation>
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144 </xs:annotation>
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145 </xs:attribute>
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146 <xs:attribute name="version" type="xs:string" default="1.0.0">
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147 <xs:annotation gxdocs:best_practices="tool-versions">
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148 <xs:documentation xml:lang="en">This string allows for tool versioning
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149 and should be increased with each new version of the tool. The value should
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150 follow the [PEP 440](https://www.python.org/dev/peps/pep-0440/) specification.
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151 It defaults to ``1.0.0`` if it is not included in the tag.</xs:documentation>
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152 </xs:annotation>
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153 </xs:attribute>
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154 <xs:attribute name="hidden" type="PermissiveBoolean" default="false">
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155 <xs:annotation>
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156 <xs:documentation xml:lang="en">Allows for tools to be loaded upon
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157 server startup, but not displayed in the tool menu. This attribute should be
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158 applied in the toolbox configuration instead and so should be considered
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159 deprecated.
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160 </xs:documentation>
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161 </xs:annotation>
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162 </xs:attribute>
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163 <xs:attribute name="display_interface" type="PermissiveBoolean">
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164 <xs:annotation>
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165 <xs:documentation xml:lang="en">Disable the display the tool's
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166 graphical tool form by setting this to ``false``.</xs:documentation>
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167 </xs:annotation>
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168 </xs:attribute>
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169 <xs:attribute name="tool_type" type="ToolTypeType">
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170 <xs:annotation>
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171 <xs:documentation xml:lang="en">Allows for certain framework
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172 functionality to be performed on certain types of tools. Normal tools that execute
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173 typical command-line jobs do not need to specify this, special kinds of tools such
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174 as [Data Source](https://galaxyproject.org/admin/internals/data-sources/) and
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175 [Data Manager](https://galaxyproject.org/admin/tools/data-managers/) tools should
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176 set this to have values such as ``data_source`` or ``manage_data``.</xs:documentation>
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177 </xs:annotation>
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178 </xs:attribute>
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179 <xs:attribute name="profile" type="xs:string">
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180 <xs:annotation>
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181 <xs:documentation xml:lang="en">This string specifies the minimum Galaxy
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182 version that should be required to run this tool. Certain legacy behaviors such
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183 as using standard error content to detect errors instead of exit code are disabled
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184 automatically if profile is set to any version newer than ``16.01``, such as
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185 ``16.04``.
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186
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187 16.04
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188
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189 - Disable implicit extra file collection. All dynamic extra file collection requires a `discover_datasets` tag.
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190 - Disable `format="input"` and require explicit metadata targets (`metadata_source`, `format_source`).
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191 - Disable `interpreter` use `$__tool_directory__`.
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192 - Disable `$param_file` use `configfile`
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193 - Disable default tool version of 1.0.0.
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194 - Use non zero exit code as default stdio error condition (before non-empty stderr).
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195
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196 18.01
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197
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198 - Use a separate home directory for each job.
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199 - Introduce `provided_metadata_style` with default `"default"` before `"legacy"`.
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200
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201 18.09
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202
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203 - References to other inputs need to be fully qualified by using `|`.
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204 - Do not allow provided but illegal default values.
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205 - Do not use Galaxy python environment for `manage_data` tools.
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206
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207 19.05
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208
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209 - Change default Python version from 2.7 to 3.5
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210
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211 20.05
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212
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213 - json config files:
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214 - unselected optional `select` and `data_column` parameters get `None` instead of `"None"`
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215 - multiple `select` and `data_column` parameters are lists (before comma separated string)
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216
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217 20.09
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218
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219 - Exit immediately if a command exits with a non-zero status (`set -e`)
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220 - Assume sort order for collection elements
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221 </xs:documentation>
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222 </xs:annotation>
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223 </xs:attribute>
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224 <xs:attribute name="license" type="xs:string">
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225 <xs:annotation>
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226 <xs:documentation xml:lang="en">This string specifies any full URI or a
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227 a short SPDX (https://spdx.org/licenses/) identifier for a license for this tool
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228 wrapper. The tool wrapper version can be indepedent of the underlying tool. This
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229 license covers the tool XML and associated scripts shipped with the tool.
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230
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231 This is interpreted as a schema.org license attribute (see also https://schema.org/license).
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232 </xs:documentation>
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233 </xs:annotation>
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234 </xs:attribute>
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235 <xs:attribute name="python_template_version" type="xs:float">
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236 <xs:annotation>
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237 <xs:documentation xml:lang="en">This string specifies the minimum Python
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238 version that is able to fill the Cheetah sections of the tool. If unset defaults
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239 to 2.7 if the profile is older than 19.05, otherwise defaults to 3.5. Galaxy will
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240 attempt to convert Python statements in Cheetah sections using [future](http://python-future.org/)
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241 if Galaxy is run on Python 3 and ``python_template_version`` is below 3.</xs:documentation>
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242 </xs:annotation>
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243 </xs:attribute>
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244 <xs:attribute name="workflow_compatible" type="xs:boolean" default="true">
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245 <xs:annotation>
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246 <xs:documentation xml:lang="en">This attribute indicates if
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247 this tool is usable within a workflow (defaults to ``true`` for normal tools and
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248 ``false`` for data sources).</xs:documentation>
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249 </xs:annotation>
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250 </xs:attribute>
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251 <xs:attribute name="URL_method" type="URLmethodType">
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252 <xs:annotation>
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253 <xs:documentation xml:lang="en">Only used if ``tool_type`` attribute value
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254 is ``data_source`` - this attribute defines the HTTP request method to use when
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255 communicating with an external data source application (the default is ``get``).</xs:documentation>
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256 </xs:annotation>
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257 </xs:attribute>
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258 </xs:complexType>
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259 </xs:element>
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260
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261 <xs:complexType name="Macros">
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262 <xs:annotation>
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263 <xs:documentation xml:lang="en">Frequently, tools may require the same XML
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264 fragments be repeated in a file (for instance similar conditional branches,
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265 repeated options, etc...) or among tools in the same repository. Galaxy tools
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266 have a macro system to address this problem.
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267
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268 For more information, see [planemo documentation](https://planemo.readthedocs.io/en/latest/writing_advanced.html#macros-reusable-elements)</xs:documentation>
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269 </xs:annotation>
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270 <xs:sequence>
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271 <xs:element name="import" type="MacroImportType" minOccurs="0" maxOccurs="unbounded">
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272 <xs:annotation>
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273 <xs:documentation xml:lang="en"><![CDATA[
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274 The ``import`` element allows specifying an XML file containing shared macro definitions that can then
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275 be reused by all the tools contained in the same directory/repository.
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276
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277 Example:
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278 ````
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279 <macros>
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280 <import>macros.xml</import>
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281 </macros>
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282 ````]]>
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283 </xs:documentation>
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284 </xs:annotation>
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285 </xs:element>
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286 <xs:element name="token" type="xs:anyType" minOccurs="0" maxOccurs="unbounded">
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287 <xs:annotation>
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288 <xs:documentation xml:lang="en"><![CDATA[
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289 The ``token`` element defines a value, like a constant, that can then be replaced anywhere in any tool importing the token.
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290
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291 Definition example:
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292 ````
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293 <macros>
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294 <token name="@TOOL_VERSION@">1.0.0</token>
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295 </macros>
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296 ````
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297
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298 Usage example:
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299 ````
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300 <requirements>
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301 <requirement type="package" version="@TOOL_VERSION@">mypackage</requirement>
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302 </requirements>
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303 ````]]>
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304 </xs:documentation>
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305 </xs:annotation>
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306 </xs:element>
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307 <xs:element name="xml" type="xs:anyType" minOccurs="0" maxOccurs="unbounded">
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308 <xs:annotation>
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309 <xs:documentation xml:lang="en">
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310 <![CDATA[
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311 The ``xml`` element, inside macros, allows defining a named XML fragment that can be reused (expanded) anywhere in the tool or tools that use the macro.
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312
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313 Definition example:
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314 ````
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315 <macros>
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316 <xml name="citations">
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317 <citations>
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318 ....
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319 </citations>
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320 </xml>
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321 </macros>
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322 ````
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323
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324 Usage example:
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325 ````
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326 <expand macro="citations" />
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327 ````
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328 ]]></xs:documentation>
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329 </xs:annotation>
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330 </xs:element>
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331 </xs:sequence>
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332 </xs:complexType>
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333
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334 <xs:complexType name="EntryPoints">
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335 <xs:annotation>
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336 <xs:documentation xml:lang="en"><![CDATA[
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337
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338 This is a container tag set for the ``entry_point`` tag that contains ``port`` and ``url`` tags
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339 described in greater detail below. ``entry_point``s describe InteractiveTool entry points
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340 to a tool.
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341
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342 ]]></xs:documentation>
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343 </xs:annotation>
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344 <xs:sequence>
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345 <xs:element name="entry_point" type="EntryPoint" minOccurs="0" maxOccurs="unbounded"/>
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346 </xs:sequence>
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347 </xs:complexType>
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348
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349 <xs:complexType name="EntryPoint" mixed="true">
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350 <xs:annotation>
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351 <xs:documentation xml:lang="en"><![CDATA[
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352
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353 This tag set is contained within the ``<entry_point>`` tag set. Access to entry point
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354 ports and urls are included in this tag set. These are used by InteractiveTools
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355 to provide access to graphical tools in real-time.
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356
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357 ```xml
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358 <entry_points>
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359 <entry_point name="Example name">
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360 <port>80</port>
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361 <url>landing/${template_enabled}/index.html</url>
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362 </entry_point>
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363 </entry_points>
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364 ```
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365
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366 ]]></xs:documentation>
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367 </xs:annotation>
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368 <xs:sequence>
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369 <xs:element name="port" type="EntryPointPort" minOccurs="1" maxOccurs="1"/>
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370 <xs:element name="url" type="EntryPointURL" minOccurs="0" maxOccurs="1"/>
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371 </xs:sequence>
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372 <xs:attribute name="name" type="xs:string" use="required">
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373 <xs:annotation>
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374 <xs:documentation xml:lang="en">This value defines the name of the entry point.</xs:documentation>
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375 </xs:annotation>
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376 </xs:attribute>
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377 <xs:attribute name="requires_domain" type="PermissiveBoolean" default="false">
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378 <xs:annotation>
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379 <xs:documentation xml:lang="en">This value declares if domain-based proxying is required. Default is False. Currently only works when True.</xs:documentation>
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380 </xs:annotation>
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381 </xs:attribute>
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382 </xs:complexType>
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383 <xs:complexType name="EntryPointPort" mixed="true">
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384 <xs:annotation>
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385 <xs:documentation xml:lang="en"><![CDATA[
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386
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387 This tag set is contained within the ``<entry_point>`` tag set. It contains the entry port.
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388
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389 ]]></xs:documentation>
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390 </xs:annotation>
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391 </xs:complexType>
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392 <xs:complexType name="EntryPointURL" mixed="true">
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393 <xs:annotation>
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394 <xs:documentation xml:lang="en"><![CDATA[
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395
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396 This tag set is contained within the ``<entry_point>`` tag set. It contains the entry URL.
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397
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398 ]]></xs:documentation>
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399 </xs:annotation>
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400 </xs:complexType>
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401
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402 <xs:complexType name="ToolAction">
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403 <xs:annotation>
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404 <xs:documentation xml:lang="en">Describe the backend Python action to execute for this Galaxy tool.</xs:documentation>
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405 </xs:annotation>
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406 <xs:sequence>
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407 </xs:sequence>
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408 <xs:attribute name="module" type="xs:string" use="required">
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409 </xs:attribute>
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410 <xs:attribute name="class" type="xs:string" use="required">
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411 </xs:attribute>
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412 </xs:complexType>
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413
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414 <xs:attributeGroup name="Thing">
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415 <xs:attribute name="name" type="xs:string" use="optional">
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416 <xs:annotation>
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417 <xs:documentation>https://schema.org/name</xs:documentation>
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418 </xs:annotation>
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419 </xs:attribute>
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420 <xs:attribute name="url" type="xs:string" use="optional">
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421 <xs:annotation>
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422 <xs:documentation>https://schema.org/url</xs:documentation>
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423 </xs:annotation>
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424 </xs:attribute>
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425 <xs:attribute name="identifier" type="xs:string" use="optional">
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426 <xs:annotation>
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427 <xs:documentation>https://schema.org/identifier</xs:documentation>
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428 </xs:annotation>
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429 </xs:attribute>
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430 <xs:attribute name="image" type="xs:string" use="optional">
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431 <xs:annotation>
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432 <xs:documentation>https://schema.org/image</xs:documentation>
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433 </xs:annotation>
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434 </xs:attribute>
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435 <xs:attribute name="address" type="xs:string" use="optional">
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436 <xs:annotation>
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437 <xs:documentation>https://schema.org/address</xs:documentation>
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438 </xs:annotation>
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439 </xs:attribute>
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440 <xs:attribute name="email" type="xs:string" use="optional">
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441 <xs:annotation>
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442 <xs:documentation>https://schema.org/email</xs:documentation>
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443 </xs:annotation>
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444 </xs:attribute>
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445 <xs:attribute name="telephone" type="xs:string" use="optional">
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446 <xs:annotation>
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447 <xs:documentation>https://schema.org/telephone</xs:documentation>
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448 </xs:annotation>
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449 </xs:attribute>
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450 <xs:attribute name="faxNumber" type="xs:string" use="optional">
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451 <xs:annotation>
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452 <xs:documentation>https://schema.org/faxNumber</xs:documentation>
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453 </xs:annotation>
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454 </xs:attribute>
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455 <xs:attribute name="alternateName" type="xs:string" use="optional">
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456 <xs:annotation>
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457 <xs:documentation>https://schema.org/alternateName</xs:documentation>
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458 </xs:annotation>
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459 </xs:attribute>
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460 </xs:attributeGroup>
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461
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462 <xs:complexType name="Person">
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463 <xs:annotation>
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464 <xs:documentation xml:lang="en"><![CDATA[
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465 Describes a person. Tries to stay close to schema.org data model - see https://schema.org/Person.
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466 ]]></xs:documentation>
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467 </xs:annotation>
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468 <xs:attributeGroup ref="Thing"/>
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469 <xs:attribute name="givenName" type="xs:string" use="optional">
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470 <xs:annotation>
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471 <xs:documentation>https://schema.org/givenName</xs:documentation>
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472 </xs:annotation>
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473 </xs:attribute>
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474 <xs:attribute name="familyName" type="xs:string" use="optional">
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475 <xs:annotation>
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476 <xs:documentation>https://schema.org/familyName</xs:documentation>
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477 </xs:annotation>
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478 </xs:attribute>
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479 <xs:attribute name="honorificPrefix" type="xs:string" use="optional">
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480 <xs:annotation>
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481 <xs:documentation>https://schema.org/honorificPrefix</xs:documentation>
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482 </xs:annotation>
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483 </xs:attribute>
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484 <xs:attribute name="honorificSuffix" type="xs:string" use="optional">
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485 <xs:annotation>
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486 <xs:documentation>https://schema.org/honorificSuffix</xs:documentation>
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487 </xs:annotation>
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488 </xs:attribute>
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489 <xs:attribute name="jobTitle" type="xs:string" use="optional">
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490 <xs:annotation>
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491 <xs:documentation>https://schema.org/jobTitle</xs:documentation>
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492 </xs:annotation>
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493 </xs:attribute>
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494 </xs:complexType>
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495
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496 <xs:complexType name="Organization">
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497 <xs:annotation>
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498 <xs:documentation xml:lang="en"><![CDATA[
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499 Describes an organization. Tries to stay close to schema.org data model - see https://schema.org/Organization.
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500 ]]></xs:documentation>
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501 </xs:annotation>
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502 <xs:attributeGroup ref="Thing"/>
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503 </xs:complexType>
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504
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505 <xs:group name="PersonOrOrganization">
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506 <xs:choice>
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507 <xs:element name="person" type="Person" />
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508 <xs:element name="organization" type="Organization" />
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509 </xs:choice>
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510 </xs:group>
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511
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512 <xs:complexType name="Creator">
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513 <xs:annotation>
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514 <xs:documentation xml:lang="en">The creator(s) of this work. See https://schema.org/creator.</xs:documentation>
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515 </xs:annotation>
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516 <xs:sequence>
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517 <xs:group ref="PersonOrOrganization" minOccurs="0" maxOccurs="unbounded"/>
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518 </xs:sequence>
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519 </xs:complexType>
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520
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521 <xs:complexType name="Requirements">
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522 <xs:annotation>
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523 <xs:documentation xml:lang="en"><![CDATA[
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524
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525 This is a container tag set for the ``requirement`` and ``container`` tags
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526 described in greater detail below. ``requirement``s describe software packages
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527 and other individual computing requirements required to execute a tool, while
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528 ``container``s describe Docker or Singularity containers that should be able to
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529 serve as complete descriptions of the runtime of a tool.
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530
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531 ]]></xs:documentation>
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532 </xs:annotation>
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533 <xs:sequence>
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534 <xs:element name="requirement" type="Requirement" minOccurs="0" maxOccurs="unbounded"/>
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535 <xs:element name="container" type="Container" minOccurs="0" maxOccurs="unbounded"/>
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536 </xs:sequence>
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537 </xs:complexType>
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538
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539 <xs:complexType name="Requirement">
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540 <xs:annotation>
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541 <xs:documentation xml:lang="en"><![CDATA[
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542
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543 This tag set is contained within the ``<requirements>`` tag set. Third party
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544 programs or modules that the tool depends upon are included in this tag set.
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545
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546 When a tool runs, Galaxy attempts to *resolve* these requirements (also called
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547 dependencies). ``requirement``s are meant to be abstract and resolvable by
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548 multiple different systems (e.g. [conda](https://conda.io/), the
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549 [Galaxy Tool Shed dependency management system](https://galaxyproject.org/toolshed/tool-features/#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories),
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550 or [environment modules](http://modules.sourceforge.net/)).
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551
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552 Read more about dependency resolvers in Galaxy on
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553 [docs.galaxyproject.org](https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html).
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554 The current best practice for tool dependencies is to target Conda, this is
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555 discussed in greater detail
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556 [here](https://docs.galaxyproject.org/en/master/admin/conda_faq.html).
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557
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558 ### Examples
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559
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560 This example shows a tool that requires the samtools 0.0.18 package.
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561
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562 This package is available via the Tool Shed (see
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563 [Tool Shed dependency management](https://galaxyproject.org/toolshed/tool-features/#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories)
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564 ) as well as [Conda](https://docs.galaxyproject.org/en/master/admin/conda_faq.html)
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565 and can be configured locally to adapt to any other package management system.
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566
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567 ```xml
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568 <requirements>
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569 <requirement type="package" version="0.1.18">samtools</requirement>
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570 </requirements>
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571 ```
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572
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573 This older example shows a tool that requires R version 2.15.1. The
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574 ``tool_dependencies.xml`` should contain matching declarations for Galaxy to
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575 actually install the R runtime. The ``set_envirornment`` type is only respected
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576 by the tool shed and is ignored by the newer and preferred conda dependency
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577 resolver.
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578
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579 ```xml
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580 <requirements>
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581 <requirement type="set_environment">R_SCRIPT_PATH</requirement>
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582 <requirement type="package" version="2.15.1">R</requirement>
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583 </requirements>
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584 ```
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585
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586 ]]></xs:documentation>
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587 </xs:annotation>
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588 <xs:simpleContent>
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589 <xs:extension base="xs:string">
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590 <xs:attribute name="type" type="RequirementType" use="required">
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591 <xs:annotation>
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592 <xs:documentation xml:lang="en">This value defines the type of the 3rd party module required by this tool.</xs:documentation>
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593 </xs:annotation>
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594 </xs:attribute>
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595 <xs:attribute name="version" type="xs:string">
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596 <xs:annotation>
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597 <xs:documentation xml:lang="en">For requirements of type ``package`` this value defines a specific version of the tool dependency.</xs:documentation>
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598 </xs:annotation>
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599 </xs:attribute>
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600 </xs:extension>
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601 </xs:simpleContent>
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602 </xs:complexType>
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603 <xs:complexType name="Container">
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604 <xs:annotation>
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605 <xs:documentation xml:lang="en"><![CDATA[
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606 This tag set is contained within the 'requirements' tag set. Galaxy can be
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607 configured to run tools within [Docker](https://www.docker.com/) or [Singularity](https://www.sylabs.io/singularity/)
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608 containers - this tag allows the tool to suggest possible valid containers for this tool. The contents of the tag should
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609 be a container image identifier appropriate for the particular container runtime being used, e.g.
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610 ``quay.io/biocontainers/fastqc:0.11.2--1`` for Docker or ``docker://quay.io/biocontainers/fastqc:0.11.2--1``
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611 (or alternatively ``/opt/containers/fastqc.simg`` if your Galaxy installation will be loading the image from a filesystem path)
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612 for Singularity. The ``requirements`` tag can contain multiple ``container`` tags describing suitable container options, in
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613 which case the first container that is found by the Galaxy container resolver at runtime will be used.
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614
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615 Example:
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616
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617 ```xml
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618 <requirements>
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619 <container type="docker">quay.io/biocontainers/fastqc:0.11.2--1</container>
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620 <requirements>
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621 ```
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622
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623 Read more about configuring Galaxy to run Docker jobs
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624 [here](https://galaxyproject.org/admin/tools/docker/).
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625 ]]></xs:documentation>
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626 </xs:annotation>
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627 <xs:simpleContent>
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628 <xs:extension base="xs:string">
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629 <xs:attribute name="type" type="ContainerType" use="required">
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630 <xs:annotation>
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631 <xs:documentation xml:lang="en">This value describes the type of container that the tool may be executed in and currently may be ``docker`` or ``singularity``.</xs:documentation>
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632 </xs:annotation>
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633 </xs:attribute>
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634 </xs:extension>
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635 </xs:simpleContent>
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636 </xs:complexType>
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637
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638 <xs:complexType name="Parallelism">
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639 <xs:annotation>
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640 <xs:documentation xml:lang="en">Documentation for Parallelism</xs:documentation>
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641 </xs:annotation>
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642 <xs:attribute name="method" type="MethodType">
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643 <xs:annotation>
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644 <xs:documentation xml:lang="en">Documentation for method</xs:documentation>
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645 </xs:annotation>
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646 </xs:attribute>
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647 <xs:attribute name="merge_outputs" type="xs:string">
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648 <xs:annotation>
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649 <xs:documentation xml:lang="en">Documentation for merge_outputs</xs:documentation>
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650 </xs:annotation>
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651 </xs:attribute>
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652 <xs:attribute name="split_inputs" type="xs:string">
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653 <xs:annotation>
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654 <xs:documentation xml:lang="en">A comma-separated list of data inputs to split for job parallelization.</xs:documentation>
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655 </xs:annotation>
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656 </xs:attribute>
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657 <xs:attribute name="split_size" type="xs:string">
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658 <xs:annotation>
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659 <xs:documentation xml:lang="en">Documentation for split_size</xs:documentation>
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660 </xs:annotation>
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661 </xs:attribute>
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662 <xs:attribute name="split_mode" type="xs:string">
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663 <xs:annotation>
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664 <xs:documentation xml:lang="en">Documentation for split_mode</xs:documentation>
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665 </xs:annotation>
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666 </xs:attribute>
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667 <xs:attribute name="shared_inputs" type="xs:string">
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668 <xs:annotation>
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669 <xs:documentation xml:lang="en">A comma-separated list of data inputs that should not be split for this tool, Galaxy will infer this if not present and so this potentially never needs to be set.</xs:documentation>
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670 </xs:annotation>
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671 </xs:attribute>
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672 </xs:complexType>
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673 <xs:complexType name="Code">
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674 <xs:annotation>
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675 <xs:documentation xml:lang="en"><![CDATA[
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676 *Deprecated*. Do not use this unless absolutely necessary.
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677
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678 The extensions described here can cause problems using your tool with certain components
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679 of Galaxy (like the workflow system). It is highly recommended to avoid these constructs
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680 unless absolutely necessary.
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681
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682 This tag set provides detailed control of the way the tool is executed. This
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683 (optional) code can be deployed in a separate file in the same directory as the
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684 tool's config file. These hooks are being replaced by new tool config features
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685 and methods in the [/lib/galaxy/tools/\__init__.py](https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/__init__.py) code file.
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686
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687 ### Examples
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688
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689 #### Dynamic Options
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690
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691 Use associated dynamic select lists where selecting an option in the first
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692 select list dynamically re-renders the options in the second select list. In
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693 this example, we are populating both dynamic select lists from metadata elements
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694 associated with a tool's single input dataset. The 2 metadata elements we're
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695 using look like this.
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696
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697 ```python
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698 MetadataElement(name="field_names", default=[], desc="Field names", readonly=True, optional=True, visible=True, no_value=[])
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699 # The keys in the field_components map to the list of field_names in the above element
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700 # which ensures order for select list options that are built from it.
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701 MetadataElement(name="field_components", default={}, desc="Field names and components", readonly=True, optional=True, visible=True, no_value={})
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702 ```
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703
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704 Our tool config includes a code file tag like this.
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705
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706 ```xml
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707 <code file="tool_form_utils.py" />
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708 ```
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709
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710 Here are the relevant input parameters in our tool config. The first parameter
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711 is the input dataset that includes the above metadata elements.
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712
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713 ```xml
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714 <param name="input" type="data" format="vtkascii,vtkbinary" label="Shape with uncolored surface field">
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715 <validator type="expression" message="Shape must have an uncolored surface field.">value is not None and len(value.metadata.field_names) > 0</validator>
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716 </param>
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717 ```
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718
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719 The following parameter dynamically renders a select list consisting of the
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720 elements in the ``field_names`` metadata element associated with the selected
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721 input dataset.
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722
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723 ```xml
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724 <param name="field_name" type="select" label="Field name" refresh_on_change="true">
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725 <options>
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726 <filter type="data_meta" ref="input" key="field_names"/>
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727 <validator type="no_options" message="The selected shape has no uncolored surface fields." />
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728 </options>
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729 </param>
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730 ```
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731
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732 The following parameter calls the ``get_field_components_options()`` function in
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733 the ``tool_form_utils.py`` code file discussed above. This function returns the
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734 value of the input dataset's ``field_components`` metadata element dictionary
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735 whose key is the currently selected ``field_name`` from the select list parameter
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736 above.
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737
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738 ```xml
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parents:
diff changeset
739 <param name="field_component_index" type="select" label="Field component index" dynamic_options="get_field_components_options(input, field_name=field_name)" help="Color will be applied to the selected field's component associated with this index." />
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diff changeset
740 ```
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diff changeset
741
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diff changeset
742 Changing the selected option in the ``field_name`` select list will dynamically
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parents:
diff changeset
743 re-render the options available in the associated ``field_component_index`` select
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diff changeset
744 list, which is the behavior we want.
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diff changeset
745
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diff changeset
746 The ``get_field_components_options()`` method looks like this.
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747
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748 ```python
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diff changeset
749 def get_field_components_options(dataset, field_name):
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diff changeset
750 options = []
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751 if dataset.metadata is None:
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752 return options
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753 if not hasattr(dataset.metadata, 'field_names'):
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diff changeset
754 return options
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755 if dataset.metadata.field_names is None:
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diff changeset
756 return options
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757 if field_name is None:
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758 # The expression validator that helps populate the select list of input
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diff changeset
759 # datsets in the icqsol_color_surface_field tool does not filter out
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760 # datasets with no field field_names, so we need this check.
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diff changeset
761 if len(dataset.metadata.field_names) == 0:
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diff changeset
762 return options
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diff changeset
763 field_name = dataset.metadata.field_names[0]
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764 field_components = dataset.metadata.field_components.get(field_name, [])
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765 for i, field_component in enumerate(field_components):
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diff changeset
766 options.append((field_component, field_component, i == 0))
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diff changeset
767 return options
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diff changeset
768 ```
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diff changeset
769
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770 #### Parameter Validation
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771
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772 This function is called before the tool is executed. If it raises any exceptions the tool execution will be aborted and the exception's value will be displayed in an error message box. Here is an example:
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773
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774 ```python
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diff changeset
775 def validate(incoming):
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diff changeset
776 """Validator for the plotting program"""
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diff changeset
777
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diff changeset
778
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diff changeset
779 bins = incoming.get("bins","")
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diff changeset
780 col = incoming.get("col","")
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diff changeset
781
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diff changeset
782
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diff changeset
783 if not bins or not col:
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diff changeset
784 raise Exception, "You need to specify a number for bins and columns"
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diff changeset
785
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diff changeset
786
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diff changeset
787 try:
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788 bins = int(bins)
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diff changeset
789 col = int(col)
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790 except:
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791 raise Exception, "Parameters are not integers, columns:%s, bins:%s" % (col, bins)
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diff changeset
792
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diff changeset
793
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794 if not 1<bins<100:
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diff changeset
795 raise Exception, "The number of bins %s must be a number between 1 and 100" % bins
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diff changeset
796 ```
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diff changeset
797
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diff changeset
798 This code will intercept a number of parameter errors and return corresponding error messages. The parameter ``incoming`` contains a dictionary with all the parameters that were sent through the web.
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diff changeset
799
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diff changeset
800 #### Pre-job and pre-process code
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diff changeset
801
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diff changeset
802 The signature of both of these is the same:
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diff changeset
803
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diff changeset
804 ```python
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diff changeset
805 def exec_before_job(inp_data, out_data, param_dict, tool):
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806 def exec_before_process(inp_data, out_data, param_dict, tool):
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diff changeset
807 ```
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diff changeset
808
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diff changeset
809 The ``param_dict`` is a dictionary that contains all the values in the ``incoming`` parameter above plus a number of keys and values generated internally by galaxy. The ``inp_data`` and the ``out_data`` are dictionaries keyed by parameter name containing the classes that represent the data.
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diff changeset
810
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diff changeset
811 Example:
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diff changeset
812
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diff changeset
813 ```python
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diff changeset
814 def exec_before_process(inp_data, out_data, param_dict, tool):
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diff changeset
815 for name, data in out_data.items():
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diff changeset
816 data.name = 'New name'
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diff changeset
817 ```
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diff changeset
818
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diff changeset
819 This custom code will change the name of the data that was created for this tool to **New name**. The difference between these two functions is that the ``exec_before_job`` executes before the page returns and the user will see the new name right away. If one were to use ``exec_before_process`` the new name would be set only once the job starts to execute.
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820
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diff changeset
821 #### Post-process code
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822
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diff changeset
823 This code executes after the background process running the tool finishes its run. The example below is more advanced one that replaces the type of the output data depending on the parameter named ``extension``:
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824
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diff changeset
825 ```python
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diff changeset
826 from galaxy import datatypes
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diff changeset
827 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
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828 ext = param_dict.get('extension', 'text')
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829 items = out_data.items()
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diff changeset
830 for name, data in items:
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diff changeset
831 newdata = datatypes.factory(ext)(id=data.id)
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832 for key, value in data. __dict__.items():
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833 setattr(newdata, key, value)
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834 newdata.ext = ext
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diff changeset
835 out_data[name] = newdata
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diff changeset
836 ```
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837
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838 The content of ``stdout`` and ``stderr`` are strings containing the output of the process.
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839
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840 ]]></xs:documentation>
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841
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842 </xs:annotation>
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843 <xs:sequence>
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844 <xs:element name="hook" type="CodeHook" minOccurs="0" maxOccurs="unbounded"/>
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845 </xs:sequence>
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846 <xs:attribute name="file" type="xs:string" use="required">
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847 <xs:annotation>
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848 <xs:documentation xml:lang="en">This value is the name of the executable code file, and is called in the ``exec_before_process()``, ``exec_before_job()``, ``exec_after_process()`` and ``exec_after_job()`` methods.</xs:documentation>
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849 </xs:annotation>
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850 </xs:attribute>
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851 </xs:complexType>
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852 <xs:complexType name="CodeHook">
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853 <xs:annotation>
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854 <xs:documentation xml:lang="en">*Deprecated*. Map a hook to a function defined in the code file.</xs:documentation>
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855 </xs:annotation>
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856 <xs:attribute name="exec_after_process" type="xs:string">
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857 <xs:annotation>
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858 <xs:documentation xml:lang="en">Function defined in the code file to which the ``exec_after_process`` hook should be mapped</xs:documentation>
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859 </xs:annotation>
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860 </xs:attribute>
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861 </xs:complexType>
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862 <xs:complexType name="UIhints">
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863 <xs:annotation>
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864 <xs:documentation xml:lang="en">Used only for data source tools, this directive contains UI options (currently only ``minwidth`` is valid).</xs:documentation>
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865 </xs:annotation>
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866 <xs:attribute name="minwidth" type="xs:integer">
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867 <xs:annotation>
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868 <xs:documentation xml:lang="en">Documentation for minwidth</xs:documentation>
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869 </xs:annotation>
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870 </xs:attribute>
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871 </xs:complexType>
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872
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873 <xs:complexType name="Options">
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874 <xs:annotation>
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875 <xs:documentation xml:lang="en">This directive is used to specify some rarely modified options.</xs:documentation>
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876 </xs:annotation>
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877 <xs:attribute name="refresh" type="PermissiveBoolean" gxdocs:deprecated="true">
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878 <xs:annotation>
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879 <xs:documentation xml:lang="en">*Deprecated*. Unused attribute.</xs:documentation>
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880 </xs:annotation>
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881 </xs:attribute>
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882 <xs:attribute name="sanitize" type="PermissiveBoolean" default="true">
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883 <xs:annotation>
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884 <xs:documentation xml:lang="en">This attribute can be used to turn off all input sanitization for a tool.</xs:documentation>
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885 </xs:annotation>
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886 </xs:attribute>
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887 </xs:complexType>
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888
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889 <xs:complexType name="TracksterConf">
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890 <xs:annotation>
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891 <xs:documentation xml:lang="en">This directive is used to specify some rarely modified trackster options.</xs:documentation>
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892 </xs:annotation>
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893 <xs:sequence>
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894 <xs:element name="action" type="TracksterAction" minOccurs="0" maxOccurs="unbounded" />
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895 </xs:sequence>
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896 </xs:complexType>
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897
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898 <xs:complexType name="TracksterAction">
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899 <xs:annotation>
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900 <xs:documentation xml:lang="en"></xs:documentation>
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901 </xs:annotation>
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902 <xs:attribute name="name" type="xs:string">
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903 <xs:annotation>
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904 <xs:documentation xml:lang="en"></xs:documentation>
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905 </xs:annotation>
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906 </xs:attribute>
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907 <xs:attribute name="output_name" type="xs:string">
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908 <xs:annotation>
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909 <xs:documentation xml:lang="en"></xs:documentation>
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910 </xs:annotation>
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911 </xs:attribute>
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912 </xs:complexType>
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913
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914 <xs:complexType name="Tests">
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915 <xs:annotation gxdocs:best_practices="tests">
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916 <xs:documentation xml:lang="en"><![CDATA[
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917
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918 Container tag set to specify tests via the ``<test>`` tag sets. Any number of tests can be included,
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919 and each test is wrapped within separate ``<test>`` tag sets. Functional tests are
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920 executed via [Planemo](https://planemo.readthedocs.io/) or the
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921 [run_tests.sh](https://github.com/galaxyproject/galaxy/blob/dev/run_tests.sh)
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922 shell script distributed with Galaxy.
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923
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diff changeset
924 The documentation contained here is mostly reference documentation, for
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925 tutorials on writing tool tests please check out Planemo's
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926 [Test-Driven Development](https://planemo.readthedocs.io/en/latest/writing_advanced.html#test-driven-development)
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927 documentation or the much older wiki content for
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928 [WritingTests](https://galaxyproject.org/admin/tools/writing-tests/).
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929
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930 ]]></xs:documentation>
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931 </xs:annotation>
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932 <xs:sequence>
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933 <xs:element name="test" type="Test" minOccurs="0" maxOccurs="unbounded"/>
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934 </xs:sequence>
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935 </xs:complexType>
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936
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937 <xs:complexType name="Test">
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938 <xs:annotation>
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939 <xs:documentation xml:lang="en"><![CDATA[
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940
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941 This tag set contains the necessary parameter values for executing the tool via
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942 the functional test framework.
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943
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944 ### Example
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945
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946 The following two tests will execute the
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947 [/tools/filters/sorter.xml](https://github.com/galaxyproject/galaxy/blob/dev/tools/filters/sorter.xml)
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948 tool. Notice the way that the tool's inputs and outputs are defined.
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949
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950 ```xml
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951 <tests>
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952 <test>
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953 <param name="input" value="1.bed" ftype="bed" />
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954 <param name="column" value="1"/>
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955 <param name="order" value="ASC"/>
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956 <param name="style" value="num"/>
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957 <output name="out_file1" file="sort1_num.bed" ftype="bed" />
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958 </test>
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959 <test>
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960 <param name="input" value="7.bed" ftype="bed" />
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961 <param name="column" value="1"/>
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962 <param name="order" value="ASC"/>
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963 <param name="style" value="alpha"/>
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964 <output name="out_file1" file="sort1_alpha.bed" ftype="bed" />
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965 </test>
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966 </tests>
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967 ```
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968
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969 The following example, tests the execution of the MAF-to-FASTA converter
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970 ([/tools/maf/maf_to_fasta.xml](https://github.com/galaxyproject/galaxy/blob/master/tools/maf/maf_to_fasta.xml)).
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971
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972 ```xml
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973 <tests>
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974 <test>
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975 <param name="input1" value="3.maf" ftype="maf"/>
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976 <param name="species" value="canFam1"/>
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977 <param name="fasta_type" value="concatenated"/>
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978 <output name="out_file1" file="cf_maf2fasta_concat.dat" ftype="fasta"/>
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979 </test>
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980 </tests>
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981 ```
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982
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983 This test demonstrates verifying specific properties about a test output instead
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984 of directly comparing it to another file. Here the file attribute is not
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985 specified and instead a series of assertions is made about the output.
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986
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987 ```xml
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988 <test>
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989 <param name="input" value="maf_stats_interval_in.dat" />
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990 <param name="lineNum" value="99999"/>
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991 <output name="out_file1">
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992 <assert_contents>
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993 <has_text text="chr7" />
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994 <not_has_text text="chr8" />
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995 <has_text_matching expression="1274\d+53" />
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996 <has_line_matching expression=".*\s+127489808\s+127494553" />
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997 <!-- &#009; is XML escape code for tab -->
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998 <has_line line="chr7&#009;127471195&#009;127489808" />
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999 <has_n_columns n="3" />
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1000 <has_n_lines n="3" />
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1001 </assert_contents>
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1002 </output>
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1003 </test>
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1004 ```
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1005
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1006 ]]></xs:documentation>
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1007 </xs:annotation>
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1008 <xs:sequence>
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1009 <xs:group ref="TestParamElement" minOccurs="0" maxOccurs="unbounded"/>
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1010 </xs:sequence>
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1011 <xs:attribute name="expect_exit_code" type="xs:integer">
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1012 <xs:annotation>
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1013 <xs:documentation xml:lang="en">Describe the job's expected exit code.</xs:documentation>
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1014 </xs:annotation>
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1015 </xs:attribute>
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1016 <xs:attribute name="expect_num_outputs" type="xs:integer">
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1017 <xs:annotation>
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1018 <xs:documentation xml:lang="en">Assert the number of outputs this test
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1019 should produce, this is useful to ensure ``filter`` directives are implemented correctly.</xs:documentation>
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1020 </xs:annotation>
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1021 </xs:attribute>
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1022 <xs:attribute name="expect_failure" type="PermissiveBoolean" default="false">
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1023 <xs:annotation>
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1024 <xs:documentation xml:lang="en">Setting this to ``true`` indicates
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1025 the expectation is for the job fail. If set to ``true`` no job output checks may
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1026 be present in ``test`` definition.</xs:documentation>
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1027 </xs:annotation>
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1028 </xs:attribute>
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1029 <xs:attribute name="maxseconds" type="xs:integer">
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1030 <xs:annotation>
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1031 <xs:documentation xml:lang="en">Maximum amount of time to let test run.</xs:documentation>
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1032 </xs:annotation>
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1033 </xs:attribute>
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1034 </xs:complexType>
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1035 <xs:group name="TestParamElement">
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1036 <xs:choice>
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1037 <xs:element name="param" type="TestParam" />
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1038 <xs:element name="repeat" type="TestRepeat" />
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1039 <xs:element name="conditional" type="TestConditional" />
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1040 <xs:element name="section" type="TestSection" />
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1041 <xs:element name="output" type="TestOutput" minOccurs="0" maxOccurs="unbounded"/>
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1042 <xs:element name="output_collection" type="TestOutputCollection"/>
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1043 <xs:element name="assert_command" type="TestAssertions">
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1044 <xs:annotation>
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1045 <xs:documentation xml:lang="en">Describe assertions about the job's
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1046 generated command-line.
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1047
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1048 $assertions
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1049 </xs:documentation>
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1050 </xs:annotation>
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1051 </xs:element>
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1052 <xs:element name="assert_stdout" type="TestAssertions">
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1053 <xs:annotation>
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1054 <xs:documentation xml:lang="en">Describe assertions about the job's
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1055 standard output.
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1056
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1057 $assertions
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1058 </xs:documentation>
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1059 </xs:annotation>
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1060 </xs:element>
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1061 <xs:element name="assert_stderr" type="TestAssertions">
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1062 <xs:annotation>
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1063 <xs:documentation xml:lang="en">Describe assertions about the job's
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1064 standard error.
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1065
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1066 $assertions
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1067 </xs:documentation>
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1068 </xs:annotation>
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1069 </xs:element>
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1070 <xs:element name="assert_command_version" type="TestAssertions">
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1071 <xs:annotation>
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1072 <xs:documentation xml:lang="en">Describe assertions about the job's
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1073 command version.
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1074
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1075 $assertions
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1076 </xs:documentation>
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1077 </xs:annotation>
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1078 </xs:element>
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1079 </xs:choice>
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1080 </xs:group>
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1081 <xs:complexType name="TestSection">
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1082 <xs:annotation>
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1083 <xs:documentation xml:lang="en"><![CDATA[
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1084
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1085 Specify test parameters below a named of a ``section`` block matching
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1086 one in ``inputs`` with this element.
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1087
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1088 ``param`` elements in a ``test`` block can be arranged into nested ``repeat``,
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1089 ``conditional``, and ``select`` structures to match the inputs. While this might
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1090 be overkill for simple tests, it helps prevent ambiguous definitions and keeps
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1091 things organized in large test cases. A future ``profile`` version of Galaxy
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1092 tools may require ``section`` blocks be explicitly defined with this
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1093 directive.
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1094
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1095 ### Examples
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1096
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1097 The test tool demonstrating sections
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1098 ([section.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/section.xml))
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1099 contains a test case demonstrating this block. This test case appears below:
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1100
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1101 ```xml
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1102 <test>
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1103 <section name="int">
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1104 <param name="inttest" value="12456" />
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1105 </section>
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1106 <section name="float">
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1107 <param name="floattest" value="6.789" />
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1108 </section>
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1109 <output name="out_file1">
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diff changeset
1110 <assert_contents>
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diff changeset
1111 <has_line line="12456" />
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1112 <has_line line="6.789" />
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1113 </assert_contents>
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diff changeset
1114 </output>
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diff changeset
1115 </test>
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diff changeset
1116 ```
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diff changeset
1117
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diff changeset
1118 ]]>
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diff changeset
1119 </xs:documentation>
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diff changeset
1120 </xs:annotation>
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diff changeset
1121 <xs:sequence>
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diff changeset
1122 <xs:group ref="TestParamElement" minOccurs="0" maxOccurs="unbounded" />
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1123 </xs:sequence>
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1124 <xs:attribute name="name" type="xs:string" use="required">
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diff changeset
1125 <xs:annotation>
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1126 <xs:documentation xml:lang="en">This value must match the name of the
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1127 associated input ``section``.</xs:documentation>
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1128 </xs:annotation>
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diff changeset
1129 </xs:attribute>
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diff changeset
1130 </xs:complexType>
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1131 <xs:complexType name="TestConditional">
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1132 <xs:annotation>
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1133 <xs:documentation xml:lang="en"><![CDATA[
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1134
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1135 Specify test parameters below a named of a ``conditional`` block matching
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diff changeset
1136 one in ``inputs`` with this element.
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diff changeset
1137
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1138 ``param`` elements in a ``test`` block can be arranged into nested ``repeat``,
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1139 ``conditional``, and ``select`` structures to match the inputs. While this might
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1140 be overkill for simple tests, it helps prevent ambiguous definitions and keeps
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diff changeset
1141 things organized in large test cases. A future ``profile`` version of Galaxy
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1142 tools may require ``conditional`` blocks be explicitly defined with this
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diff changeset
1143 directive.
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diff changeset
1144
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diff changeset
1145 ### Examples
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1146
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diff changeset
1147 The following example demonstrates disambiguation of a parameter (named ``use``)
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1148 which appears in multiple ``param`` names in ``conditional``s in the ``inputs``
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diff changeset
1149 definition of the [disambiguate_cond.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/disambiguate_cond.xml)
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diff changeset
1150 tool.
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diff changeset
1151
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diff changeset
1152 ```xml
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diff changeset
1153 <!-- Can use nested conditional blocks as shown below to disambiguate
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1154 various nested parameters. -->
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diff changeset
1155 <test>
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diff changeset
1156 <conditional name="p1">
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diff changeset
1157 <param name="use" value="False"/>
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diff changeset
1158 </conditional>
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diff changeset
1159 <conditional name="p2">
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diff changeset
1160 <param name="use" value="True"/>
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diff changeset
1161 </conditional>
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diff changeset
1162 <conditional name="p3">
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1163 <param name="use" value="False"/>
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1164 </conditional>
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diff changeset
1165 <conditional name="files">
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diff changeset
1166 <param name="attach_files" value="True" />
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diff changeset
1167 <conditional name="p4">
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1168 <param name="use" value="True"/>
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1169 <param name="file" value="simple_line_alternative.txt" />
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1170 </conditional>
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1171 </conditional>
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diff changeset
1172 <output name="out_file1">
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diff changeset
1173 <assert_contents>
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diff changeset
1174 <has_line line="7 4 7" />
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1175 <has_line line="This is a different line of text." />
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1176 </assert_contents>
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diff changeset
1177 </output>
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diff changeset
1178 </test>
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diff changeset
1179 ```
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diff changeset
1180
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diff changeset
1181 The [tophat2](https://github.com/galaxyproject/tools-devteam/blob/master/tools/tophat2/tophat2_wrapper.xml)
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1182 tool demonstrates a real tool that benefits from more structured test cases
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1183 using the ``conditional`` test directive. One such test case from that tool is
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diff changeset
1184 shown below.
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diff changeset
1185
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diff changeset
1186 ```xml
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1187 <!-- Test base-space paired-end reads with user-supplied reference fasta and full parameters -->
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diff changeset
1188 <test>
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diff changeset
1189 <!-- TopHat commands:
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diff changeset
1190 tophat2 -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search +report_discordant_pairs tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
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diff changeset
1191 Replace the + with double-dash
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diff changeset
1192 Rename the files in tmp_dir appropriately
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diff changeset
1193 -->
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diff changeset
1194 <conditional name="singlePaired">
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1195 <param name="sPaired" value="paired"/>
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1196 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
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1197 <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/>
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1198 <param name="mate_inner_distance" value="20"/>
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1199 <param name="report_discordant_pairs" value="Yes" />
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1200 </conditional>
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1201 <param name="genomeSource" value="indexed"/>
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diff changeset
1202 <param name="index" value="tophat_test"/>
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diff changeset
1203 <conditional name="params">
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diff changeset
1204 <param name="settingsType" value="full"/>
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1205 <param name="library_type" value="FR Unstranded"/>
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diff changeset
1206 <param name="read_mismatches" value="5"/>
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1207 <!-- Error: the read mismatches (5) and the read gap length (2) should be less than or equal to the read edit dist (2) -->
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1208 <param name="read_edit_dist" value="5" />
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1209 <param name="bowtie_n" value="Yes"/>
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1210 <param name="mate_std_dev" value="20"/>
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diff changeset
1211 <param name="anchor_length" value="8"/>
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diff changeset
1212 <param name="splice_mismatches" value="0"/>
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diff changeset
1213 <param name="min_intron_length" value="70"/>
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diff changeset
1214 <param name="max_intron_length" value="500000"/>
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1215 <param name="max_multihits" value="40"/>
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1216 <param name="min_segment_intron" value="50" />
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diff changeset
1217 <param name="max_segment_intron" value="500000" />
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1218 <param name="seg_mismatches" value="2"/>
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diff changeset
1219 <param name="seg_length" value="25"/>
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diff changeset
1220 <conditional name="indel_search">
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1221 <param name="allow_indel_search" value="No"/>
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1222 </conditional>
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1223 <conditional name="own_junctions">
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1224 <param name="use_junctions" value="Yes" />
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1225 <conditional name="gene_model_ann">
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1226 <param name="use_annotations" value="No" />
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1227 </conditional>
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1228 <conditional name="raw_juncs">
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diff changeset
1229 <param name="use_juncs" value="No" />
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diff changeset
1230 </conditional>
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diff changeset
1231 <conditional name="no_novel_juncs">
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parents:
diff changeset
1232 <param name="no_novel_juncs" value="No" />
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diff changeset
1233 </conditional>
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diff changeset
1234 </conditional>
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diff changeset
1235 <conditional name="coverage_search">
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parents:
diff changeset
1236 <param name="use_search" value="No" />
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diff changeset
1237 </conditional>
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diff changeset
1238 <param name="microexon_search" value="Yes" />
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parents:
diff changeset
1239 <conditional name="bowtie2_settings">
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diff changeset
1240 <param name="b2_settings" value="No" />
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1241 </conditional>
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parents:
diff changeset
1242 <!-- Fusion search params -->
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diff changeset
1243 <conditional name="fusion_search">
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diff changeset
1244 <param name="do_search" value="Yes" />
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1245 <param name="anchor_len" value="21" />
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1246 <param name="min_dist" value="10000021" />
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1247 <param name="read_mismatches" value="3" />
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diff changeset
1248 <param name="multireads" value="4" />
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parents:
diff changeset
1249 <param name="multipairs" value="5" />
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diff changeset
1250 <param name="ignore_chromosomes" value="chrM"/>
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1251 </conditional>
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1252 </conditional>
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diff changeset
1253 <conditional name="readGroup">
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diff changeset
1254 <param name="specReadGroup" value="no" />
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1255 </conditional>
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diff changeset
1256 <output name="junctions" file="tophat2_out4j.bed" />
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diff changeset
1257 <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" />
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1258 </test>
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diff changeset
1259 ```
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diff changeset
1260
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diff changeset
1261 ]]></xs:documentation>
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diff changeset
1262 </xs:annotation>
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diff changeset
1263 <xs:sequence>
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diff changeset
1264 <xs:group ref="TestParamElement" minOccurs="0" maxOccurs="unbounded" />
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1265 </xs:sequence>
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diff changeset
1266 <xs:attribute name="name" type="xs:string" use="required">
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diff changeset
1267 <xs:annotation>
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diff changeset
1268 <xs:documentation xml:lang="en">This value must match the name of the
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diff changeset
1269 associated input ``conditional``.</xs:documentation>
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1270 </xs:annotation>
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diff changeset
1271 </xs:attribute>
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diff changeset
1272 </xs:complexType>
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diff changeset
1273 <xs:complexType name="TestRepeat">
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diff changeset
1274 <xs:annotation>
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diff changeset
1275 <xs:documentation xml:lang="en"><![CDATA[
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diff changeset
1276
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diff changeset
1277 Specify test parameters below an iteration of a ``repeat`` block with this
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diff changeset
1278 element.
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diff changeset
1279
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1280 ``param`` elements in a ``test`` block can be arranged into nested ``repeat``,
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1281 ``conditional``, and ``select`` structures to match the inputs. While this might
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1282 be overkill for simple tests, it helps prevent ambiguous definitions and keeps
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diff changeset
1283 things organized in large test cases. A future ``profile`` version of Galaxy
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1284 tools may require ``repeat`` blocks be explicitly defined with this directive.
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diff changeset
1285
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diff changeset
1286 ### Examples
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diff changeset
1287
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diff changeset
1288 The test tool [disambiguate_repeats.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/disambiguate_repeats.xml)
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diff changeset
1289 demonstrates the use of this directive.
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diff changeset
1290
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diff changeset
1291 This first test case demonstrates that this block allows different values for
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diff changeset
1292 the ``param`` named ``input`` to be tested even though this parameter name
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diff changeset
1293 appears in two different ``<repeat>`` elements in the ``<inputs>`` definition.
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1294
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diff changeset
1295 ```xml
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1296 <!-- Can disambiguate repeats and specify multiple blocks using,
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parents:
diff changeset
1297 nested structure. -->
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diff changeset
1298 <test>
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diff changeset
1299 <repeat name="queries">
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diff changeset
1300 <param name="input" value="simple_line.txt"/>
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diff changeset
1301 </repeat>
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diff changeset
1302 <repeat name="more_queries">
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diff changeset
1303 <param name="input" value="simple_line_alternative.txt"/>
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diff changeset
1304 </repeat>
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diff changeset
1305 <output name="out_file1">
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diff changeset
1306 <assert_contents>
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diff changeset
1307 <has_line line="This is a line of text." />
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diff changeset
1308 <has_line line="This is a different line of text." />
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diff changeset
1309 </assert_contents>
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diff changeset
1310 </output>
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diff changeset
1311 </test>
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diff changeset
1312 ```
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diff changeset
1313
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diff changeset
1314 The second definition in that file demonstrates repeated ``<repeat>`` blocks
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diff changeset
1315 allowing multiple instances of a single repeat to be specified.
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diff changeset
1316
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diff changeset
1317 ```xml
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diff changeset
1318 <!-- Multiple such blocks can be specified but only with newer API
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1319 driven tests. -->
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diff changeset
1320 <test>
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diff changeset
1321 <repeat name="queries">
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diff changeset
1322 <param name="input" value="simple_line.txt"/>
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diff changeset
1323 </repeat>
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diff changeset
1324 <repeat name="queries">
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diff changeset
1325 <param name="input" value="simple_line_alternative.txt"/>
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diff changeset
1326 </repeat>
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diff changeset
1327 <repeat name="more_queries">
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diff changeset
1328 <param name="input" value="simple_line.txt"/>
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diff changeset
1329 </repeat>
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diff changeset
1330 <repeat name="more_queries">
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diff changeset
1331 <param name="input" value="simple_line_alternative.txt"/>
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diff changeset
1332 </repeat>
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diff changeset
1333 <output name="out_file1" file="simple_lines_interleaved.txt"/>
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diff changeset
1334 </test>
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diff changeset
1335 ```
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diff changeset
1336
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diff changeset
1337 ]]></xs:documentation>
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diff changeset
1338 </xs:annotation>
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diff changeset
1339 <xs:sequence>
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1340 <xs:group ref="TestParamElement" minOccurs="0" maxOccurs="unbounded" />
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1341 </xs:sequence>
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diff changeset
1342 <xs:attribute name="name" type="xs:string" use="required">
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diff changeset
1343 <xs:annotation>
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1344 <xs:documentation xml:lang="en">This value must match the name of the
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1345 associated input ``repeat``.</xs:documentation>
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diff changeset
1346 </xs:annotation>
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1347 </xs:attribute>
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diff changeset
1348 </xs:complexType>
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1349 <xs:complexType name="TestParam">
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diff changeset
1350 <xs:annotation>
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diff changeset
1351 <xs:documentation xml:lang="en"><![CDATA[
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diff changeset
1352
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1353 This tag set defines the tool's input parameters for executing the tool via the
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1354 functional test framework. See [test](#tool-tests-test) documentation for
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1355 some simple examples of parameters.
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1356
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1357 ### Parameter Types
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1358
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1359 #### ``text``, ``integer``, and ``float``
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1360
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1361 Values for these parameters are simply given by the desired value.
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1362
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1363 #### ``boolean``
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1364
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1365 The value of the test parameter should be set to `true` or `false` corresponding
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1366 to the cases that the parameter is checked or not. Alternatively the value
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1367 specified as `truevalue` or `falsevalue` can be given.
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1368
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1369 #### ``data``
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1370
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1371 Data input parameters can be given as a file name. The file should exist in the
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1372 `test-data` folder. Multiple files can be specified as comma separated list.
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