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63
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1 <tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" >
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62
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2 <description>Scripts into tools v2.0</description>
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48
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3 <macros>
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50
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4 <xml name="tool_metadata">
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49
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5 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
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6 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
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7 <param name="tool_desc" label="Tool Description" type="text" value=""
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8 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
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9 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
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10 value="**What it Does**"
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11 help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
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12 <sanitizer>
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13 <valid initial="string.printable">
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14 </valid>
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15 <mapping initial="none"/>
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16 </sanitizer>
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17 </param>
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18 <repeat name="citations" title="Citation">
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19 <conditional name="citation_type">
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20 <param name="type" type="select" display="radio" label="Citation Type">
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21 <option value="doi">DOI</option>
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22 <option value="bibtex">BibTeX</option>
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23 </param>
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24 <when value="doi">
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25 <param name="doi" label="DOI" type="text" value=""
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64
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26 help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) to be cited when this tool is used in published research." />
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49
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27 </when>
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28 <when value="bibtex">
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29 <param name="bibtex" label="BibTex" type="text" area="true"
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30 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
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31 <sanitizer>
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32 <valid initial="string.printable">
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33 </valid>
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34 <mapping initial="none"/>
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35 </sanitizer>
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36 </param>
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37 </when>
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38 </conditional>
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39 </repeat>
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40 </xml>
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48
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41 <xml name="io">
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42 <repeat name="history_inputs" title="Add a data file from your history to pass in to the script. Use the '+' button as needed"
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49
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43 help="USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool">
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48
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44 <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false"
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45 help=""/>
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46 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
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47 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
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48 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
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49 <column name="value" index="0"/>
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50 </options>
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51 </param>
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52 <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative"
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53 help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" >
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54 <sanitizer invalid_char="">
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55 <valid initial="string.printable"> <remove value='~~~'/> </valid>
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56 <mapping initial="none"/>
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57 </sanitizer>
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58 </param>
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63
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59 <param name="input_help" type="text" value="" label="This will become help text on the form."
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48
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60 help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation">
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61 <sanitizer invalid_char="">
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62 <valid initial="string.printable"> <remove value='~~~'/> </valid>
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63 <mapping initial="none"/>
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64 </sanitizer>
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65 </param>
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66 <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
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67 help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value="">
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68 </param>
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69 </repeat>
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70 <repeat name="history_outputs" title="Add a tool run output file to the user's history from your tool - Use the '+' button to add as many as needed"
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71 help="The name will become a history item for users of the new tool you are making containing one of it's outputs">
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72 <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" help=""/>
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73 <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
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74 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
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75 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
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76 <column name="value" index="0"/>
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77 </options>
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78 </param>
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79 <param name="history_CL" type="text" label="Positional: ordinal integer. Argparse: argument name expected for this output parameter. Use STDOUT if '>' required."
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80 help="If positional parameters, enter the integer ordinal expected for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""/>
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49
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81 <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation"
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82 help="Available options are diff:lines, sim_size" value="diff:2"/>
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48
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83 </repeat>
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84 </xml>
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85 <xml name="additparam">
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86 <param name="edit_params" type="select" display="radio" label="Add any additional parameters to the generated tool form so they are user editable?"
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87 help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
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63
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88 <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
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89 <option value="no">No - use the fixed values for all additional parameters - no user editing</option>
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48
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90 </param>
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91
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92 <repeat name="additional_parameters" title="Pass additional parameters to the script"
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93 help="See examples below to see how these can be parsed by scripts in the various languages">
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63
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94 <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!">
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48
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95 <sanitizer invalid_char="">
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96 <valid initial="string.letters,string.digits"/>
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97 <mapping initial="none"/>
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98 </sanitizer>
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99 </param>
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100 <param name="param_type" type="select" label="Select the type for this parameter">
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101 <option value="text" selected="true">text</option>
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102 <option value="integer">integer</option>
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103 <option value="float">float</option>
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104 </param>
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105 <param name="param_value" type="text" value="" label="Enter this parameter's default value"
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106 help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" >
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107 <sanitizer invalid_char="">
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108 <valid initial="string.printable"> <remove value='~~~'/> </valid>
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109 <mapping initial="none"/>
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110 </sanitizer>
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111 </param>
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63
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112 <param name="param_label" type="text" value="" label="Enter this parameter's label for the form"
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48
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113 help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" >
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114 <sanitizer invalid_char="">
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115 <valid initial="string.printable"> <remove value='~~~'/> </valid>
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116 <mapping initial="none"/>
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117 </sanitizer>
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118 </param>
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63
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119 <param name="param_help" type="text" value="" label="Help for this parameter"
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48
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120 help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" >
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121 <sanitizer invalid_char="">
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122 <valid initial="string.printable"> <remove value='~~~'/> </valid>
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123 <mapping initial="none"/>
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124 </sanitizer>
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125 </param>
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49
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126 <param name="param_CL" type="text" label="Positional ordinal | argparse argument name"
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48
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127 help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value="" />
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128 <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed"
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49
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129 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
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48
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130 </repeat>
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131 </xml>
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132 </macros>
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56
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133
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50
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134 <requirements>
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62
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135 <requirement type="package" version="0.72.0" >planemo</requirement>
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136 <requirement type="package" version="0.4.11" >galaxyxml</requirement>
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63
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137
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50
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138 </requirements>
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63
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139
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50
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140 <command ><![CDATA[
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48
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141 #import os
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142 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
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143 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
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144 python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
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48
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145 #else:
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146 python3 $__tool_directory__/rgToolFactory2.py
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49
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147 #if len(str($cl_prefix)) > 3:
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148 --cl_prefix "$cl_prefix"
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149 #end if
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150 #if $cover.commover == "yes":
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151 #if len(str($cover.command_override)) > 10:
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152 --command_override "$commandoverride"
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153 #end if
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154 #if len(str($cover.test_override)) > 10:
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155 --test_override "$testoverride"
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156 #end if
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48
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157 #end if
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63
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158 --packages "$packages"
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159 #if $usescript.choosescript == "yes":
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160 --script_path "$runme"
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161 --sysexe "$usescript.scriptrunner"
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49
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162 #end if
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163 --tool_name="$tool_name" --user_email="$__user_email__" --citations="$citeme" --parampass="$ppass.parampass"
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63
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164
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49
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165 #if str($makeMode.make_Tool)!="runonly":
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48
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166 --make_Tool="$makeMode.make_Tool"
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167 --tool_desc="$makeMode.tool_desc"
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168 --tool_version="$makeMode.tool_version"
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169 --help_text="$helpme"
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170 --new_tool="$new_tool"
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63
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171 --toolshed_api_key="$makeMode.toolshed_apikey"
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172 --galaxy_api_key="$makeMode.galaxy_apikey"
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173 --toolshed_url="$makeMode.toolshed_url"
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174 --galaxy_url="$makeMode.galaxy_url"
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48
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175 #end if
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176 #if $ppass.parampass != '0':
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177 #if str($ppass.edit_params) == "yes":
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178 --edit_additional_parameters
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179 #end if
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180 #for apar in $ppass.additional_parameters:
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181 --additional_parameters="$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed"
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182 #end for
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183 #end if
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184 #for $intab in $ppass.history_inputs:
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185 --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help"
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186 #end for
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187 #for $otab in $ppass.history_outputs:
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49
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188 --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
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48
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189 #end for
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63
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190 --galaxy_root "$__root_dir__"
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48
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191 #end if
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192 ]]></command>
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193 <configfiles>
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194 <configfile name="runme">
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49
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195 $usescript.dynScript
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48
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196 </configfile>
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49
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197 <configfile name="commandoverride">
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198 #if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1:
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199 $cover.command_override
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200 #end if
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63
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201 </configfile>
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49
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202 <configfile name="testoverride">
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203 #if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1:
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204 $cover.test_override
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205 #end if
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63
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206 </configfile>
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48
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207 <configfile name="helpme">
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49
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208 #if $makeMode.make_Tool != "runonly":
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48
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209 ${makeMode.help_text}
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210 #else
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211 $tool_name help goes here
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212 #end if
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213 </configfile>
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214 <configfile name="citeme">
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49
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215 #if $makeMode.make_Tool != "runonly":
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48
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216 #for $citation in $makeMode.citations:
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217 #if $citation.citation_type.type == "bibtex":
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218 **ENTRY**bibtex
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219 ${citation.citation_type.bibtex}
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220 #else
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221 **ENTRY**doi
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222 ${citation.citation_type.doi}
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223 #end if
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224 #end for
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225 #end if
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226 </configfile>
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227 </configfiles>
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228 <inputs>
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229 <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs"
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49
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230 help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only">
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48
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231 <sanitizer invalid_char="">
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232 <valid initial="string.letters,string.digits">
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233 <add value="_"/>
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234 </valid>
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235 </sanitizer>
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236 </param>
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63
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237 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes"
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238 optional="false" help="Use :[ver] for specific version - 'bwa:0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported" />
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239
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240 <conditional name="usescript">
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241 <param name="choosescript" type="select" display="radio" label="Supply a script to either a dependency (e.g. python/R/bash) or a system executable such as Bash"
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242 help = "For script interpreters like Python or bash. Parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them">
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243 <option value="no" selected="true">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>
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244 <option value="yes">Yes, a script is ready to be pasted below</option>
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48
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245 </param>
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49
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246 <when value="no">
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247 <param name="dynScript" type="hidden" value="" />
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63
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248 <param name="scriptrunner" type="hidden" value="" />
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49
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249 </when>
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250 <when value="yes">
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63
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251 <param name="scriptrunner" type="text" value="" label="Interpreter for the script pasted below - eg bash or python. Can be one of the dependencies named above or a system executable"
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252 help="Scripts are interpreted by the executable named here. Use bash for bash scripts, or a conda dependency such as R or Python for those scripts">
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253 <sanitizer invalid_char="">
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254 <valid initial="string.letters,string.digits">
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255 <add value="_"/>
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256 </valid>
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257 </sanitizer>
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258 </param>
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259 <param name="dynScript" type="text" area="True" value="" label="Script for executable below to interpret. It can be one of the Conda dependency names "
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50
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260 help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below">
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49
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261 <sanitizer>
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262 <valid initial="string.printable">
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263 </valid>
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264 <mapping initial="none"/>
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265 </sanitizer>
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266 </param>
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267 </when>
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268 </conditional>
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63
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269
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49
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270 <conditional name="ppass">
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48
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271 <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use">
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50
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272 <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option>
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49
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273 <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option>
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50
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274 <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option>
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48
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275 </param>
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49
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276 <when value="argparse">
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48
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277 <expand macro="io" />
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278 <expand macro="additparam" />
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279 </when>
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49
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280 <when value="positional">
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48
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281 <expand macro="io" />
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282 <expand macro="additparam" />
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283 </when>
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49
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284 <when value="0">
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48
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285 <expand macro="io"/>
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286 </when>
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287 </conditional>
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49
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288 <param name="cl_prefix" type="text" value="" label="Prefix for generated command line. Prepends generated i/o and parameter CL. Use override below to replace completely"
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289 help="Text will replace generated executable/script elements. Sometimes required before i/o and parameters in the generated command line." />
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290 <conditional name="cover">
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291 <param name="commover" type="select" display="radio" label="Add Human wrought code to override the generated XML command and/or test section - DIY"
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292 help = "For arbitrary and artfull command lines. All i/o and parameters must be passed. Choose No unless needed. Not for the faint of heart">
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50
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293 <option value="no" selected="true">No. Use automatically generated command/test XML </option>
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294 <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option>
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63
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295 </param>
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49
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296 <when value="no">
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297 <param name="command_override" type="hidden" value="" />
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298 <param name="test_override" type="hidden" value="" />
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48
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299 </when>
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49
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300 <when value="yes">
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301 <param name="command_override" type="text" area="True" value="" label="Optional. Human wrought command element override XML/template - e.g. for bwa"
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302 help="For arbitrary and artfull command lines. All i/o and parameters must be passed. Leave blank unless needed. Not for the faint of heart">
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303 <sanitizer>
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304 <valid initial="string.printable">
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305 </valid>
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306 <mapping initial="none"/>
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307 </sanitizer>
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308 </param>
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309 <param name="test_override" type="text" area="True" value="" label="Optional. Human wrought test element override XML/template - e.g. for bwa"
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310 help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart">
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311 <sanitizer>
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312 <valid initial="string.printable">
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313 </valid>
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314 <mapping initial="none"/>
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315 </sanitizer>
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63
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316 </param>
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48
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317 </when>
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318 </conditional>
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49
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319
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320 <conditional name="makeMode">
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50
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321 <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. The TF Docker container is recommended for local installation"
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63
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322 help="Installation in this Galaxy is optional" >
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50
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323 <option value="gentest" selected="true">Test with planemo after generating.</option>
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324 <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option>
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49
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325 </param>
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62
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326 <when value="gentest">
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63
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327 <param name="galaxy_apikey" value="" type="hidden" ></param>
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328 <param name="toolshed_apikey" value="" type="hidden" ></param>
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329 <param name="galaxy_url" value="" type="hidden" ></param>
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330 <param name="toolshed_url" value="" type="hidden" ></param>
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50
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331 <expand macro="tool_metadata" />
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49
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332 </when>
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333 <when value="gentestinstall">
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63
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334 <param name="galaxy_url" type="text" value="http://localhost:8080" label="URL for the Galaxy server where the new tool should be installed"
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335 help="Default is localhost">
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336 <sanitizer>
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337 <valid initial="string.printable">
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338 </valid>
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339 <mapping initial="none"/>
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340 </sanitizer>
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341 </param>
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64
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342 <param name="galaxy_apikey" type="text" value="fakekey" label="API key for the Galaxy to install the new tool"
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63
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343 help="Cut and paste from the admin user properties screen">
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344 <sanitizer>
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345 <valid initial="string.letters,string.digits">
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346 </valid>
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347 <mapping initial="none"/>
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348 </sanitizer>
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349 </param>
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350 <param name="toolshed_url" type="text" value="http://localhost:9009" label="URL for the Toolshed where the new tool should be installed"
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351 help="Default value is localhost:9009">
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352 <sanitizer>
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353 <valid initial="string.printable">
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354 </valid>
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355 <mapping initial="none"/>
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356 </sanitizer>
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357 </param>
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64
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358 <param name="toolshed_apikey" type="text" value="fakekey" label="API key for the local toolshed to use when installing the tool"
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63
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359 help="Cut and paste from the admin user properties screen">
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360 <sanitizer>
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361 <valid initial="string.letters,string.digits">
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362 </valid>
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363 <mapping initial="none"/>
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364 </sanitizer>
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365 </param>
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366
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50
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367 <expand macro="tool_metadata" />
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49
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368 </when>
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369 </conditional>
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370
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48
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371 </inputs>
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372 <outputs>
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373
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374 <data format="tgz" name="new_tool" label="${tool_name}_toolshed.tgz" >
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49
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375 <filter>makeMode['make_Tool'] != "runonly"</filter>
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48
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376 </data>
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377
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378 <collection name="TF_run_report" type="list" label="${tool_name} outputs">
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379 <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
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380 </collection>
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381 </outputs>
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382 <tests>
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383 <test>
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50
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384 <param name="user_email" value="admin@galaxy.org"/>
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48
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385 <param name="input_files" value="input1_sample" />
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386 <param name="input_CL" value="1" />
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387 <param name="input_formats" value="txt" />
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388 <param name="input_label" value="input" />
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389 <param name="input_help" value="help" />
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390 <param name="tool_name" value="pyrevpos" />
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391 <param name="parampass" value="positional" />
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49
|
392 <param name="make_Tool" value="generate" />
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48
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393 <param name="tool_version" value="0.01" />
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394 <param name="tool_desc" value="positional reverse" />
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395 <param name="help_text" value="help text goes here" />
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50
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396 <param name="packages" value="python"/>
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397 <param name="history_name" value="output2" />
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48
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398 <param name="history_format" value="txt" />
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399 <param name="history_CL" value="2" />
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400 <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/>
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50
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401 <param name="choosescript" value="yes" />
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402 <param name="script_path" value="$runme"/>
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48
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403 <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
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63
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404
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48
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405 </test>
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406 </tests>
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407 <help>
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408
|
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409 .. class:: warningmark
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410
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411 **Details and attribution**
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412 (see GTF_)
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413
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414 **Local Admins ONLY**
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415 Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
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416
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417 **If you find a bug**
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418 Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_
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419
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420 **What it does**
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421 This tool optionally generates normal workflow compatible first class Galaxy tools
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422
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423 Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form.
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424 Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user.
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425 Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example.
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426
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427 Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime.
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428 These can be editable by the downstream user or baked in.
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429
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430 When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical
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431 set of outputs - these are used to construct a test for the new tool.
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432
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433 If tool generation is required, a new tarball compatible with any Galaxy toolshed is created.
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434 It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or
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435 installed into any toolshed from where it can be installed into your Galaxy.
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436
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437
|
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438 .. class:: warningmark
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439
|
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440 **Note to system administrators**
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441 This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
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442 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
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443
|
|
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444 .. class:: warningmark
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445
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446 **Use on public servers** is STRONGLY discouraged for obvious reasons
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447
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448 The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation.
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449 We recommend that you follow the good code hygiene practices associated with safe toolshed practices.
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450
|
|
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451 Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing:
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452
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453 ::
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454
|
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455 # reverse order of text by row
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456 import sys
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457 inp = sys.argv[1]
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458 outp = sys.argv[2]
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|
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459 i = open(inp,'r').readlines()
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|
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460 o = open(outp,'w')
|
|
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461 for row in i:
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|
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462 rs = row.rstrip()
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|
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463 rs = list(rs)
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|
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464 rs.reverse()
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|
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465 o.write(''.join(rs))
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|
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466 o.write('\n')
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|
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467 o.close()
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468
|
|
|
469 With argparse style parameters:
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470
|
|
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471 ::
|
|
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472
|
|
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473 # reverse order of text by row
|
|
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474 import argparse
|
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475 parser = argparse.ArgumentParser()
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|
|
476 a = parser.add_argument
|
|
|
477 a('--infile',default='')
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|
|
478 a('--outfile',default=None)
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|
|
479 args = parser.parse_args()
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|
|
480 inp = args.infile
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|
|
481 outp = args.outfile
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|
|
482 i = open(inp,'r').readlines()
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|
|
483 o = open(outp,'w')
|
|
|
484 for row in i:
|
|
|
485 rs = row.rstrip()
|
|
|
486 rs = list(rs)
|
|
|
487 rs.reverse()
|
|
|
488 o.write(''.join(rs))
|
|
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489 o.write('\n')
|
|
|
490 o.close()
|
|
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491
|
|
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492
|
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493
|
|
63
|
494 Paper_
|
|
48
|
495
|
|
50
|
496 *Licensing*
|
|
48
|
497
|
|
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498 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
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499 All rights reserved.
|
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500 Licensed under the LGPL_
|
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501
|
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502 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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503 .. _GTF: https://github.com/fubar2/toolfactory
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504 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573
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505
|
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506
|
|
|
507 </help>
|
|
|
508 <citations>
|
|
|
509 <citation type="doi">10.1093/bioinformatics/bts573</citation>
|
|
|
510 </citations>
|
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511 </tool>
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512
|
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513
|
