annotate toolfactory/rgToolFactory2.xml @ 139:6b414af9ca11 draft

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author fubar
date Sat, 17 Apr 2021 05:02:01 +0000
parents 1dba6c7687a9
children 7c8f9793127d
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1 <tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" >
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2 <description>Scripts into tools v2.0</description>
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3 <macros>
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4 <xml name="singleText">
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5 <param name="param_value" type="text" value="" label="Enter this parameter's default text value">
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6 </param>
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7 </xml>
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8 <xml name="singleInt">
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9 <param name="param_value" type="integer" value="" label="Enter this parameter's default integer value" >
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10 </param>
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11 </xml>
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12 <xml name="singleFloat">
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13 <param name="param_value" type="float" value="" label="Enter this parameter's default value">
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14 </param>
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15 </xml>
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16 <xml name="singleBoolean">
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17 <param name="param_value" type="boolean" value="" label="Enter this parameter's default value" />
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18 <param name="truevalue" type="text" value="True" label="Command line value to emit when True" />
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19 <param name="falsevalue" type="boolean" value="True" label="Command line value to emit when False" />
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20 </xml>
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21 <xml name="selectText">
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22 <repeat name="selectTexts" title="Add each option to be presented in a text select box" min="2" default="2"
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23 help="Each text added here will also have a value to be emitted on the command line when the text is chosen">
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24 <param name="select_text" type="text" value="" label="Enter the explanatory text the user will see for this choice" >
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25 </param>
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26 <param name="select_value" type="text" value="" label="Enter the value for the command line when the user selects this option">
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27 </param>
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28 </repeat>
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29 </xml>
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30 <xml name="tool_metadata">
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31 <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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32 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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33 <param name="tool_desc" label="Tool Synopsis" type="text" value=""
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34 help="Supply a brief tool description for the Galaxy tool menu entry" />
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35 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
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36 value="**What it Does**"
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37 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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38 <sanitizer>
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39 <valid initial="string.printable" />
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40 <mapping initial="none"/>
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41 </sanitizer>
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42 </param>
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43 <repeat name="citations" title="Citation">
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44 <conditional name="citation_type">
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45 <param name="type" type="select" display="radio" label="Citation Type">
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46 <option value="doi">DOI</option>
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47 <option value="bibtex">BibTeX</option>
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48 </param>
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49 <when value="doi">
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50 <param name="doi" label="DOI" type="text" value=""
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51 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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52 </when>
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53 <when value="bibtex">
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54 <param name="bibtex" label="BibTex" type="text" area="true"
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55 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
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56 <sanitizer>
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57 <valid initial="string.printable" />
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58 <mapping initial="none"/>
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59 </sanitizer>
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60 </param>
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61 </when>
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62 </conditional>
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63 </repeat>
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64 </xml>
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65 <xml name="io">
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66 <section name="io" title="Input and output files" expanded="true">
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67 <repeat name="history_inputs" title="zero or more input data files to pass on the command line to the executable."
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68 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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69 <param name="input_files" type="data" format="data" label="Select an input file from your history" multiple="false"
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70 help=""/>
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71 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
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72 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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73 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
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74 <column name="value" index="0"/>
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75 </options>
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76 </param>
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77 <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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78 </param>
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79 <param name="input_help" type="text" value="" label="This will become help text on the form." >
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80 </param>
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81 <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
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82 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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83 </param>
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84 <param name="input_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this input as many times as wanted - script/executable must parse these."/>
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85 </repeat>
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86 <repeat name="history_outputs" title="one or more new history items output by the executable to appear in the user history after the tool runs"
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87 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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88 <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false"
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89 help="No spaces! Argparse will also use this name as --[name]">
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90 <sanitizer invalid_char="_">
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91 <valid initial="string.ascii_letters,string.digits" >
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92 <add value="_" />
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93 </valid>
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94 </sanitizer>
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95 </param>
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96 <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
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97 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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98 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
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99 <column name="value" index="0"/>
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100 </options>
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101 </param>
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102 <param name="history_CL" type="text" label="Positional: ordinal integer. Use STDOUT if '>' required. Otherwise ignored if argparse because name is used"
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103 help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/>
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104 <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation"
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105 help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/>
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106 </repeat>
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107 <repeat name="collection_outputs" title="zero or more new history collections to appear in the user history after the tool runs"
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108 help="Hides outputs not needed for downstream tools such as images and intermediate reports." default="0">
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109 <param name="name" type="text" label="Name for new collection with all outputs not individually passed to history outputs"
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110 help="No spaces! Script MUST create and fill a directory with the same name and the tool test MUST be overwritten - see the plotter example for hints">
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111 <sanitizer invalid_char="_">
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112 <valid initial="string.ascii_letters,string.digits" >
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113 <add value="_" />
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114 </valid>
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115 </sanitizer>
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116 </param>
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117 <param name="kind" type="select" multiple="false" label="Select the kind of collection for this output"
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118 help="">
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119 <option value="list" selected="true">List</option>
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120 <option value="paired">Paired</option>
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121 <option value="list:paired">List of paired</option>
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122 </param>
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123 <param name="label" type="text" label="Label for this collection" help="" value=""/>
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124 <param name="discover" type="text" label="Discover datasets expression" help="__name_and_ext__ should catch all filenames with extensions" value="__name_and_ext__"/>
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125 </repeat>
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126
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127 </section>
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128 </xml>
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129 <xml name="additparam">
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130 <section name="addparam" title="Executable or script settings passed on the command line other than I/O files" expanded="true">
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131 <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?"
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132 help="If no, 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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133 <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
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134 <option value="no">No - use the fixed values for all additional parameters - no user editing</option>
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135 </param>
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136 <repeat name="additional_parameters" title="zero or more command line settings for the user to pass to the executable"
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137 help="See examples below to see how these can be parsed by scripts in the various languages">
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138 <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!">
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139 <sanitizer invalid_char="">
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140 <valid initial="string.ascii_letters,string.digits"/>
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141 <mapping initial="none"/>
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142 </sanitizer>
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143 </param>
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144 <conditional name="ap_type">
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145 <param name="param_type" type="select" label="Select the type for this parameter">
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146 <option value="text" selected="true">Text string</option>
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147 <option value="integer">Integer</option>
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148 <option value="float">Float</option>
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149 <option value="boolean">Boolean</option>
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150 <option value="selecttext">Select text string</option>
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151 </param>
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152 <when value = "text">
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153 <expand macro="singleText" />
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154 </when>
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155 <when value = "integer">
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156 <expand macro="singleInt" />
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157 </when>
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158 <when value = "float">
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159 <expand macro="singleFloat" />
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160 </when>
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161 <when value = "boolean">
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162 <expand macro="singleBoolean" />
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163 </when>
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164 <when value = "selecttext">
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165 <expand macro="selectText" />
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166 </when>
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167 </conditional>
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168 <param name="param_label" type="text" value="" label="Enter this parameter's label for the form">
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169 </param>
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170 <param name="param_help" type="text" value="" label="Help for this parameter">
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171 </param>
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172 <param name="param_CL" type="text" label="Positional ordinal | argparse argument name"
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173 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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174 <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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175 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
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176 <param name="param_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this as many times as needed." />
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177 </repeat>
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178 </section>
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179 </xml>
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180 </macros>
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181
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182 <!--<requirements>
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183 <container type="docker"> quay.io/biocontainers/mulled-v2-a561fe5ac66db40ea5722f302d4555ea221ab3ec:1f00bdd160a9bd56118d529588d255e34b5efae2-0</container>
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184 </requirements>-->
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185 <requirements>
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186 <requirement type="package" version="0.4.14">galaxyxml</requirement>
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187 <requirement type="package" version="0.15.0">bioblend</requirement>
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188 <requirement type="package" version="0.10.6">ephemeris</requirement>
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189 <requirement type="package" version="0.74.3">planemo</requirement>
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190 </requirements>
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191
139
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192 <command detect_errors="exit_code"><![CDATA[
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193 #import os
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194 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
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195 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
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196 python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
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197 #else:
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198 python3 $__tool_directory__/rgToolFactory2.py
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199 #if len(str($cl_suffix)) > 0:
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200 --cl_suffix "$cl_suffix"
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201 #end if
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202 #if $cover.commover == "yes":
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203 #if len(str($cover.command_override)) > 10:
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204 --command_override "$commandoverride"
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205 #end if
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206 #if len(str($cover.test_override)) > 10:
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207 --test_override "$testoverride"
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208 #end if
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209 #end if
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210 --packages "$deps.packages"
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211 #if $deps.usescript.choosescript == "yes":
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212 --script_path "$runme"
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213 --sysexe "$deps.usescript.scriptrunner"
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214 #end if
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215 --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$io_param.ppass.parampass"
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216
121
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217 #if str($make.makeMode.make_Tool)!="runonly":
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218 --make_Tool "$make.makeMode.make_Tool"
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219 --tool_desc "$make.makeMode.tool_desc"
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220 --tool_version "$make.makeMode.tool_version"
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221 --help_text "$helpme"
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222 --new_tool "$new_tool"
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223 --toolshed_api_key "$make.makeMode.toolshed_apikey"
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224 --galaxy_api_key "$make.makeMode.galaxy_apikey"
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225 --toolshed_url "$make.makeMode.toolshed_url"
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226 --galaxy_url "$make.makeMode.galaxy_url"
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227 #end if
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228 #if $io_param.ppass.parampass != '0':
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229 #if str($io_param.ppass.addparam.edit_params) == "yes":
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230 --edit_additional_parameters
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231 #end if
126
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232 #for $apar in $io_param.ppass.addparam.additional_parameters:
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233 #if $apar.ap_type.param_type=="selecttext":
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234 --selecttext_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help",
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235 "type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [
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236 #for $i,$st in enumerate($apar.ap_type.selectTexts):
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237 "$st.select_value"
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238 #if ($i < (len($apar.ap_type.selectTexts)-1)):
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239 ,
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240 #end if
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241 #end for
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242 ], "texts": [
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243 #for $i,$st in enumerate($apar.ap_type.selectTexts):
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244 "$st.select_text"
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245 #if ($i < (len($apar.ap_type.selectTexts)-1)):
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246 ,
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247 #end if
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248
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249 #end for
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250 ]
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251 }'
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252 #else:
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253 --additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help",
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254 "type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed", "repeat": "$apar.param_repeat"}'
126
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255 #end if
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256 #end for
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257 #end if
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258 #for $intab in $io_param.ppass.io.history_inputs:
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259 --input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label", "help": "$intab.input_help", "repeat": "$intab.input_repeat"}'
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260 #end for
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261 #for $otab in $io_param.ppass.io.history_outputs:
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262 --output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"}'
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263 #end for
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264 #for $collect in $io_param.ppass.io.collection_outputs:
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265 --collection '{"name": "$collect.name", "kind": "$collect.kind", "discover": "$collect.discover", "label": "$collect.label"}'
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266 #end for
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267 --galaxy_root "$__root_dir__"
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268 --tool_dir "$__tool_directory__"
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269 #end if
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270 ]]></command>
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271 <configfiles>
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272 <configfile name="runme">
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273 $deps.usescript.dynScript
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274 </configfile>
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275 <configfile name="commandoverride">
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276 #if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1:
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277 $cover.command_override
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278 #end if
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279 </configfile>
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280 <configfile name="testoverride">
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281 #if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1:
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282 $cover.test_override
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283 #end if
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284 </configfile>
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285 <configfile name="helpme">
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286 #if $make.makeMode.make_Tool != "runonly":
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287 ${make.makeMode.help_text}
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288 #else
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289 $tool_name help goes here
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290 #end if
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291 </configfile>
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292 <configfile name="citeme">
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293 #if $make.makeMode.make_Tool != "runonly":
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294 #for $citation in $make.makeMode.citations:
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295 #if $citation.citation_type.type == "bibtex":
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296 **ENTRY**bibtex
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297 ${citation.citation_type.bibtex}
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298 #else
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299 **ENTRY**doi
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300 ${citation.citation_type.doi}
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301 #end if
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302 #end for
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303 #end if
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304 </configfile>
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305 </configfiles>
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306 <inputs>
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307 <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs"
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308 help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only">
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309 <sanitizer invalid_char="">
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310 <valid initial="string.ascii_lowercase,string.digits">
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311 <add value="_"/>
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312 </valid>
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313 </sanitizer>
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314 </param>
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315
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316 <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true">
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317
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318 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes"
126
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319 help="Use =[ver] or :[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" />
121
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320
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diff changeset
321 <conditional name="usescript">
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322 <param name="choosescript" type="select" display="radio" label="Supply a script for a dependency (e.g. python/R/bash) or a system executable such as Bash"
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323 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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324 <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>
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325 <option value="yes" selected="true">Yes, a script is ready to be pasted below</option>
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326 </param>
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327 <when value="no">
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328 <param name="dynScript" type="hidden" value="" />
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329 <param name="scriptrunner" type="hidden" value="" />
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330 </when>
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331 <when value="yes">
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332 <param name="scriptrunner" type="text" value="" label="Interpreter for the script - eg bash or python. Can be one of the dependencies named above or a system executable"
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333 help="Scripts are interpreted by the executable named here. For conda r-base, 'Rscript --vanilla' or for conda planemo, 'planemo test' for example">
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334 </param>
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335 <param name="dynScript" type="text" area="True" value="" label="Script for executable above to interpret. It can be one of the Conda dependency names "
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336 help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below">
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337 <sanitizer>
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338 <valid initial="string.printable"/>
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339 <mapping initial="none"/>
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340 </sanitizer>
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341 </param>
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342 </when>
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343 </conditional>
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344 </section>
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345 <section name="io_param" title="Data file input, output and settings forming the executable or script command line" expanded="true">
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346 <conditional name="ppass">
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347 <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use">
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348 <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option>
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349 <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option>
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350 <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option>
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351 </param>
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352 <when value="argparse">
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353 <expand macro="io" />
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354 <expand macro="additparam" />
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355 </when>
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356 <when value="positional">
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357 <expand macro="io" />
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358 <expand macro="additparam" />
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359 </when>
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360 <when value="0">
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361 <expand macro="io"/>
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362 </when>
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363 </conditional>
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364 </section>
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365 <param name="cl_suffix" type="text" value="" label="Suffix for generated command line. Useful for bash post processing. Use override below to replace completely"
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366 help="';' separated bash commands can be used here for post processing - added at end of autogenerated command line">
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367 <sanitizer>
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368 <valid initial="string.printable" />
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369 <mapping initial="none"/>
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370 </sanitizer>
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371 </param>
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372 <conditional name="cover">
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373 <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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parents:
diff changeset
374 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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parents:
diff changeset
375 <option value="no" selected="true">No. Use automatically generated command/test XML </option>
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parents:
diff changeset
376 <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option>
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parents:
diff changeset
377 </param>
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parents:
diff changeset
378 <when value="no">
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parents:
diff changeset
379 <param name="command_override" type="hidden" value="" />
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parents:
diff changeset
380 <param name="test_override" type="hidden" value="" />
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parents:
diff changeset
381 </when>
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fubar
parents:
diff changeset
382 <when value="yes">
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fubar
parents:
diff changeset
383 <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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fubar
parents:
diff changeset
384 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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parents:
diff changeset
385 <sanitizer>
126
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parents: 123
diff changeset
386 <valid initial="string.printable"/>
121
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parents:
diff changeset
387 <mapping initial="none"/>
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parents:
diff changeset
388 </sanitizer>
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parents:
diff changeset
389 </param>
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fubar
parents:
diff changeset
390 <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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fubar
parents:
diff changeset
391 help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart">
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fubar
parents:
diff changeset
392 <sanitizer>
126
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parents: 123
diff changeset
393 <valid initial="string.printable" />
121
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parents:
diff changeset
394 <mapping initial="none"/>
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parents:
diff changeset
395 </sanitizer>
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parents:
diff changeset
396 </param>
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parents:
diff changeset
397 </when>
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parents:
diff changeset
398 </conditional>
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fubar
parents:
diff changeset
399 <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true">
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fubar
parents:
diff changeset
400 <conditional name="makeMode">
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parents:
diff changeset
401 <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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parents:
diff changeset
402 help="Installation in this Galaxy is optional" >
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parents:
diff changeset
403 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
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parents:
diff changeset
404 <option value="gentest" selected="true">Test with planemo after generating.</option>
126
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diff changeset
405 <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option>
121
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406 </param>
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diff changeset
407 <when value="generate">
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parents:
diff changeset
408 <param name="galaxy_apikey" value="" type="hidden" ></param>
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parents:
diff changeset
409 <param name="toolshed_apikey" value="" type="hidden" ></param>
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parents:
diff changeset
410 <param name="galaxy_url" value="" type="hidden" ></param>
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parents:
diff changeset
411 <param name="toolshed_url" value="" type="hidden" ></param>
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parents:
diff changeset
412 <expand macro="tool_metadata" />
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parents:
diff changeset
413 </when>
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parents:
diff changeset
414 <when value="gentest">
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fubar
parents:
diff changeset
415 <param name="galaxy_apikey" value="" type="hidden" ></param>
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parents:
diff changeset
416 <param name="toolshed_apikey" value="" type="hidden" ></param>
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parents:
diff changeset
417 <param name="galaxy_url" value="" type="hidden" ></param>
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parents:
diff changeset
418 <param name="toolshed_url" value="" type="hidden" ></param>
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fubar
parents:
diff changeset
419 <expand macro="tool_metadata" />
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parents:
diff changeset
420 </when>
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parents:
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421 <when value="gentestinstall">
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parents:
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422 <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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parents:
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423 help="Default is localhost">
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parents:
diff changeset
424 <sanitizer>
126
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diff changeset
425 <valid initial="string.printable" />
121
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parents:
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426 <mapping initial="none"/>
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parents:
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427 </sanitizer>
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parents:
diff changeset
428 </param>
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parents:
diff changeset
429 <param name="galaxy_apikey" type="text" value="fakekey" label="API key for the Galaxy to install the new tool"
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fubar
parents:
diff changeset
430 help="Cut and paste from the admin user properties screen">
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parents:
diff changeset
431 <sanitizer>
126
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parents: 123
diff changeset
432 <valid initial="string.ascii_letters,string.digits" />
121
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parents:
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433 <mapping initial="none"/>
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parents:
diff changeset
434 </sanitizer>
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parents:
diff changeset
435 </param>
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parents:
diff changeset
436 <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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parents:
diff changeset
437 help="Default value is localhost:9009">
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parents:
diff changeset
438 <sanitizer>
126
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parents: 123
diff changeset
439 <valid initial="string.printable" />
121
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parents:
diff changeset
440 <mapping initial="none"/>
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parents:
diff changeset
441 </sanitizer>
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parents:
diff changeset
442 </param>
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parents:
diff changeset
443 <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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fubar
parents:
diff changeset
444 help="Cut and paste from the admin user properties screen">
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parents:
diff changeset
445 <sanitizer>
126
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parents: 123
diff changeset
446 <valid initial="string.ascii_letters,string.digits" />
121
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parents:
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447 <mapping initial="none"/>
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parents:
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448 </sanitizer>
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parents:
diff changeset
449 </param>
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parents:
diff changeset
450 <expand macro="tool_metadata" />
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parents:
diff changeset
451 </when>
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parents:
diff changeset
452 </conditional>
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parents:
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453 </section>
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parents:
diff changeset
454 </inputs>
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parents:
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455 <outputs>
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456
126
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457 <data format="toolshed.gz" name="new_tool" label="${tool_name}_toolshed.gz" >
121
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parents:
diff changeset
458 <filter>makeMode['make_Tool'] != "runonly"</filter>
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parents:
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459 </data>
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parents:
diff changeset
460
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parents:
diff changeset
461 <collection name="TF_run_report" type="list" label="${tool_name} outputs">
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parents:
diff changeset
462 <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
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parents:
diff changeset
463 </collection>
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parents:
diff changeset
464 </outputs>
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parents:
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465 <tests>
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parents:
diff changeset
466 <test>
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parents:
diff changeset
467 <param name="user_email" value="admin@galaxy.org"/>
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parents:
diff changeset
468 <param name="input_files" value="input1_sample" />
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parents:
diff changeset
469 <param name="input_CL" value="1" />
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parents:
diff changeset
470 <param name="input_formats" value="txt" />
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parents:
diff changeset
471 <param name="input_label" value="input" />
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parents:
diff changeset
472 <param name="input_help" value="help" />
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parents:
diff changeset
473 <param name="tool_name" value="pyrevpos" />
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parents:
diff changeset
474 <param name="parampass" value="positional" />
126
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475 <param name="make_Tool" value="gentest" />
121
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parents:
diff changeset
476 <param name="tool_version" value="0.01" />
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parents:
diff changeset
477 <param name="tool_desc" value="positional reverse" />
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parents:
diff changeset
478 <param name="help_text" value="help text goes here" />
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parents:
diff changeset
479 <param name="packages" value="python"/>
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parents:
diff changeset
480 <param name="history_name" value="output2" />
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parents:
diff changeset
481 <param name="history_format" value="txt" />
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parents:
diff changeset
482 <param name="history_CL" value="2" />
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parents:
diff changeset
483 <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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parents:
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484 <param name="choosescript" value="yes" />
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parents:
diff changeset
485 <param name="script_path" value="$runme"/>
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parents:
diff changeset
486 <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
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parents:
diff changeset
487 </test>
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parents:
diff changeset
488 </tests>
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parents:
diff changeset
489 <help>
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parents:
diff changeset
490
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parents:
diff changeset
491 .. class:: warningmark
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parents:
diff changeset
492
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parents:
diff changeset
493 **Details and attribution**
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parents:
diff changeset
494 (see GTF_)
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parents:
diff changeset
495
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parents:
diff changeset
496 **Local Admins ONLY**
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parents:
diff changeset
497 Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
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parents:
diff changeset
498
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parents:
diff changeset
499 **If you find a bug**
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parents:
diff changeset
500 Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_
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parents:
diff changeset
501
2050b2475ae5 Uploaded
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parents:
diff changeset
502 **What it does**
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parents:
diff changeset
503 This tool optionally generates normal workflow compatible first class Galaxy tools
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parents:
diff changeset
504
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parents:
diff changeset
505 Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form.
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parents:
diff changeset
506 Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user.
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parents:
diff changeset
507 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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parents:
diff changeset
508
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parents:
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509 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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parents:
diff changeset
510 These can be editable by the downstream user or baked in.
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parents:
diff changeset
511
2050b2475ae5 Uploaded
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parents:
diff changeset
512 When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical
2050b2475ae5 Uploaded
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parents:
diff changeset
513 set of outputs - these are used to construct a test for the new tool.
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parents:
diff changeset
514
2050b2475ae5 Uploaded
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parents:
diff changeset
515 If tool generation is required, a new tarball compatible with any Galaxy toolshed is created.
2050b2475ae5 Uploaded
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parents:
diff changeset
516 It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or
2050b2475ae5 Uploaded
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parents:
diff changeset
517 installed into any toolshed from where it can be installed into your Galaxy.
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parents:
diff changeset
518
2050b2475ae5 Uploaded
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parents:
diff changeset
519
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parents:
diff changeset
520 .. class:: warningmark
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parents:
diff changeset
521
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parents:
diff changeset
522 **Note to system administrators**
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parents:
diff changeset
523 This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
2050b2475ae5 Uploaded
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parents:
diff changeset
524 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
2050b2475ae5 Uploaded
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parents:
diff changeset
525
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parents:
diff changeset
526 .. class:: warningmark
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parents:
diff changeset
527
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parents:
diff changeset
528 **Use on public servers** is STRONGLY discouraged for obvious reasons
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parents:
diff changeset
529
2050b2475ae5 Uploaded
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parents:
diff changeset
530 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.
2050b2475ae5 Uploaded
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parents:
diff changeset
531 We recommend that you follow the good code hygiene practices associated with safe toolshed practices.
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parents:
diff changeset
532
2050b2475ae5 Uploaded
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parents:
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533 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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parents:
diff changeset
534
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parents:
diff changeset
535 ::
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536
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parents:
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537 # reverse order of text by row
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parents:
diff changeset
538 import sys
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parents:
diff changeset
539 inp = sys.argv[1]
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parents:
diff changeset
540 outp = sys.argv[2]
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parents:
diff changeset
541 i = open(inp,'r').readlines()
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fubar
parents:
diff changeset
542 o = open(outp,'w')
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fubar
parents:
diff changeset
543 for row in i:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
544 rs = row.rstrip()
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fubar
parents:
diff changeset
545 rs = list(rs)
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parents:
diff changeset
546 rs.reverse()
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parents:
diff changeset
547 o.write(''.join(rs))
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parents:
diff changeset
548 o.write('\n')
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fubar
parents:
diff changeset
549 o.close()
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parents:
diff changeset
550
2050b2475ae5 Uploaded
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parents:
diff changeset
551 With argparse style parameters:
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parents:
diff changeset
552
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parents:
diff changeset
553 ::
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parents:
diff changeset
554
2050b2475ae5 Uploaded
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parents:
diff changeset
555 # reverse order of text by row
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parents:
diff changeset
556 import argparse
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parents:
diff changeset
557 parser = argparse.ArgumentParser()
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parents:
diff changeset
558 a = parser.add_argument
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parents:
diff changeset
559 a('--infile',default='')
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parents:
diff changeset
560 a('--outfile',default=None)
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parents:
diff changeset
561 args = parser.parse_args()
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parents:
diff changeset
562 inp = args.infile
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fubar
parents:
diff changeset
563 outp = args.outfile
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parents:
diff changeset
564 i = open(inp,'r').readlines()
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parents:
diff changeset
565 o = open(outp,'w')
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
566 for row in i:
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fubar
parents:
diff changeset
567 rs = row.rstrip()
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fubar
parents:
diff changeset
568 rs = list(rs)
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fubar
parents:
diff changeset
569 rs.reverse()
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parents:
diff changeset
570 o.write(''.join(rs))
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fubar
parents:
diff changeset
571 o.write('\n')
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parents:
diff changeset
572 o.close()
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parents:
diff changeset
573
126
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parents: 123
diff changeset
574 R script to draw some plots - use a collection.
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parents: 123
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575
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parents: 123
diff changeset
576 ::
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diff changeset
577
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578
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579 \# note this script takes NO input because it generates random data
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580 dir.create('plots')
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581 for (i in 1:10) {
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582 foo = runif(100)
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583 bar = rnorm(100)
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584 bar = foo + 0.05*bar
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585 pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_'))
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586 plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6)
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587 dev.off()
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588 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
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589 bar = as.matrix(foo)
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590 pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_'))
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591 heatmap(bar,main='Random Heatmap')
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592 dev.off()
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593 }
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594
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595
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596
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597 Paper_
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598
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599 *Licensing*
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600
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601 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
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602 All rights reserved.
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603 Licensed under the LGPL_
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604
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605 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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606 .. _GTF: https://github.com/fubar2/toolfactory
126
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607 .. _Paper: https://academic.oup.com/bioinformatics/article/28/23/3139/192853
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608
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609
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610 </help>
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611 <citations>
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612 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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613 </citations>
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614 </tool>
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615
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616