annotate toolfactory/rgToolFactory2.xml @ 131:72d190989c68 draft

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author fubar
date Fri, 09 Apr 2021 23:23:12 +0000
parents e8e8071c9d0c
children 7805fdac70ed
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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 <requirement type="package" version="0.4.13">galaxyxml</requirement>
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184 <requirement type="package" version="0.14.0">bioblend</requirement>
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185 <requirement type="package" version="0.10.6">ephemeris</requirement>
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186 <requirement type="package" version="0.74.3">planemo</requirement>
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187 </requirements>
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188
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189 <command ><![CDATA[
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190 #import os
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191 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
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192 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
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193 python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
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194 #else:
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195 python3 $__tool_directory__/rgToolFactory2.py
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196 #if len(str($cl_suffix)) > 0:
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197 --cl_suffix "$cl_suffix"
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198 #end if
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199 #if $cover.commover == "yes":
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200 #if len(str($cover.command_override)) > 10:
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201 --command_override "$commandoverride"
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202 #end if
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203 #if len(str($cover.test_override)) > 10:
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204 --test_override "$testoverride"
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205 #end if
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206 #end if
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207 --packages "$deps.packages"
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208 #if $deps.usescript.choosescript == "yes":
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209 --script_path "$runme"
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210 --sysexe "$deps.usescript.scriptrunner"
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211 #end if
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212 --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$io_param.ppass.parampass"
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213
121
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214 #if str($make.makeMode.make_Tool)!="runonly":
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215 --make_Tool "$make.makeMode.make_Tool"
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216 --tool_desc "$make.makeMode.tool_desc"
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217 --tool_version "$make.makeMode.tool_version"
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218 --help_text "$helpme"
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219 --new_tool "$new_tool"
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220 --toolshed_api_key "$make.makeMode.toolshed_apikey"
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221 --galaxy_api_key "$make.makeMode.galaxy_apikey"
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222 --toolshed_url "$make.makeMode.toolshed_url"
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223 --galaxy_url "$make.makeMode.galaxy_url"
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224 #end if
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225 #if $io_param.ppass.parampass != '0':
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226 #if str($io_param.ppass.addparam.edit_params) == "yes":
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227 --edit_additional_parameters
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228 #end if
126
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229 #for $apar in $io_param.ppass.addparam.additional_parameters:
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230 #if $apar.ap_type.param_type=="selecttext":
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231 --selecttext_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help",
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232 "type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [
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233 #for $i,$st in enumerate($apar.ap_type.selectTexts):
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234 "$st.select_value"
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235 #if ($i < (len($apar.ap_type.selectTexts)-1)):
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236 ,
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237 #end if
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238 #end for
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239 ], "texts": [
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240 #for $i,$st in enumerate($apar.ap_type.selectTexts):
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241 "$st.select_text"
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242 #if ($i < (len($apar.ap_type.selectTexts)-1)):
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243 ,
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244 #end if
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245
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246 #end for
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247 ]
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248 }'
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249 #else:
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250 --additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help",
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251 "type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed", "repeat": "$apar.param_repeat"}'
126
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252 #end if
121
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253 #end for
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254 #end if
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255 #for $intab in $io_param.ppass.io.history_inputs:
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256 --input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label", "help": "$intab.input_help", "repeat": "$intab.input_repeat"}'
121
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257 #end for
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258 #for $otab in $io_param.ppass.io.history_outputs:
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259 --output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"}'
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260 #end for
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261 #for $collect in $io_param.ppass.io.collection_outputs:
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262 --collection '{"name": "$collect.name", "kind": "$collect.kind", "discover": "$collect.discover", "label": "$collect.label"}'
121
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263 #end for
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264 --galaxy_root "$__root_dir__"
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265 --tool_dir "$__tool_directory__"
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266 #end if
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267 ]]></command>
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268 <configfiles>
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269 <configfile name="runme">
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270 $deps.usescript.dynScript
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271 </configfile>
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272 <configfile name="commandoverride">
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273 #if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1:
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274 $cover.command_override
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275 #end if
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276 </configfile>
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277 <configfile name="testoverride">
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278 #if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1:
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279 $cover.test_override
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280 #end if
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281 </configfile>
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282 <configfile name="helpme">
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283 #if $make.makeMode.make_Tool != "runonly":
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284 ${make.makeMode.help_text}
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285 #else
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286 $tool_name help goes here
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287 #end if
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288 </configfile>
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289 <configfile name="citeme">
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290 #if $make.makeMode.make_Tool != "runonly":
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291 #for $citation in $make.makeMode.citations:
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292 #if $citation.citation_type.type == "bibtex":
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293 **ENTRY**bibtex
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294 ${citation.citation_type.bibtex}
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295 #else
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296 **ENTRY**doi
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297 ${citation.citation_type.doi}
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298 #end if
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299 #end for
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300 #end if
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301 </configfile>
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302 </configfiles>
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303 <inputs>
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304 <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs"
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305 help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only">
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306 <sanitizer invalid_char="">
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307 <valid initial="string.ascii_lowercase,string.digits">
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308 <add value="_"/>
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309 </valid>
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310 </sanitizer>
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311 </param>
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312
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313 <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true">
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314
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315 <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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316 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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317
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318 <conditional name="usescript">
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319 <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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320 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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321 <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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322 <option value="yes" selected="true">Yes, a script is ready to be pasted below</option>
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323 </param>
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324 <when value="no">
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325 <param name="dynScript" type="hidden" value="" />
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parents:
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326 <param name="scriptrunner" type="hidden" value="" />
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327 </when>
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328 <when value="yes">
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329 <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"
126
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330 help="Scripts are interpreted by the executable named here. For conda r-base, 'Rscript --vanilla' or for conda planemo, 'planemo test' for example">
121
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331 </param>
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332 <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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333 help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below">
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334 <sanitizer>
126
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335 <valid initial="string.printable"/>
121
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336 <mapping initial="none"/>
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337 </sanitizer>
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338 </param>
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339 </when>
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340 </conditional>
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341 </section>
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342 <section name="io_param" title="Data file input, output and settings forming the executable or script command line" expanded="true">
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343 <conditional name="ppass">
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344 <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use">
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345 <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option>
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346 <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option>
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347 <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option>
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348 </param>
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349 <when value="argparse">
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350 <expand macro="io" />
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351 <expand macro="additparam" />
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352 </when>
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353 <when value="positional">
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parents:
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354 <expand macro="io" />
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355 <expand macro="additparam" />
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356 </when>
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357 <when value="0">
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358 <expand macro="io"/>
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359 </when>
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360 </conditional>
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361 </section>
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362 <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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363 help="';' separated bash commands can be used here for post processing - added at end of autogenerated command line">
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364 <sanitizer>
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365 <valid initial="string.printable" />
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366 <mapping initial="none"/>
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367 </sanitizer>
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368 </param>
121
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369 <conditional name="cover">
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370 <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:
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371 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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372 <option value="no" selected="true">No. Use automatically generated command/test XML </option>
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373 <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option>
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374 </param>
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diff changeset
375 <when value="no">
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parents:
diff changeset
376 <param name="command_override" type="hidden" value="" />
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fubar
parents:
diff changeset
377 <param name="test_override" type="hidden" value="" />
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fubar
parents:
diff changeset
378 </when>
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fubar
parents:
diff changeset
379 <when value="yes">
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fubar
parents:
diff changeset
380 <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
381 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
382 <sanitizer>
126
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parents: 123
diff changeset
383 <valid initial="string.printable"/>
121
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parents:
diff changeset
384 <mapping initial="none"/>
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fubar
parents:
diff changeset
385 </sanitizer>
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parents:
diff changeset
386 </param>
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fubar
parents:
diff changeset
387 <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
388 help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart">
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fubar
parents:
diff changeset
389 <sanitizer>
126
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parents: 123
diff changeset
390 <valid initial="string.printable" />
121
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parents:
diff changeset
391 <mapping initial="none"/>
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fubar
parents:
diff changeset
392 </sanitizer>
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parents:
diff changeset
393 </param>
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fubar
parents:
diff changeset
394 </when>
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parents:
diff changeset
395 </conditional>
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fubar
parents:
diff changeset
396 <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true">
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fubar
parents:
diff changeset
397 <conditional name="makeMode">
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parents:
diff changeset
398 <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
399 help="Installation in this Galaxy is optional" >
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fubar
parents:
diff changeset
400 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
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parents:
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401 <option value="gentest" selected="true">Test with planemo after generating.</option>
126
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diff changeset
402 <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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parents:
diff changeset
403 </param>
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parents:
diff changeset
404 <when value="generate">
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fubar
parents:
diff changeset
405 <param name="galaxy_apikey" value="" type="hidden" ></param>
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fubar
parents:
diff changeset
406 <param name="toolshed_apikey" value="" type="hidden" ></param>
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parents:
diff changeset
407 <param name="galaxy_url" value="" type="hidden" ></param>
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parents:
diff changeset
408 <param name="toolshed_url" value="" type="hidden" ></param>
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fubar
parents:
diff changeset
409 <expand macro="tool_metadata" />
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parents:
diff changeset
410 </when>
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parents:
diff changeset
411 <when value="gentest">
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fubar
parents:
diff changeset
412 <param name="galaxy_apikey" value="" type="hidden" ></param>
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fubar
parents:
diff changeset
413 <param name="toolshed_apikey" value="" type="hidden" ></param>
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fubar
parents:
diff changeset
414 <param name="galaxy_url" value="" type="hidden" ></param>
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fubar
parents:
diff changeset
415 <param name="toolshed_url" value="" type="hidden" ></param>
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fubar
parents:
diff changeset
416 <expand macro="tool_metadata" />
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parents:
diff changeset
417 </when>
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parents:
diff changeset
418 <when value="gentestinstall">
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parents:
diff changeset
419 <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:
diff changeset
420 help="Default is localhost">
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parents:
diff changeset
421 <sanitizer>
126
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parents: 123
diff changeset
422 <valid initial="string.printable" />
121
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parents:
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423 <mapping initial="none"/>
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parents:
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424 </sanitizer>
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parents:
diff changeset
425 </param>
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fubar
parents:
diff changeset
426 <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
427 help="Cut and paste from the admin user properties screen">
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fubar
parents:
diff changeset
428 <sanitizer>
126
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parents: 123
diff changeset
429 <valid initial="string.ascii_letters,string.digits" />
121
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parents:
diff changeset
430 <mapping initial="none"/>
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parents:
diff changeset
431 </sanitizer>
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parents:
diff changeset
432 </param>
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parents:
diff changeset
433 <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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fubar
parents:
diff changeset
434 help="Default value is localhost:9009">
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fubar
parents:
diff changeset
435 <sanitizer>
126
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parents: 123
diff changeset
436 <valid initial="string.printable" />
121
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parents:
diff changeset
437 <mapping initial="none"/>
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parents:
diff changeset
438 </sanitizer>
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parents:
diff changeset
439 </param>
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fubar
parents:
diff changeset
440 <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
441 help="Cut and paste from the admin user properties screen">
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fubar
parents:
diff changeset
442 <sanitizer>
126
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parents: 123
diff changeset
443 <valid initial="string.ascii_letters,string.digits" />
121
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parents:
diff changeset
444 <mapping initial="none"/>
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parents:
diff changeset
445 </sanitizer>
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parents:
diff changeset
446 </param>
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fubar
parents:
diff changeset
447 <expand macro="tool_metadata" />
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parents:
diff changeset
448 </when>
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parents:
diff changeset
449 </conditional>
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parents:
diff changeset
450 </section>
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parents:
diff changeset
451 </inputs>
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parents:
diff changeset
452 <outputs>
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diff changeset
453
126
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454 <data format="toolshed.gz" name="new_tool" label="${tool_name}_toolshed.gz" >
121
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parents:
diff changeset
455 <filter>makeMode['make_Tool'] != "runonly"</filter>
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parents:
diff changeset
456 </data>
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parents:
diff changeset
457
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parents:
diff changeset
458 <collection name="TF_run_report" type="list" label="${tool_name} outputs">
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parents:
diff changeset
459 <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
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parents:
diff changeset
460 </collection>
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parents:
diff changeset
461 </outputs>
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parents:
diff changeset
462 <tests>
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fubar
parents:
diff changeset
463 <test>
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parents:
diff changeset
464 <param name="user_email" value="admin@galaxy.org"/>
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fubar
parents:
diff changeset
465 <param name="input_files" value="input1_sample" />
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parents:
diff changeset
466 <param name="input_CL" value="1" />
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parents:
diff changeset
467 <param name="input_formats" value="txt" />
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parents:
diff changeset
468 <param name="input_label" value="input" />
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parents:
diff changeset
469 <param name="input_help" value="help" />
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parents:
diff changeset
470 <param name="tool_name" value="pyrevpos" />
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parents:
diff changeset
471 <param name="parampass" value="positional" />
126
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472 <param name="make_Tool" value="gentest" />
121
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parents:
diff changeset
473 <param name="tool_version" value="0.01" />
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parents:
diff changeset
474 <param name="tool_desc" value="positional reverse" />
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fubar
parents:
diff changeset
475 <param name="help_text" value="help text goes here" />
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parents:
diff changeset
476 <param name="packages" value="python"/>
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fubar
parents:
diff changeset
477 <param name="history_name" value="output2" />
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fubar
parents:
diff changeset
478 <param name="history_format" value="txt" />
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parents:
diff changeset
479 <param name="history_CL" value="2" />
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parents:
diff changeset
480 <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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481 <param name="choosescript" value="yes" />
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parents:
diff changeset
482 <param name="script_path" value="$runme"/>
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parents:
diff changeset
483 <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
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parents:
diff changeset
484 </test>
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parents:
diff changeset
485 </tests>
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parents:
diff changeset
486 <help>
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parents:
diff changeset
487
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parents:
diff changeset
488 .. class:: warningmark
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parents:
diff changeset
489
2050b2475ae5 Uploaded
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parents:
diff changeset
490 **Details and attribution**
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parents:
diff changeset
491 (see GTF_)
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parents:
diff changeset
492
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parents:
diff changeset
493 **Local Admins ONLY**
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parents:
diff changeset
494 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
495
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parents:
diff changeset
496 **If you find a bug**
2050b2475ae5 Uploaded
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parents:
diff changeset
497 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
498
2050b2475ae5 Uploaded
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parents:
diff changeset
499 **What it does**
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parents:
diff changeset
500 This tool optionally generates normal workflow compatible first class Galaxy tools
2050b2475ae5 Uploaded
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parents:
diff changeset
501
2050b2475ae5 Uploaded
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parents:
diff changeset
502 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
503 Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user.
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fubar
parents:
diff changeset
504 Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example.
2050b2475ae5 Uploaded
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parents:
diff changeset
505
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parents:
diff changeset
506 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
507 These can be editable by the downstream user or baked in.
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parents:
diff changeset
508
2050b2475ae5 Uploaded
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parents:
diff changeset
509 When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
510 set of outputs - these are used to construct a test for the new tool.
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fubar
parents:
diff changeset
511
2050b2475ae5 Uploaded
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parents:
diff changeset
512 If tool generation is required, a new tarball compatible with any Galaxy toolshed is created.
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
513 It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
514 installed into any toolshed from where it can be installed into your Galaxy.
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
515
2050b2475ae5 Uploaded
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parents:
diff changeset
516
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parents:
diff changeset
517 .. class:: warningmark
2050b2475ae5 Uploaded
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parents:
diff changeset
518
2050b2475ae5 Uploaded
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parents:
diff changeset
519 **Note to system administrators**
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
520 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
521 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
522
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
523 .. class:: warningmark
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parents:
diff changeset
524
2050b2475ae5 Uploaded
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parents:
diff changeset
525 **Use on public servers** is STRONGLY discouraged for obvious reasons
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parents:
diff changeset
526
2050b2475ae5 Uploaded
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parents:
diff changeset
527 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
528 We recommend that you follow the good code hygiene practices associated with safe toolshed practices.
2050b2475ae5 Uploaded
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parents:
diff changeset
529
2050b2475ae5 Uploaded
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parents:
diff changeset
530 Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing:
2050b2475ae5 Uploaded
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parents:
diff changeset
531
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parents:
diff changeset
532 ::
2050b2475ae5 Uploaded
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parents:
diff changeset
533
2050b2475ae5 Uploaded
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parents:
diff changeset
534 # reverse order of text by row
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parents:
diff changeset
535 import sys
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
536 inp = sys.argv[1]
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fubar
parents:
diff changeset
537 outp = sys.argv[2]
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fubar
parents:
diff changeset
538 i = open(inp,'r').readlines()
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fubar
parents:
diff changeset
539 o = open(outp,'w')
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fubar
parents:
diff changeset
540 for row in i:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
541 rs = row.rstrip()
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fubar
parents:
diff changeset
542 rs = list(rs)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
543 rs.reverse()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
544 o.write(''.join(rs))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
545 o.write('\n')
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
546 o.close()
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fubar
parents:
diff changeset
547
2050b2475ae5 Uploaded
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parents:
diff changeset
548 With argparse style parameters:
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fubar
parents:
diff changeset
549
2050b2475ae5 Uploaded
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parents:
diff changeset
550 ::
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parents:
diff changeset
551
2050b2475ae5 Uploaded
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parents:
diff changeset
552 # reverse order of text by row
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fubar
parents:
diff changeset
553 import argparse
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fubar
parents:
diff changeset
554 parser = argparse.ArgumentParser()
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fubar
parents:
diff changeset
555 a = parser.add_argument
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fubar
parents:
diff changeset
556 a('--infile',default='')
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fubar
parents:
diff changeset
557 a('--outfile',default=None)
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fubar
parents:
diff changeset
558 args = parser.parse_args()
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fubar
parents:
diff changeset
559 inp = args.infile
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fubar
parents:
diff changeset
560 outp = args.outfile
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fubar
parents:
diff changeset
561 i = open(inp,'r').readlines()
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fubar
parents:
diff changeset
562 o = open(outp,'w')
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
563 for row in i:
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fubar
parents:
diff changeset
564 rs = row.rstrip()
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fubar
parents:
diff changeset
565 rs = list(rs)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
566 rs.reverse()
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fubar
parents:
diff changeset
567 o.write(''.join(rs))
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fubar
parents:
diff changeset
568 o.write('\n')
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parents:
diff changeset
569 o.close()
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parents:
diff changeset
570
126
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parents: 123
diff changeset
571 R script to draw some plots - use a collection.
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parents: 123
diff changeset
572
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parents: 123
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573 ::
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parents: 123
diff changeset
574
def0f754ee1b Uploaded
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diff changeset
575
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parents: 123
diff changeset
576 \# note this script takes NO input because it generates random data
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parents: 123
diff changeset
577 dir.create('plots')
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fubar
parents: 123
diff changeset
578 for (i in 1:10) {
def0f754ee1b Uploaded
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parents: 123
diff changeset
579 foo = runif(100)
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580 bar = rnorm(100)
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581 bar = foo + 0.05*bar
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582 pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_'))
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583 plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6)
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584 dev.off()
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585 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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586 bar = as.matrix(foo)
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587 pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_'))
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588 heatmap(bar,main='Random Heatmap')
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589 dev.off()
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590 }
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591
121
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592
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593
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594 Paper_
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595
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596 *Licensing*
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597
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598 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
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599 All rights reserved.
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600 Licensed under the LGPL_
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601
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602 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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603 .. _GTF: https://github.com/fubar2/toolfactory
126
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604 .. _Paper: https://academic.oup.com/bioinformatics/article/28/23/3139/192853
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605
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606
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607 </help>
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608 <citations>
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609 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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610 </citations>
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611 </tool>
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612
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613