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1
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1 <tool id="toolfactory" name="toolfactory" version="3.0" profile="22.05" >
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2 <description>Scripts into tools v3.0</description>
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3 <macros>
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4 <xml name="dataColumn">
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5 <param name="param_dataref" type="text" value="" label="Input data name to use as source of data column names"/>
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6 <param name="param_multiple" type="boolean" truevalue="1" falsevalue="" value = ""
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7 label="Allow user to make multiple selections" help="default is single selection"/>
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8 <param name="param_value" type="text" value="" label="Default column value">
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9 </param>
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10 </xml>
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11 <xml name="singleText">
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12 <param name="param_value" type="text" value="" label="Default text value">
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13 <sanitizer invalid_char="_">
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14 <valid initial="string.printable" >
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15 </valid>
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16 </sanitizer>
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17 </param>
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18 </xml>
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19 <xml name="singleInt">
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20 <param name="param_value" type="integer" value="" label="Default integer value" >
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21 </param>
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22 </xml>
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23 <xml name="singleFloat">
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24 <param name="param_value" type="float" value="" label="Default value">
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25 </param>
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26 </xml>
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27 <xml name="singleBoolean">
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28 <param name="param_value" type="boolean" value="" label="Default value" />
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29 <param name="truevalue" type="text" value="True" label="Command line value when True" />
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30 <param name="falsevalue" type="boolean" value="True" label="Command line value when False" />
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31 </xml>
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32 <xml name="selectText">
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33 <repeat name="selectTexts" title="Add each option to be presented" min="2" default="2"
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34 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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35 <param name="select_text" type="text" value="" label="Explanatory text the user will see for this choice" >
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36 <sanitizer invalid_char="_">
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37 <valid initial="string.printable" >
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38 </valid>
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39 </sanitizer>
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40 </param>
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41 <param name="select_value" type="text" value="" label="Value for the command line when the user selects this option">
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42 <sanitizer invalid_char="_">
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43 <valid initial="string.printable" >
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44 </valid>
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45 </sanitizer>
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46 </param>
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47 </repeat>
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48 </xml>
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49 <xml name="selectFlag">
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50 <repeat name="selectFlags" title="Add mutually exclusive flag selection" min="2" default="2"
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51 help="Supply the corresponding mutually exclusive flag as it should appear on the command line if each option is selected">
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52 <param name="select_text" type="text" value="" label="Explanatory text the user will see for this choice" >
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53 </param>
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54 <param name="select_value" type="text" value="" label="Value for the command line when the user selects this option"
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55 help="Supply the corresponding mutually exclusive flag as it should appear on the command line if each option is selected">
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56 </param>
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57 </repeat>
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58 </xml>
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59 <xml name="tool_metadata">
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60 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text"
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61 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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62 <param name="tool_desc" label="Tool Synopsis" type="text" value=""
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63 help="Supply a brief tool description for the Galaxy tool menu entry">
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64 </param>
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65 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
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66 value="**What it Does**"
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67 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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68 <sanitizer>
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69 <valid initial="string.printable" >
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70 </valid>
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71 </sanitizer>
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72 </param>
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73 <repeat name="citations" title="Citation">
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74 <conditional name="citation_type">
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75 <param name="type" type="select" display="radio" label="Citation Type">
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76 <option value="doi">DOI</option>
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77 <option value="bibtex">BibTeX</option>
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78 </param>
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79 <when value="doi">
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80 <param name="doi" label="DOI" type="text"
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81 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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82 <sanitizer>
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83 <valid initial="string.printable" >
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84 </valid>
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85 </sanitizer>
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86 </param>
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87 </when>
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88 <when value="bibtex">
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89 <param name="bibtex" label="BibTex" type="text" area="true"
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90 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
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91 <sanitizer>
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92 <valid initial="string.printable" >
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93 </valid>
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94 </sanitizer>
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95 </param>
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96 </when>
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97 </conditional>
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98 </repeat>
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99 </xml>
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100 <xml name="io">
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101 <section name="io" title="Input and output files" expanded="true">
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102 <repeat name="history_inputs" title="Inputs" min="0"
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103 help="Input data files to pass on the command line to the executable. USE SMALL SAMPLES for the new tool's test.
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104 Prompts will form a history item selector as input for users of this new tool">
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105 <param name="input_files" type="data" format="data" label="Select an input file from your history" multiple="true"
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106 help="Note that multiple inputs can be selected if this input parameter will allow multiple selections"/>
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107 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
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108 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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109 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
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110 <column name="value" index="0"/>
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111 </options>
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112 </param>
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113 <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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114 </param>
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115 <param name="input_help" type="text" value="" label="This will become help text on the form." >
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116 </param>
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117 <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
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118 help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if
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119 single character">
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120 </param>
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121 <param name="input_required" type="select" label="Input mode - optional, required, repeated optional or 1 or more repeated required.">
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122 <option value="required" selected="true">Required single input</option>
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123 <option value="optional">Optional single input</option>
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124 <option value="required1">Required. 1 or more repeats</option>
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125 <option value="optional1">Optional. 1 or more repeats</option>
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126 </param>
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127 </repeat>
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128 <repeat name="history_outputs" min="0" title="Outputs"
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129 help="New history items output by the executable to appear in the user history after the tool runs. The name will become a history item for
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130 users of the new tool you are making containing one of it's outputs">
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131 <param name="history_name" type="text" label="Output Name" optional="false"
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132 help="Name used for this output in history. No spaces. Digits and letters only please. Argparse should look for this name on the command line.">
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133 <sanitizer invalid_char="_">
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134 <valid initial="string.ascii_letters,string.digits" >
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135 <add value="_" />
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136 </valid>
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137 </sanitizer>
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138 </param>
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139 <param name="history_label" type="text" label="Output label. Allows template substitution" value=""
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140 help="Label used for this output - for example 'Plotlytabular $title on $input_tab.element_identifier' where variable templates are informative." >
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141 <sanitizer>
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142 <valid initial="string.printable" >
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143 </valid>
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144 </sanitizer>
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145 </param>
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146 <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
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147 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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148 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
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149 <column name="value" index="0"/>
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150 </options>
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151 </param>
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152 <param name="history_CL" type="text" label="Position"
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153 help="Positional: ordinal integer or 'STDOUT' if '>' required. Ignored if argparse because output name is used.
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154 If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/>
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155 <param name="history_test" type="text" label="Output test criteria"
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156 help="Pass/fail decision criterion for this output compared to test generation. Accepted variants include diff:100, sim_size:100 and sim_size:0.1"
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157 value="diff:0"/>
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158 <repeat name="history_whens" title="Optional change_format on this data" min="0" help="ADVANCED option only!! Easy to get wrong!">
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159 <param name="history_when" type="text" label="Add a 'when' expression for this output so format can depend on another parameter"
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160 help="Supply the three key=value pairs needed as shown - no quotes: input=image_format value=small_png format=png" value="">
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161 </param>
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162 </repeat>
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163 </repeat>
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164 <repeat name="collection_outputs" title="Output Collections" min="0"
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165 help="New history collections to appear in the user history after the tool runs. Hides outputs not needed for downstream tools such as
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166 images and intermediate reports." default="0">
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167 <param name="name" type="text" label="Name"
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168 help="for new collection with all outputs not individually passed to history outputs. No spaces! Script MUST create and fill a directory
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169 with the same name and the tool test MUST be overwritten - see the plotter example for hints">
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170 </param>
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171 <param name="kind" type="select" multiple="false" label="Select the kind of collection for this output"
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172 help="">
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173 <option value="list" selected="true">List</option>
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174 <option value="paired">Paired</option>
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175 <option value="list:paired">List of paired</option>
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176 </param>
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177 <param name="label" type="text" label="Collection label. Allows template substitution" value=""
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178 help="Label used for this output - for example 'Plotlytabular $title on $input_tab.element_identifier' where variable templates are informative." >
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179 <sanitizer>
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180 <valid initial="string.printable" >
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181 </valid>
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182 </sanitizer>
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183 </param>
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184 <param name="discover" type="text" label="Discover datasets expression" help="__name_and_ext__ should catch all filenames with extensions"
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185 value="__name_and_ext__"/>
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186 </repeat>
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187
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188 </section>
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189 </xml>
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190 <xml name="additparam">
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191 <section name="addparam" title="Arguments" help="Executable or script settings passed on the command line other than I/O files" expanded="true">
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192 <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?"
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193 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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194 <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
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195 <option value="no">No - use the fixed values for all additional parameters - no user editing</option>
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196 </param>
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197 <repeat name="additional_parameters" title="Command Line Parameters" min="0"
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198 help="Command line settings for the user to pass to the executable. See examples below to see how these can be parsed by scripts in the various languages">
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199 <param name="param_name" type="text" value="" label="Name for this parameter. Underscore, letters and digits only. No spaces allowed">
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200 <sanitizer invalid_char="_">
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201 <valid initial="string.ascii_letters,string.digits">
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202 <add value="_"/>
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203 </valid>
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204 </sanitizer>
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205 </param>
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206 <conditional name="ap_type">
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207 <param name="param_type" type="select" label="Type for this parameter">
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208 <option value="text" selected="true">Text string</option>
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209 <option value="integer">Integer</option>
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210 <option value="float">Float</option>
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211 <option value="boolean">Boolean</option>
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212 <option value="selecttext">Select text string</option>
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213 <option value="selectflag">Select from a mutually exclusive list of command line flags to pass</option>
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214 <option value="clflag">Flag - user can set. Only used for argparse parameter passing style</option>
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215 <option value="datacolumn">Data column - user selects from an input tabular file column name/header values</option>
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216 </param>
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217 <when value = "text">
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218 <expand macro="singleText" />
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219 </when>
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220 <when value = "integer">
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221 <expand macro="singleInt" />
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222 </when>
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223 <when value = "float">
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224 <expand macro="singleFloat" />
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225 </when>
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226 <when value = "boolean">
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227 <expand macro="singleBoolean" />
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228 </when>
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229 <when value = "selecttext">
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230 <expand macro="selectText" />
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231 </when>
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232 <when value = "selectflag">
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233 <expand macro="selectFlag" />
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234 </when>
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235 <when value = "clflag">
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236 <param name="param_value" type="select" value="notset">
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237 <option value='notset'>DO NOT set this flag</option>
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238 <option value='set'>SET this flag</option>
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239 </param>
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240 </when>
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241 <when value = "datacolumn">
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242 <expand macro="dataColumn" />
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243 </when>
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244 </conditional>
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245 <param name="param_label" type="text" value="" label="Label for the form">
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246 <sanitizer>
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247 <valid initial="string.printable" >
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248 </valid>
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249 </sanitizer>
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250 </param>
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251 <param name="param_help" type="text" value="" label="Help for this parameter">
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252 <sanitizer>
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253 <valid initial="string.printable" >
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254 </valid>
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255 </sanitizer>
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256 </param>
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257 <param name="param_CL" type="text" label="Positional ordinal | argparse argument name"
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258 help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style,
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259 '--' will be prepended on the CL" value="" />
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260 <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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261 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="">
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262 <sanitizer invalid_char="_">
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263 <valid initial="string.printable" >
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264 <remove value="'" />
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265 </valid>
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266 </sanitizer>
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267 </param>
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268 <param name="param_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0"
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269 label="Allow user to repeat this as many times as needed." />
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270 </repeat>
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271 </section>
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272 </xml>
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273 </macros>
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274 <requirements>
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275 <requirement type="package" version="3.10.12">python</requirement>
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276 <requirement type="package" version="0.5.3">galaxyxml</requirement>
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277 <requirement type="package" version="1.2.0">bioblend</requirement>
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278 <requirement type="package" version="0.75.20">planemo</requirement>
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279 <requirement type="package" version="0.10.10">ephemeris</requirement>
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280 </requirements>
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281
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282 <command detect_errors="exit_code"><![CDATA[
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283 #import os
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284 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
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285 #if not $__user_email__
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286 #set useremail = 'admin@galaxy.this'
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287 #else
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288 #set useremail = $__user_email__
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289 #end if
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290 #if not $dev_env and ( $__user_email__ not in $__admin_users__ )
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291 python3 $__tool_directory__/toolfactory.py --bad_user $__user_email__
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292 #else
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293 python3 $__tool_directory__/toolfactory.py
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294 #if len(str($cl_options.cl_suffix)) > 0
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295 --cl_suffix "$clsuffix"
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296 #end if
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297 #if len(str($cl_options.cl_prefix)) > 0
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298 --cl_prefix "$clprefix"
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299 #end if
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300 #if len(str($cl_options.cl_override)) > 0
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301 --cl_override "$commandoverride"
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302 #end if
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303 #if len(str($cl_options.test_override)) > 0
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304 --test_override "$testoverride"
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305 #end if
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306 #if $deps.packages > "":
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307 --packages "$deps.packages"
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308 #end if
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309 #if $deps.usescript.choosescript == "yes"
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310 --script_path "$runscript"
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311 --sysexe "$deps.usescript.scriptrunner"
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312 #end if
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313 --tool_name "$tool_name" --user_email "$useremail" --citations "$citeme" --parampass "$io_param.ppass.parampass"
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314 --tool_desc "$tool_desc"
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315 --tool_version "$tool_version"
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316 --help_text "$helpme"
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317 #if $io_param.ppass.parampass != '0'
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318 #if str($io_param.ppass.addparam.edit_params) == "yes"
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319 --edit_additional_parameters
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320 #end if
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321 #for $apar in $io_param.ppass.addparam.additional_parameters
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322 #if $apar.ap_type.param_type=="selecttext"
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323 --selecttext_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help",
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324 "type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [
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325 #for $i,$st in enumerate($apar.ap_type.selectTexts):
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326 "$st.select_value"
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327 #if ($i < (len($apar.ap_type.selectTexts)-1)):
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328 ,
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329 #end if
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330 #end for
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331 ], "texts": [
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332 #for $i,$st in enumerate($apar.ap_type.selectTexts):
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333 "$st.select_text"
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334 #if ($i < (len($apar.ap_type.selectTexts)-1)):
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335 ,
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336 #end if
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337
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338 #end for
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339 ]
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340 }'
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341 #else if $apar.ap_type.param_type=="selectflag"
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342 --selectflag_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help",
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343 "type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [
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344 #for $i,$st in enumerate($apar.ap_type.selectFlags):
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345 "$st.select_value"
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346 #if ($i < (len($apar.ap_type.selectFlags)-1)):
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347 ,
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348 #end if
|
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349 #end for
|
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350 ], "texts": [
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351 #for $i,$st in enumerate($apar.ap_type.selectFlags):
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352 "$st.select_text"
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353 #if ($i < (len($apar.ap_type.selectFlags)-1)):
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354 ,
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355 #end if
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356
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357 #end for
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358 ]
|
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359 }'
|
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360 #else if $apar.ap_type.param_type=="datacolumn"
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361 --additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help",
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362 "type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed", "repeat": "$apar.param_repeat", "multiple": "$apar.ap_type.param_multiple",
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363 "dataref": "$apar.ap_type.param_dataref"}'
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364 #else:
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365 --additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help",
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366 "type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed", "repeat": "$apar.param_repeat"}'
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367 #end if
|
|
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368 #end for
|
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369 #end if
|
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370 #for $intab in $io_param.ppass.io.history_inputs
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371 --input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label",
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372 "help": "$intab.input_help", "required": "$intab.input_required"}'
|
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373 #end for
|
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374 #for $otab in $io_param.ppass.io.history_outputs
|
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375 #if str($otab.history_label) > ""
|
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376 --output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test", "label": "$otab.history_label"
|
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377 #else
|
|
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378 --output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"
|
|
|
379 #end if
|
|
|
380 #if $otab.history_whens
|
|
|
381 , "when": [
|
|
|
382 #for $i, $hw in enumerate($otab.history_whens)
|
|
|
383 "$hw.history_when"
|
|
|
384 #if ($i < (len($otab.history_whens)-1))
|
|
|
385 ,
|
|
|
386 #end if
|
|
|
387 #end for
|
|
|
388 ]
|
|
|
389 #end if
|
|
|
390 }'
|
|
|
391 #end for
|
|
|
392 #for $collect in $io_param.ppass.io.collection_outputs
|
|
|
393 --collection '{"name": "$collect.name", "kind": "$collect.kind", "discover": "$collect.discover", "label": "$collect.label"}'
|
|
|
394 #end for
|
|
|
395 --tfcollection 'toolgen'
|
|
|
396 --tested_tool_out "$untested_tool"
|
|
|
397 --nftest
|
|
|
398 --galaxy_root "$__root_dir__"
|
|
|
399 --toolfactory_dir "$__tool_directory__"
|
|
|
400 #if $cl_options.xtracond.needxtra == "yes"
|
|
|
401 #for $x in $cl_options.xtracond.xtra_files
|
|
|
402 --xtra_file '{"fpath":"$x", "fname":"$x.element_identifier"}'
|
|
|
403 #end for
|
|
|
404 #end if
|
|
|
405 #end if
|
|
|
406 ]]>
|
|
|
407 </command>
|
|
|
408 <configfiles>
|
|
|
409 <configfile name="runscript">
|
|
|
410 ${deps.usescript.dynScript}
|
|
|
411 </configfile>
|
|
|
412 <configfile name="commandoverride">
|
|
|
413 #if len(str($cl_options.cl_override).strip()) > 1:
|
|
|
414 ${cl_options.cl_override}
|
|
|
415 #end if
|
|
|
416 </configfile>
|
|
|
417 <configfile name="testoverride">
|
|
|
418 #if len(str($cl_options.test_override).strip()) > 1:
|
|
|
419 ${cl_options.test_override}
|
|
|
420 #end if
|
|
|
421 </configfile>
|
|
|
422 <configfile name="clprefix">
|
|
|
423 #if len(str($cl_options.cl_prefix).strip()) > 1:
|
|
|
424 ${cl_options.cl_prefix}
|
|
|
425 #end if
|
|
|
426 </configfile>
|
|
|
427 <configfile name="clsuffix">
|
|
|
428 #if len(str($cl_options.cl_suffix).strip()) > 1:
|
|
|
429 ${cl_options.cl_suffix}
|
|
|
430 #end if
|
|
|
431 </configfile>
|
|
|
432 <configfile name="helpme">
|
|
|
433 ${help_text}
|
|
|
434 </configfile>
|
|
|
435 <configfile name="citeme">
|
|
|
436
|
|
|
437 #for $citation in $citations:
|
|
|
438 #if $citation.citation_type.type == "bibtex":
|
|
|
439 **ENTRY**bibtex
|
|
|
440 ${citation.citation_type.bibtex}
|
|
|
441 #else
|
|
|
442 **ENTRY**doi
|
|
|
443 ${citation.citation_type.doi}
|
|
|
444 #end if
|
|
|
445 #end for
|
|
|
446
|
|
|
447 </configfile>
|
|
|
448 </configfiles>
|
|
|
449 <inputs>
|
|
|
450 <param name="tool_name" type="text" value="my_tool" label="New tool ID and title for outputs"
|
|
|
451 help="Toolshed repository name so lower case, digits and underscores only. Choose thoughtfully to avoid namespace clashes with other tool writers.">
|
|
|
452 <sanitizer invalid_char="_">
|
|
|
453 <valid initial="string.ascii_lowercase,string.digits">
|
|
|
454 <add value="_"/>
|
|
|
455 </valid>
|
|
|
456 </sanitizer>
|
|
|
457 </param>
|
|
|
458
|
|
|
459 <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true">
|
|
|
460
|
|
|
461 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...].
|
|
|
462 These will always be available when this tool executes" help="Use =[ver] or :[ver] for specific version - 'bwa=0.17.0'.
|
|
|
463 Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported" />
|
|
|
464
|
|
|
465 <conditional name="usescript">
|
|
|
466 <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"
|
|
|
467 help = "For script interpreters like Python or bash, parameters and i/o specified below must match script's expectations - i
|
|
|
468 f you pass parameters, the script must deal with them">
|
|
|
469 <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>
|
|
|
470 <option value="yes" selected="true">Yes, a script is ready to be pasted below</option>
|
|
|
471 </param>
|
|
|
472 <when value="no">
|
|
|
473 <param name="dynScript" type="hidden" value="" />
|
|
|
474 <param name="scriptrunner" type="hidden" value="" />
|
|
|
475 </when>
|
|
|
476 <when value="yes">
|
|
|
477 <param name="scriptrunner" type="text" value="" label="Interpreter for the script - eg bash or python. Can be one of the dependencies named
|
|
|
478 above or a system executable" help="Scripts are interpreted by the executable named here. For conda r-base, 'Rscript --vanilla' or for
|
|
|
479 conda planemo, 'planemo test' for example">
|
|
|
480 </param>
|
|
|
481 <param name="dynScript" type="text" area="True" value="" label="Script for executable above to interpret. It can be one of the Conda dependency names"
|
|
|
482 help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below">
|
|
|
483 <sanitizer>
|
|
|
484 <valid initial="string.printable"/>
|
|
|
485 </sanitizer>
|
|
|
486 </param>
|
|
|
487 </when>
|
|
|
488 </conditional>
|
|
|
489 </section>
|
|
|
490 <section name="io_param" title="Data file input, output and settings forming the executable or script command line" expanded="true">
|
|
|
491 <conditional name="ppass">
|
|
|
492 <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use">
|
|
|
493 <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option>
|
|
|
494 <option value="embed">Script has Cheetah templates for parameters embedded into the code</option>
|
|
|
495 <option value="embednfmod">Specialised embed with nf-core module pixie dust</option>
|
|
|
496 <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option>
|
|
|
497 <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option>
|
|
|
498 </param>
|
|
|
499 <when value="argparse">
|
|
|
500 <expand macro="io" />
|
|
|
501 <expand macro="additparam" />
|
|
|
502 </when>
|
|
|
503 <when value="embed">
|
|
|
504 <expand macro="io" />
|
|
|
505 <expand macro="additparam" />
|
|
|
506 </when>
|
|
|
507 <when value="embednfmod">
|
|
|
508 <expand macro="io" />
|
|
|
509 <expand macro="additparam" />
|
|
|
510 </when>
|
|
|
511 <when value="positional">
|
|
|
512 <expand macro="io" />
|
|
|
513 <expand macro="additparam" />
|
|
|
514 </when>
|
|
|
515 <when value="0">
|
|
|
516 <expand macro="io"/>
|
|
|
517 </when>
|
|
|
518 </conditional>
|
|
|
519 </section>
|
|
|
520 <section name="cl_options" title="ADVANCED DIY MANUAL REPLACEMENT OPTIONS: Test or command line prefix, suffix or DIY command line" expanded="false" >
|
|
|
521 <param name="cl_prefix" type="text" area="True" value="" label="Prefix for generated command line. Useful for bash pre processing.
|
|
|
522 Use override below to replace completely"
|
|
|
523 help="';' separated bash commands can be used here for pre processing like renaming or copying datasets for the script -
|
|
|
524 added at start of autogenerated command line">
|
|
|
525 <sanitizer>
|
|
|
526 <valid initial="string.printable" />
|
|
|
527 </sanitizer>
|
|
|
528 </param>
|
|
|
529 <param name="cl_suffix" type="text" area="True" value="" label="Suffix for generated command line. Useful for bash post processing.
|
|
|
530 Use override below to replace completely"
|
|
|
531 help="';' separated bash commands can be used here for post processing - added at end of autogenerated command line" >
|
|
|
532 <sanitizer>
|
|
|
533 <valid initial="string.printable" />
|
|
|
534 </sanitizer>
|
|
|
535 </param>
|
|
|
536 <param name="cl_override" type="text" area="True" label="Optional. Human wrought command element override XML/template - e.g. for bwa"
|
|
|
537 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" value="">
|
|
|
538 <sanitizer>
|
|
|
539 <valid initial="string.printable"/>
|
|
|
540 </sanitizer>
|
|
|
541 </param>
|
|
|
542 <param name="test_override" type="text" area="True" label="Optional. Human wrought test element override XML/template - e.g. for bwa"
|
|
|
543 help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart" value="">
|
|
|
544 <sanitizer>
|
|
|
545 <valid initial="string.printable" />
|
|
|
546 </sanitizer>
|
|
|
547 </param>
|
|
|
548 <conditional name="xtracond">
|
|
|
549 <param name="needxtra" type="select" display="radio" label="Specific files from the history must be available in the tool directory"
|
|
|
550 help = "If you need a java .jar file or special data file for your script to be able to access, upload it to the history and select it here">
|
|
|
551 <option value="no" selected="true">No special files need to be available in the tool directory for the script to use</option>
|
|
|
552 <option value="yes">Yes - some special files must be copied into the tool directory</option>
|
|
|
553 </param>
|
|
|
554 <when value="no">
|
|
|
555 <param name="xtra_files" type="hidden" value="" />
|
|
|
556 </when>
|
|
|
557 <when value="yes">
|
|
|
558 <param name="xtra_files" type="data" format="data" label="Select all files from your history to add to tool directory for the script to use" multiple="true"
|
|
|
559 help="If your script needs access to a .jar or other specific permanent resource, upload it before building, so you can select it here.
|
|
|
560 All those selected history items will be added to the tool directory. That path is available at execution as $__tool_directory__, for use in the command section.
|
|
|
561 These need to be expanded and used as parameters for the script where needed: $__tool_directory__/BlastTools.jar for example"/>
|
|
|
562 </when>
|
|
|
563 </conditional>
|
|
|
564 </section>
|
|
|
565 <expand macro="tool_metadata" />
|
|
|
566 <param name="useremail" type="hidden" value="" />
|
|
|
567 <param name="script_path" type="hidden" value="" />
|
|
|
568 </inputs>
|
|
|
569 <outputs>
|
|
|
570 <collection name="toolgen" type="list" label="${tool_name} generated components">
|
|
|
571 <discover_datasets pattern="__name_and_ext__" directory="toolgen" visible="false"/>
|
|
|
572 </collection>
|
|
|
573 <data name="untested_tool" format="tgz" label = "${tool_name}_toolshed_archive"/>
|
|
|
574 </outputs>
|
|
|
575 <tests>
|
|
|
576 <test>
|
|
|
577 <param name="useremail" value="admin.galaxy.here" />
|
|
|
578 <param name="input_files" value="input1_sample" />
|
|
|
579 <param name="input_CL" value="1" />
|
|
|
580 <param name="input_formats" value="txt" />
|
|
|
581 <param name="input_label" value="input" />
|
|
|
582 <param name="input_help" value="help" />
|
|
|
583 <param name="tool_name" value="pyrevpos" />
|
|
|
584 <param name="parampass" value="positional" />
|
|
|
585 <param name="tool_version" value="0.01" />
|
|
|
586 <param name="tool_desc" value="positional reverse" />
|
|
|
587 <param name="help_text" value="help text goes here" />
|
|
|
588 <param name="packages" value="python" />
|
|
|
589 <param name="history_name" value="output2" />
|
|
|
590 <param name="history_format" value="txt" />
|
|
|
591 <param name="history_CL" value="2" />
|
|
|
592 <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines();
|
|
|
593 o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()" />
|
|
|
594 <param name="choosescript" value="yes" />
|
|
|
595 <param name="script_path" value="$runscript" />
|
|
|
596 <output name="untested_tool" file="pyrevpos_not_tested.toolshed_sample" ftype="tgz" compare="sim_size" delta_frac="0.1" />
|
|
|
597 </test>
|
|
|
598 </tests>
|
|
|
599 <help>
|
|
|
600
|
|
|
601 **Details and attribution**
|
|
|
602 (see GTF_)
|
|
|
603
|
|
|
604 **Local Admins ONLY**
|
|
|
605 Only users with emails in the local admin_user configuration setting in config/galaxy.yml can run this tool.
|
|
|
606
|
|
|
607 **If you find a bug**
|
|
|
608 Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_
|
|
|
609
|
|
|
610 **What it does**
|
|
|
611 This tool contains an automated code generator, and creates normal, workflow compatible Galaxy tools as Toolshed ready archives. The
|
|
|
612 new tool is immediately installed and available for use - a page refresh will be needed to see the new tool in the "Local" tool section.
|
|
|
613
|
|
|
614 Generated tools can use existing Conda packages. These become requirements for optional scripts pasted into this tool form.
|
|
|
615 Pasted scripts *cannot be adjusted* by the downstream user.
|
|
|
616
|
|
|
617 Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime.
|
|
|
618 These can be editable by the downstream user or baked in.
|
|
|
619
|
|
|
620 A new tarball compatible with any Galaxy toolshed is created in your history, including a test based on the supplied default parameter
|
|
|
621 values and input history datasets.
|
|
|
622
|
|
|
623 .. class:: warningmark
|
|
|
624
|
|
|
625 **Note to system administrators**
|
|
|
626 This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
|
|
|
627 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
|
|
|
628
|
|
|
629 .. class:: warningmark
|
|
|
630
|
|
|
631 **Use on public servers** is STRONGLY discouraged for obvious reasons
|
|
|
632
|
|
|
633 The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools,
|
|
|
634 should always be checked carefully before installation. We recommend that you follow the good code hygiene practices associated with safe toolshed practices.
|
|
|
635
|
|
|
636
|
|
|
637 Paper_
|
|
|
638
|
|
|
639 *Licensing*
|
|
|
640
|
|
|
641 Copyright Ross Lazarus May 2012
|
|
|
642 Licensed under the MIT_ licence.
|
|
|
643
|
|
|
644 .. _MIT: https://mit-license.org/
|
|
|
645 .. _GTF: https://github.com/fubar2/galaxy_tf_overlay
|
|
|
646 .. _Paper: https://academic.oup.com/bioinformatics/article/28/23/3139/192853
|
|
|
647
|
|
|
648
|
|
|
649 </help>
|
|
|
650 <citations>
|
|
|
651 <citation type="doi">10.1093/bioinformatics/bts573</citation>
|
|
|
652 </citations>
|
|
|
653 </tool>
|
|
|
654
|
|
|
655
|
