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comparison elastic_r_package_wrappers_macros.xml @ 8:ea3271940757 draft

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planemo upload
author mingchen0919
date Tue, 27 Mar 2018 23:42:53 -0400
parents 01eaa66fcc2e
children 06f38d3febdc
comparison
equal deleted inserted replaced
7:01eaa66fcc2e 8:ea3271940757
1 <macros> 1 <macros>
2 2
3 <xml name="rmarkdown_requirements"> 3 <xml name="rmarkdown_requirements">
4 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> 4 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
5 <requirement type="package" version="1.6">r-rmarkdown</requirement> 5 <requirement type="package" version="1.6">r-rmarkdown</requirement>
6 <requirement type="package" version="1.2.1">r-tidyverse</requirement> 6 <requirement type="package" version="1.1.1">r-tidyverse</requirement>
7 </xml> 7 </xml>
8 8
9 <xml name="stdio"> 9 <xml name="stdio">
10 <stdio> 10 <stdio>
11 <regex match="XXX" source="stderr" level="warning" 11 <regex match="XXX" source="stderr" level="warning"
13 </stdio> 13 </stdio>
14 </xml> 14 </xml>
15 15
16 <xml name="function_components"> 16 <xml name="function_components">
17 <repeat name="function_component_repeat" title="Call a function" min="1" default="1"> 17 <repeat name="function_component_repeat" title="Call a function" min="1" default="1">
18 <expand macro="function_name" /> 18 <param type="select" name="function_name" multiple="false" label="==== Call function ====">
19 <option value="ggplot" selected="false">ggplot</option>
20 <option value="aes" selected="false">ggplot</option>
21 <option value="read.table" selected="false">read.table</option>
22 <option value="write.csv" selected="false">write.csv</option>
23 </param>
19 <expand macro="function_arguments" /> 24 <expand macro="function_arguments" />
25 <param type="select" name="operator" label="connect to next function">
26 <option value="%>%" selected="false">pipe (%>%)</option>
27 <option value="+" selected="false">plus (+)</option>
28 </param>
20 </repeat> 29 </repeat>
21 </xml> 30 </xml>
22 31
23 <!--Tool name-->
24 <xml name="function_name">
25 <param type="select" name="function_name" multiple="false" label="==== Call function ====">
26 <option value="ggplot" selected="false">ggplot</option>
27 <option value="aes" selected="false">ggplot</option>
28 <option value="read.table" selected="false">read.table</option>
29 <option value="write.csv" selected="false">write.csv</option>
30 </param>
31 </xml>
32
33 <!--input values: string, float and integer-->
34 <xml name="function_arguments"> 32 <xml name="function_arguments">
35 <repeat name="regular_argument_value" title="--------Argument value: from user input" min="0" default="0"> 33 <repeat name="regular_argument_value" title="Argument value: from user input" min="0" default="0">
36 <param type="text" name="argument" label="argument" /> 34 <param type="text" name="argument" label="argument" />
37 <param type="text" name="argument_value" label="argument value" /> 35 <param type="text" name="argument_value" label="argument value" />
38 <param type="select" name="argument_type" label="argument type"> 36 <param type="select" name="argument_type" label="argument type">
39 <option value="string" selected="true">string</option> 37 <option value="string" selected="true">string</option>
40 <option value="numeric" selected="true">numeric</option> 38 <option value="numeric" selected="false">numeric</option>
41 <option value="boolean" selected="true">boolean</option> 39 <option value="boolean" selected="false">boolean</option>
40 <option value="variable" selected="false">variable</option>
42 </param> 41 </param>
43 </repeat> 42 </repeat>
44 <repeat name="rdata_argument_value" title="--------Argument value: from RData" min="0" default="0"> 43 <repeat name="rdata_argument_value" title="Argument value: from RData" min="0" default="0">
45 <param type="text" name="argument" label="argument" /> 44 <param type="text" name="argument" label="argument" />
46 <param type="data" format="rdata" name="argument_value" optional="false" label="RData output" /> 45 <param type="data" format="rdata" name="argument_value" optional="false" label="RData output" />
47 </repeat> 46 </repeat>
48 <repeat name="function_argument_value" title="--------Argument value: from function return" min="0" default="0">
49 <param type="text" name="argument" optional="false" label="argument" />
50 <expand macro="function_name" />
51 <expand macro="nested_function_arguments" />
52 </repeat>
53 <param type="select" name="connect_to_next_function" label="connect to next function">
54 <option value="%>%" selected="false">pipe (%>%)</option>
55 <option value="+" selected="false">plus (+)</option>
56 </param>
57 </xml> 47 </xml>
58
59 <xml name="nested_function_arguments">
60 <repeat name="regular_argument_value" title="--------Argument value: from user input" min="0" default="0">
61 <param type="text" name="argument" label="argument" />
62 <param type="text" name="argument_value" label="argument value" />
63 <param type="select" name="argument_type" label="argument type">
64 <option value="string" selected="true">string</option>
65 <option value="numeric" selected="true">numeric</option>
66 <option value="boolean" selected="true">boolean</option>
67 </param>
68 </repeat>
69 <repeat name="rdata_argument_value" title="--------Argument value: from RData" min="0" default="0">
70 <param type="text" name="argument" label="argument" />
71 <param type="text" name="argument_value" label="RData output" />
72 </repeat>
73 </xml>
74
75 <!--&lt;!&ndash;OPTION/ARGUMENT PAIRS and INPUT types&ndash;&gt;-->
76 <!--&lt;!&ndash;input files&ndash;&gt;-->
77 <!--<xml name="option_argument_single_dataset">-->
78 <!--<repeat name="option_argument_single_dataset_repeat" title="INPUT DATA FROM HISTORY: single data set" min="0" default="0">-->
79 <!--<param type="text" name="flag" optional="true" label="flag" />-->
80 <!--<param name="value" type="data" optional="false" multiple="false" label="value"/>-->
81 <!--</repeat>-->
82 <!--</xml>-->
83
84 <!--<xml name="option_argument_multiple_datasets">-->
85 <!--<repeat name="option_argument_multiple_datasets_repeat" title="INPUT DATA FROM HISTORY: multiple data sets" min="0" default="0">-->
86 <!--<param type="text" name="flag" optional="true" label="flag" />-->
87 <!--<param name="value" type="data" optional="false" multiple="true" label="value"/>-->
88 <!--<param type="select" name="delimiter" multiple="false" label="file delimiter">-->
89 <!--<option value=" " selected="false">space</option>-->
90 <!--<option value="," selected="false">comma</option>-->
91 <!--</param>-->
92 <!--</repeat>-->
93 <!--</xml>-->
94
95 <!--&lt;!&ndash;input path&ndash;&gt;-->
96 <!--<xml name="option_argument_path_relative_to_a_tool">-->
97 <!--<repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="0" default="0">-->
98 <!--<param type="text" name="flag" optional="true" label="flag" />-->
99 <!--<param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>-->
100 <!--<param type="text" name="value" optional="true" label="value" />-->
101 <!--</repeat>-->
102 <!--</xml>-->
103 <!--<xml name="option_argument_path_relative_to_this_tool">-->
104 <!--<repeat name="option_argument_path_relative_to_this_tool_repeat" title="OUTPUT PATH: relative to this tool output directory" min="0" default="0">-->
105 <!--<param type="text" name="flag" optional="true" label="flag" />-->
106 <!--<param type="text" name="value" optional="false" label="value" />-->
107 <!--<param type="select" name="path_type" multiple="false" label="path type">-->
108 <!--<option value="file_path" selected="false">file path</option>-->
109 <!--<option value="dir_path" selected="false">directory path</option>-->
110 <!--</param>-->
111 <!--</repeat>-->
112 <!--</xml>-->
113
114 48
115 49
116 <!--output set--> 50 <!--output set-->
117 <xml name="output_set"> 51 <xml name="output_set">
118 <data format="html" name="report" label="${tool.name} report"/> 52 <data format="html" name="report" label="${tool.name} report"/>
119 <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/> 53 <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
120 <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/>
121 <data format="txt" name="tool_log" label="${tool.name} log" /> 54 <data format="txt" name="tool_log" label="${tool.name} log" />
122 </xml> 55 </xml>
123 56
124 57
125 <!--shell command fragment--> 58 <!--shell command fragment-->
126 <xml name="shell_command"> 59 <xml name="shell_command">
127 <command><![CDATA[ 60 <command><![CDATA[
128 61
129 ############ first, create a directory to store all files 62 ############ 1. create a directory to store all files
130 mkdir -p $report.files_path && 63 mkdir -p $report.files_path &&
131 64
132 65
133 ############ save the tool installation directory to an environment variable 66 ############ 2. save the tool installation directory to an environment variable
134 export TOOL_INSTALL_DIR='${__tool_directory__}' && 67 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
135 68
136 69
137 ######################### 70 ############ 3. save user inputs into arguments.txt
138 ##
139 ## save user input option/argument pairs into a file
140 ##
141 #########################
142 71
143 ## first line will be the header 72 ############ 3.1 table header
144 echo 'type|flag|value|path_type' > $report.files_path/options_and_arguments.txt && 73 echo 'function|input_type|argument|argument_value|argument_value_type|operator' > $report.files_path/arguments.txt &&
145
146 ############ function_name
147 ##-t '$function_name'
148 echo "function_name|not available|${function_name}|not available" >> $report.files_path/options_and_arguments.txt &&
149
150 ####################################################
151 ## loop through repeats to get option/argument pairs
152 ####################################################
153
154 ############ option_argument_single_dataset
155 #for i in $option_argument_single_dataset_repeat:
156 #set $item = 'single_dataset|' + str($i.flag) + "|" + str($i.value) + "|"
157 echo '$item' >> $report.files_path/options_and_arguments.txt &&
158 #end for
159
160 ############ option_argument_multiple_datasets
161 #for i in $option_argument_multiple_datasets_repeat:
162 #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|"
163 echo '$item' >> $report.files_path/options_and_arguments.txt &&
164 #end for
165 74
166 75
167 ############ option_argument_path_relative_to_a_tool 76 ############ 3.2 loop through function component repeat
168 #for i in $option_argument_path_relative_to_a_tool_repeat: 77 #for $fun_component in $function_components:
169 #set $item = 'path_relative_to_a_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir) 78 #for reg_arg in $fun_component.regular_argument_value
170 echo '$item' >> $report.files_path/options_and_arguments.txt && 79 echo '$fun_component.function_name|regular|$reg_arg.argument|$arg_arg.argument_value|$arg_arg.argument_value_type|$fun_component.operator' >> $report.files_path/arguments.txt &&
171 #end for 80 #end for
172 81
173 ############ option_argument_path_relative_to_this_tool 82 #for rdata_arg in $fun_component.rdata_argument_value
174 #for i in $option_argument_path_relative_to_this_tool_repeat: 83 echo '$fun_component.function_name|rdata|$rdata_arg.argument|$arg_arg.argument_value|rdata|$fun_component.operator' >> $report.files_path/arguments.txt &&
175 #set $item = 'path_relative_to_this_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.path_type) 84 #end for
176 echo '$item' >> $report.files_path/options_and_arguments.txt &&
177 #end for
178
179 ############ option_argument_string_float_integer
180 #for i in $option_argument_string_float_integer_repeat:
181 #set $item = 'value|' + str($i.flag) + "|" + str($i.value) + "|"
182 echo '$item' >> $report.files_path/options_and_arguments.txt &&
183 #end for
184 85
185 ############ output_set 86 ############ output_set
186 ## '$report' 87 ## '$report'
187 ## '$report.files_path' 88 ## '$report.files_path'
188 ## '$tool_help_doc' 89 ## '$tool_help_doc'
189 ## '$tool_output_dir'
190 ## '$tool_log' 90 ## '$tool_log'
191 ####################### 91 #######################
192 export REPORT='$report' && 92 export REPORT='$report' &&
193 export REPORT_FILES_PATH='$report.files_path' && 93 export REPORT_FILES_PATH='$report.files_path' &&
194 export TOOL_HELP_DOC='$tool_help_doc' && 94 export TOOL_HELP_DOC='$tool_help_doc' &&
195 export TOOL_OUTPUT_DIR='$tool_output_dir' &&
196 export TOOL_LOG='$tool_log' && 95 export TOOL_LOG='$tool_log' &&
197 96
198 97
199 ############ run render R script to render R markdowns 98 ############ run render R script to render R markdowns
200 Rscript '${__tool_directory__}/elastic_tool_render.R' 99 Rscript '${__tool_directory__}/elastic_tool_render.R'