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annotate dynamic_tool_wrappers_macros.xml @ 2:a9579c344a90 draft default tip
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author | mingchen0919 |
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date | Fri, 23 Mar 2018 21:50:16 -0400 |
parents | ddc3c3527f49 |
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rev | line source |
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0 | 1 <macros> |
2 | |
3 <xml name="rmarkdown_requirements"> | |
4 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> | |
5 <requirement type="package" version="1.6">r-rmarkdown</requirement> | |
1 | 6 <requirement type="package" version="2.5.4a">star</requirement> |
0 | 7 </xml> |
8 | |
9 <xml name="stdio"> | |
10 <stdio> | |
11 <regex match="XXX" source="stderr" level="warning" | |
12 description="Check the tool log output file for more details."/> | |
13 </stdio> | |
14 </xml> | |
15 | |
16 <!--Tool name--> | |
17 <xml name="tool_name"> | |
18 <param type="select" name="tool_name" multiple="false" label="Tool name"> | |
19 <option value="STAR" selected="false">STAR</option> | |
20 </param> | |
21 </xml> | |
22 | |
23 <!--OPTION/ARGUMENT PAIRS and INPUT types--> | |
24 <!--input files--> | |
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25 <xml name="option_argument_single_dataset"> |
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26 <repeat name="option_argument_single_dataset_repeat" title="INPUT SINGLE DATASET" min="0" default="0"> |
0 | 27 <param type="text" name="flag" optional="true" label="flag" /> |
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28 <param name="value" type="data" optional="false" multiple="false" label="value"/> |
0 | 29 </repeat> |
30 </xml> | |
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31 |
0 | 32 <xml name="option_argument_multiple_datasets"> |
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33 <repeat name="option_argument_multiple_datasets_repeat" title="INPUT MULTIPLE DATASETS" min="0" default="0"> |
0 | 34 <param type="text" name="flag" optional="true" label="flag" /> |
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35 <param name="value" type="data" optional="false" multiple="true" label="value"/> |
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36 <param type="select" name="delimiter" multiple="false" label="file delimiter"> |
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37 <option value=" " selected="false">space</option> |
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38 <option value="," selected="false">comma</option> |
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39 </param> |
0 | 40 </repeat> |
41 </xml> | |
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42 |
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43 <!--input path--> |
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44 <xml name="option_argument_path_relative_to_a_tool"> |
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45 <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT PATH: path relative to a tool" min="0" default="0"> |
0 | 46 <param type="text" name="flag" optional="true" label="flag" /> |
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47 <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/> |
0 | 48 <param type="text" name="value" optional="true" label="value" /> |
49 </repeat> | |
50 </xml> | |
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51 <xml name="option_argument_path_relative_to_this_tool"> |
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52 <repeat name="option_argument_path_relative_to_this_tool_repeat" title="INPUT PATH: path relative to this tool" min="0" default="0"> |
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53 <param type="text" name="flag" optional="true" label="flag" /> |
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54 <param type="text" name="value" optional="false" label="value" /> |
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55 <param type="select" name="path_type" multiple="false" label="path type"> |
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56 <option value="file_path" selected="false">file path</option> |
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57 <option value="dir_path" selected="false">directory path</option> |
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58 </param> |
0 | 59 </repeat> |
60 </xml> | |
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61 |
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62 <!--input values: string, float and integer--> |
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63 <xml name="option_argument_string_float_integer"> |
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64 <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0" default="0"> |
0 | 65 <param type="text" name="flag" label="flag" /> |
66 <param type="text" name="value" label="value" /> | |
67 </repeat> | |
68 </xml> | |
69 | |
70 <!--output set--> | |
71 <xml name="output_set"> | |
72 <data format="html" name="report" label="${tool.name} report"/> | |
73 <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/> | |
74 <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/> | |
75 <data format="txt" name="tool_log" label="${tool.name} log" /> | |
76 </xml> | |
77 | |
78 | |
79 <!--shell command fragment--> | |
80 <xml name="shell_command"> | |
81 <command><![CDATA[ | |
82 | |
83 ############ first, create a directory to store all files | |
84 mkdir -p $report.files_path && cd $report.files_path && | |
85 | |
86 | |
87 ############ save the tool installation directory to an environment variable | |
88 export TOOL_INSTALL_DIR='${__tool_directory__}' && | |
89 | |
90 | |
91 ######################### | |
92 ## | |
93 ## save user input option/argument pairs into a file | |
94 ## | |
95 ######################### | |
96 | |
97 ## first line will be the header | |
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98 echo 'type|flag|value|path_type' > options_and_arguments.txt && |
0 | 99 |
100 ############ tool_name | |
101 ##-t '$tool_name' | |
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102 echo "tool_name|not available|${tool_name}|not available" >> options_and_arguments.txt && |
0 | 103 |
104 #################################################### | |
105 ## loop through repeats to get option/argument pairs | |
106 #################################################### | |
107 | |
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108 ############ option_argument_single_dataset |
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109 #for i in $option_argument_single_dataset_repeat: |
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110 #set $item = 'single_dataset|' + str($i.flag) + "|" + str($i.value) + "|" |
0 | 111 echo '$item' >> options_and_arguments.txt && |
112 #end for | |
113 | |
114 ############ option_argument_multiple_datasets | |
115 #for i in $option_argument_multiple_datasets_repeat: | |
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116 #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|" |
0 | 117 echo '$item' >> options_and_arguments.txt && |
118 #end for | |
119 | |
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120 |
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121 ############ option_argument_path_relative_to_a_tool |
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122 #for i in $option_argument_path_relative_to_a_tool_repeat: |
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123 #set $item = 'path_relative_to_a_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir) |
0 | 124 echo '$item' >> options_and_arguments.txt && |
125 #end for | |
126 | |
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127 ############ option_argument_path_relative_to_this_tool |
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128 #for i in $option_argument_path_relative_to_this_tool_repeat: |
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129 #set $item = 'path_relative_to_this_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.path_type) |
0 | 130 echo '$item' >> options_and_arguments.txt && |
131 #end for | |
132 | |
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133 ############ option_argument_string_float_integer |
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134 #for i in $option_argument_string_float_integer_repeat: |
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135 #set $item = 'value|' + str($i.flag) + "|" + str($i.value) + "|" |
0 | 136 echo '$item' >> options_and_arguments.txt && |
137 #end for | |
138 | |
139 ############ output_set | |
140 ## '$report' | |
141 ## '$report.files_path' | |
142 ## '$tool_help_doc' | |
143 ## '$tool_output_dir' | |
144 ## '$tool_log' | |
145 ####################### | |
146 export REPORT='$report' && | |
147 export REPORT_FILES_PATH='$report.files_path' && | |
148 export TOOL_HELP_DOC='$tool_help_doc' && | |
149 export TOOL_OUTPUT_DIR='$tool_output_dir' && | |
150 export TOOL_LOG='$tool_log' && | |
151 | |
152 | |
153 ############ run render R script to render R markdowns | |
154 Rscript '${__tool_directory__}/dynamic_tool_render.R' | |
155 | |
156 ]]></command> | |
157 </xml> | |
158 | |
159 <!--tool citations--> | |
160 <xml name="citations"> | |
161 <citation type="bibtex"><![CDATA[ | |
162 @article{allaire2016rmarkdown, | |
163 title={rmarkdown: Dynamic Documents for R, 2016}, | |
164 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff | |
165 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, | |
166 journal={R package version 0.9}, | |
167 volume={6}, | |
168 year={2016} | |
169 } | |
170 ]]></citation> | |
171 <citation type="bibtex"><![CDATA[ | |
172 @book{xie2015dynamic, | |
173 title={Dynamic Documents with R and knitr}, | |
174 author={Xie, Yihui}, | |
175 volume={29}, | |
176 year={2015}, | |
177 publisher={CRC Press} | |
178 } | |
179 ]]></citation> | |
180 </xml> | |
181 </macros> |