Mercurial > repos > mingchen0919 > dynamic_star
comparison dynamic_tool_wrappers_macros.xml @ 2:a9579c344a90 draft default tip
planemo upload commit 8f84e3911c6ff4103c0ad5fb8dd774f80d9b2559
| author | mingchen0919 |
|---|---|
| date | Fri, 23 Mar 2018 21:50:16 -0400 |
| parents | ddc3c3527f49 |
| children |
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| 1:ddc3c3527f49 | 2:a9579c344a90 |
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| 20 </param> | 20 </param> |
| 21 </xml> | 21 </xml> |
| 22 | 22 |
| 23 <!--OPTION/ARGUMENT PAIRS and INPUT types--> | 23 <!--OPTION/ARGUMENT PAIRS and INPUT types--> |
| 24 <!--input files--> | 24 <!--input files--> |
| 25 <xml name="option_argument_one_dataset"> | 25 <xml name="option_argument_single_dataset"> |
| 26 <repeat name="option_argument_one_dataset_repeat" title="OPTION and ARGUMENT: input one dataset" min="0" default="0"> | 26 <repeat name="option_argument_single_dataset_repeat" title="INPUT SINGLE DATASET" min="0" default="0"> |
| 27 <param type="text" name="flag" optional="true" label="flag" /> | 27 <param type="text" name="flag" optional="true" label="flag" /> |
| 28 <param name="value" type="data" optional="true" multiple="false" label="value"/> | 28 <param name="value" type="data" optional="false" multiple="false" label="value"/> |
| 29 </repeat> | 29 </repeat> |
| 30 </xml> | 30 </xml> |
| 31 | |
| 31 <xml name="option_argument_multiple_datasets"> | 32 <xml name="option_argument_multiple_datasets"> |
| 32 <repeat name="option_argument_multiple_datasets_repeat" title="OPTION and ARGUMENT: input multiple datasets" min="0" default="0"> | 33 <repeat name="option_argument_multiple_datasets_repeat" title="INPUT MULTIPLE DATASETS" min="0" default="0"> |
| 33 <param type="text" name="flag" optional="true" label="flag" /> | 34 <param type="text" name="flag" optional="true" label="flag" /> |
| 34 <param name="value" type="data" optional="true" multiple="true" label="value" /> | 35 <param name="value" type="data" optional="false" multiple="true" label="value"/> |
| 36 <param type="select" name="delimiter" multiple="false" label="file delimiter"> | |
| 37 <option value=" " selected="false">space</option> | |
| 38 <option value="," selected="false">comma</option> | |
| 39 </param> | |
| 35 </repeat> | 40 </repeat> |
| 36 </xml> | 41 </xml> |
| 37 <xml name="option_argument_path_relative_to_upstream_tool"> | 42 |
| 38 <repeat name="option_argument_path_relative_to_upstream_tool_repeat" title="OPTION and ARGUMENT: path relative to upstream tool" min="0" default="0"> | 43 <!--input path--> |
| 44 <xml name="option_argument_path_relative_to_a_tool"> | |
| 45 <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT PATH: path relative to a tool" min="0" default="0"> | |
| 39 <param type="text" name="flag" optional="true" label="flag" /> | 46 <param type="text" name="flag" optional="true" label="flag" /> |
| 40 <param name="upstream_tool_output_dir" type="data" optional="true" multiple="false" label="upstream tool output directory"/> | 47 <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/> |
| 41 <param type="text" name="value" optional="true" label="value" /> | 48 <param type="text" name="value" optional="true" label="value" /> |
| 42 </repeat> | 49 </repeat> |
| 43 </xml> | 50 </xml> |
| 44 | 51 <xml name="option_argument_path_relative_to_this_tool"> |
| 45 <!--input values: string, float and integer--> | 52 <repeat name="option_argument_path_relative_to_this_tool_repeat" title="INPUT PATH: path relative to this tool" min="0" default="0"> |
| 46 <xml name="option_argument_string"> | 53 <param type="text" name="flag" optional="true" label="flag" /> |
| 47 <repeat name="option_argument_string_repeat" title="OPTION and ARGUMENT: input string" min="0" default="0"> | 54 <param type="text" name="value" optional="false" label="value" /> |
| 48 <param type="text" name="flag" label="flag" /> | 55 <param type="select" name="path_type" multiple="false" label="path type"> |
| 49 <param type="text" name="value" label="value" /> | 56 <option value="file_path" selected="false">file path</option> |
| 57 <option value="dir_path" selected="false">directory path</option> | |
| 58 </param> | |
| 50 </repeat> | 59 </repeat> |
| 51 </xml> | 60 </xml> |
| 52 <xml name="option_argument_float"> | 61 |
| 53 <repeat name="option_argument_float_repeat" title="OPTION and ARGUMENT: input float" min="0" default="0"> | 62 <!--input values: string, float and integer--> |
| 54 <param type="text" name="flag" label="flag" /> | 63 <xml name="option_argument_string_float_integer"> |
| 55 <param type="text" name="value" label="value" /> | 64 <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0" default="0"> |
| 56 </repeat> | |
| 57 </xml> | |
| 58 <xml name="option_argument_integer"> | |
| 59 <repeat name="option_argument_integer_repeat" title="OPTION and ARGUMENT: input integer" min="0" default="0"> | |
| 60 <param type="text" name="flag" label="flag" /> | 65 <param type="text" name="flag" label="flag" /> |
| 61 <param type="text" name="value" label="value" /> | 66 <param type="text" name="value" label="value" /> |
| 62 </repeat> | 67 </repeat> |
| 63 </xml> | 68 </xml> |
| 64 | 69 |
| 88 ## save user input option/argument pairs into a file | 93 ## save user input option/argument pairs into a file |
| 89 ## | 94 ## |
| 90 ######################### | 95 ######################### |
| 91 | 96 |
| 92 ## first line will be the header | 97 ## first line will be the header |
| 93 echo 'type|flag|value' > options_and_arguments.txt && | 98 echo 'type|flag|value|path_type' > options_and_arguments.txt && |
| 94 | 99 |
| 95 ############ tool_name | 100 ############ tool_name |
| 96 ##-t '$tool_name' | 101 ##-t '$tool_name' |
| 97 echo "tool_name|tool_flag|${tool_name}" >> options_and_arguments.txt && | 102 echo "tool_name|not available|${tool_name}|not available" >> options_and_arguments.txt && |
| 98 | 103 |
| 99 #################################################### | 104 #################################################### |
| 100 ## loop through repeats to get option/argument pairs | 105 ## loop through repeats to get option/argument pairs |
| 101 #################################################### | 106 #################################################### |
| 102 | 107 |
| 103 ############ option_argument_one_dataset | 108 ############ option_argument_single_dataset |
| 104 #for i in $option_argument_one_dataset_repeat: | 109 #for i in $option_argument_single_dataset_repeat: |
| 105 #set $item = 'one_dataset|' + str($i.flag) + "|" + str($i.value) | 110 #set $item = 'single_dataset|' + str($i.flag) + "|" + str($i.value) + "|" |
| 106 echo '$item' >> options_and_arguments.txt && | 111 echo '$item' >> options_and_arguments.txt && |
| 107 #end for | 112 #end for |
| 108 | 113 |
| 109 ############ option_argument_multiple_datasets | 114 ############ option_argument_multiple_datasets |
| 110 #for i in $option_argument_multiple_datasets_repeat: | 115 #for i in $option_argument_multiple_datasets_repeat: |
| 111 #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value) | 116 #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|" |
| 112 echo '$item' >> options_and_arguments.txt && | 117 echo '$item' >> options_and_arguments.txt && |
| 113 #end for | 118 #end for |
| 114 | 119 |
| 115 ############ option_argument_path_relative_to_upstream_tool | 120 |
| 116 #for i in $option_argument_path_relative_to_upstream_tool_repeat: | 121 ############ option_argument_path_relative_to_a_tool |
| 117 #set $item = 'path_relative_to_upstream_tool|' + str($i.flag) + "|" + str($i.value) | 122 #for i in $option_argument_path_relative_to_a_tool_repeat: |
| 123 #set $item = 'path_relative_to_a_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir) | |
| 118 echo '$item' >> options_and_arguments.txt && | 124 echo '$item' >> options_and_arguments.txt && |
| 119 #end for | 125 #end for |
| 120 | 126 |
| 121 ############ option_argument_string | 127 ############ option_argument_path_relative_to_this_tool |
| 122 #for i in $option_argument_string_repeat: | 128 #for i in $option_argument_path_relative_to_this_tool_repeat: |
| 123 #set $item = 'string|' + str($i.flag) + "|" + str($i.value) | 129 #set $item = 'path_relative_to_this_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.path_type) |
| 124 echo '$item' >> options_and_arguments.txt && | 130 echo '$item' >> options_and_arguments.txt && |
| 125 #end for | 131 #end for |
| 126 | 132 |
| 127 ############ option_argument_float | 133 ############ option_argument_string_float_integer |
| 128 #for i in $option_argument_float_repeat: | 134 #for i in $option_argument_string_float_integer_repeat: |
| 129 #set $item = 'float|' + str($i.flag) + "|" + str($i.value) | 135 #set $item = 'value|' + str($i.flag) + "|" + str($i.value) + "|" |
| 130 echo '$item' >> options_and_arguments.txt && | 136 echo '$item' >> options_and_arguments.txt && |
| 131 #end for | 137 #end for |
| 132 | |
| 133 | |
| 134 ############ option_argument_integer | |
| 135 #for i in $option_argument_integer_repeat: | |
| 136 #set $item = 'integer|' + str($i.flag) + "|" + str($i.value) | |
| 137 echo '$item' >> options_and_arguments.txt && | |
| 138 #end for | |
| 139 | |
| 140 | 138 |
| 141 ############ output_set | 139 ############ output_set |
| 142 ## '$report' | 140 ## '$report' |
| 143 ## '$report.files_path' | 141 ## '$report.files_path' |
| 144 ## '$tool_help_doc' | 142 ## '$tool_help_doc' |
| 149 export REPORT_FILES_PATH='$report.files_path' && | 147 export REPORT_FILES_PATH='$report.files_path' && |
| 150 export TOOL_HELP_DOC='$tool_help_doc' && | 148 export TOOL_HELP_DOC='$tool_help_doc' && |
| 151 export TOOL_OUTPUT_DIR='$tool_output_dir' && | 149 export TOOL_OUTPUT_DIR='$tool_output_dir' && |
| 152 export TOOL_LOG='$tool_log' && | 150 export TOOL_LOG='$tool_log' && |
| 153 | 151 |
| 154 | |
| 155 ############ save tool files path to a tool output so that it can be accessed from galaxy history | |
| 156 echo '$report.files_path' > $tool_output_dir && | |
| 157 | 152 |
| 158 ############ run render R script to render R markdowns | 153 ############ run render R script to render R markdowns |
| 159 Rscript '${__tool_directory__}/dynamic_tool_render.R' | 154 Rscript '${__tool_directory__}/dynamic_tool_render.R' |
| 160 | 155 |
| 161 ]]></command> | 156 ]]></command> |