Mercurial > repos > iuc > ega_download_client
comparison pyega3.xml @ 2:e82175804eb1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit eb28ccaa03633b3500b38e2eb304c55e1682c489
| author | iuc |
|---|---|
| date | Tue, 14 Jun 2022 17:06:07 +0000 |
| parents | 1162bfd9f782 |
| children | 8bbe09a52904 |
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| 1:1162bfd9f782 | 2:e82175804eb1 |
|---|---|
| 1 <tool id="pyega3" name="EGA Download Client" version="@TOOL_VERSION@+galaxy0" profile="21.01" > | 1 <tool id="pyega3" name="EGA Download Client" version="@TOOL_VERSION@+galaxy1" profile="21.01" > |
| 2 <macros> | 2 <macros> |
| 3 <token name="@TOOL_VERSION@">4.0.0</token> | 3 <token name="@TOOL_VERSION@">4.0.0</token> |
| 4 </macros> | 4 </macros> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="@TOOL_VERSION@">pyega3</requirement> | 6 <requirement type="package" version="@TOOL_VERSION@">pyega3</requirement> |
| 30 pyega3 -c \${PYEGA_CONNECTIONS:-30} -cf '$credentials' | 30 pyega3 -c \${PYEGA_CONNECTIONS:-30} -cf '$credentials' |
| 31 fetch '$action.file_id' | 31 fetch '$action.file_id' |
| 32 --max-retries 10 | 32 --max-retries 10 |
| 33 #if $action.range.reference_name | 33 #if $action.range.reference_name |
| 34 --reference-name '$action.range.reference_name' | 34 --reference-name '$action.range.reference_name' |
| 35 #if $action.range.start | 35 #if str($action.range.start) |
| 36 --start $action.range.start | 36 --start $action.range.start |
| 37 #end if | 37 #end if |
| 38 #if $action.range.end | 38 #if $action.range.end |
| 39 --end $action.range.end | 39 --end $action.range.end |
| 40 #end if | 40 #end if |
| 50 pyega3 -c \${PYEGA_CONNECTIONS:-30} -cf '$credentials' | 50 pyega3 -c \${PYEGA_CONNECTIONS:-30} -cf '$credentials' |
| 51 fetch '$f' | 51 fetch '$f' |
| 52 --max-retries 10 | 52 --max-retries 10 |
| 53 #if $action.range.reference_name | 53 #if $action.range.reference_name |
| 54 --reference-name '$action.range.reference_name' | 54 --reference-name '$action.range.reference_name' |
| 55 #if $action.range.start | 55 #if str($action.range.start) |
| 56 --start $action.range.start | 56 --start $action.range.start |
| 57 #end if | 57 #end if |
| 58 #if $action.range.end | 58 #if $action.range.end |
| 59 --end $action.range.end | 59 --end $action.range.end |
| 60 #end if | 60 #end if |
| 163 </test> | 163 </test> |
| 164 <test expect_num_outputs="1"> <!-- download a single file, with genomic range specified --> | 164 <test expect_num_outputs="1"> <!-- download a single file, with genomic range specified --> |
| 165 <param name="action_type" value="download_file"/> | 165 <param name="action_type" value="download_file"/> |
| 166 <param name="file_id" value="EGAF00001753756"/> | 166 <param name="file_id" value="EGAF00001753756"/> |
| 167 <param name="reference_name" value="1"/> | 167 <param name="reference_name" value="1"/> |
| 168 <param name="start" value="100"/> | 168 <param name="start" value="0"/> |
| 169 <param name="end" value="10000"/> | 169 <param name="end" value="10000"/> |
| 170 <output name="downloaded_file" ftype="bam" md5="e576a38748feec45aa45191f6e902ce2"/> | 170 <output name="downloaded_file" ftype="bam" md5="e576a38748feec45aa45191f6e902ce2"/> |
| 171 </test> | 171 </test> |
| 172 <test expect_num_outputs="1"> <!-- download multiple files --> | 172 <test expect_num_outputs="1"> <!-- download multiple files --> |
| 173 <param name="action_type" value="download_files"/> | 173 <param name="action_type" value="download_files"/> |
| 181 <test expect_num_outputs="1"> <!-- download multiple files, in combination with a genomic range --> | 181 <test expect_num_outputs="1"> <!-- download multiple files, in combination with a genomic range --> |
| 182 <param name="action_type" value="download_files"/> | 182 <param name="action_type" value="download_files"/> |
| 183 <param name="id_table" value="filelist2.tabular"/> | 183 <param name="id_table" value="filelist2.tabular"/> |
| 184 <param name="id_column" value="1"/> | 184 <param name="id_column" value="1"/> |
| 185 <param name="reference_name" value="1"/> | 185 <param name="reference_name" value="1"/> |
| 186 <param name="start" value="100"/> | 186 <param name="start" value="0"/> |
| 187 <param name="end" value="10000"/> | 187 <param name="end" value="10000"/> |
| 188 <output_collection name="downloaded_file_collection" count="2"> | 188 <output_collection name="downloaded_file_collection" count="2"> |
| 189 <element name="NA19239_genomic_range_1_100_10000" md5="bcdcf18846233cbe5cc8afd95168552c" /> | 189 <element name="NA19239_genomic_range_1_0_10000" md5="bcdcf18846233cbe5cc8afd95168552c" /> |
| 190 <element name="NA19240_genomic_range_1_100_10000" md5="e576a38748feec45aa45191f6e902ce2" /> | 190 <element name="NA19240_genomic_range_1_0_10000" md5="e576a38748feec45aa45191f6e902ce2" /> |
| 191 </output_collection> | 191 </output_collection> |
| 192 </test> | 192 </test> |
| 193 </tests> | 193 </tests> |
| 194 <help><![CDATA[ | 194 <help><![CDATA[ |
| 195 The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets. | 195 The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets. |