Mercurial > repos > iuc > packaged_annotation_loader
annotate load_annotations.xml @ 0:0de428c589f3 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
author | iuc |
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date | Tue, 04 Jan 2022 18:34:48 +0000 |
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0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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1 <tool id="packaged_annotation_loader" name="Load packaged annotation data" version="0.1" profile="20.05"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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2 <description>as a collection</description> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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3 <requirements> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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4 <requirement type="package" version="3.9">python</requirement> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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5 <requirement type="package" version="6.0">pyyaml</requirement> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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6 </requirements> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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7 <command detect_errors="exit_code"><![CDATA[ |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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8 cp $c1 galaxy.json |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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9 #if str($retrieve_meta): |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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10 && python '$__tool_directory__/retrieve_meta.py' --format $retrieve_meta -o meta.out galaxy.json |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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11 #end if |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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12 ]]> </command> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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13 <configfiles> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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14 <configfile name="c1"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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15 #set $elems=",".join(['{{"name": "%s", "ext": "%s", "filename": "{0}/%s", "dbkey": "{1}"}}' % (i, f, i) for i, f in zip($annotation, $annotation.fields.format.split(','))]) |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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16 #set $elems=$elems.format($packaged_data.fields.path, $packaged_data.fields.dbkey) |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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17 {"list_output": {"elements": [$elems]}} |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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18 </configfile> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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19 </configfiles> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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20 <inputs> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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21 <param name="packaged_data" type="select" label="Annotation data package to load"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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22 <options from_data_table="packaged_annotation_data"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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23 <column name="name" index="6" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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24 <column name="value" index="5" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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25 <column name="path" index="7" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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26 <column name="dbkey" index="1" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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27 <filter type="unique_value" column="value" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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28 <filter type="sort_by" column="name" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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29 <validator type="no_options" message="No annotation paackage available" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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30 </options> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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31 </param> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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32 <param name="annotation" type="select" multiple="true" optional="false" label="Packaged annotations to load into collection"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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33 <options from_data_table="packaged_annotation_data"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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34 <column name="name" index="2" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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35 <column name="value" index="3" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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36 <column name="format" index="4" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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37 <column name="package_id" index="5" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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38 <filter type="param_value" ref="packaged_data" column="package_id" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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39 <validator type="no_options" message="No annotation data available" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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40 </options> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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41 </param> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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42 <param name="retrieve_meta" type="select" label="Retrieve annotation sources metadata as separate dataset?"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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43 <option value="">No metadata</option> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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44 <option value="yaml">Return the metadata in orignal yaml format</option> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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45 <option value="tab">Return tabular annotation source/version info</option> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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46 </param> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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47 </inputs> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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48 <outputs> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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49 <collection name="list_output" type="list" label="Output List"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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50 <discover_datasets from_provided_metadata="true" visible="false" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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51 </collection> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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52 <data name="meta_out" format="tabular" label="Loaded annotations metadata" from_work_dir="meta.out"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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53 <filter>bool(str(retrieve_meta))</filter> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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54 <change_format> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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55 <when input="retrieve_meta" value="yaml" format="yaml" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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56 </change_format> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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57 </data> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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58 </outputs> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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59 <tests> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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60 <test expect_num_outputs="1"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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61 <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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62 <param name="annotation" value="hotspots.data.test" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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63 <output_collection name="list_output" type="list" count="1"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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64 <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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65 <metadata name="dbkey" value="hg19" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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66 </element> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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67 </output_collection> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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68 </test> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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69 <test expect_num_outputs="1"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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70 <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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71 <param name="annotation" value="hotspots.data.test,civic.variants.test" /> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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72 <output_collection name="list_output" type="list" count="2"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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73 <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test"> |
0de428c589f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"
iuc
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74 <metadata name="dbkey" value="hg19" /> |
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75 </element> |
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76 <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test"> |
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77 <metadata name="dbkey" value="hg19" /> |
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78 </element> |
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79 </output_collection> |
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80 </test> |
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81 <test expect_num_outputs="2"> |
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82 <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" /> |
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83 <param name="annotation" value="hotspots.data.test,civic.variants.test" /> |
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84 <param name="retrieve_meta" value="yaml" /> |
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85 <output_collection name="list_output" type="list" count="2"> |
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86 <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test"> |
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87 <metadata name="dbkey" value="hg19" /> |
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88 </element> |
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89 <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test"> |
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90 <metadata name="dbkey" value="hg19" /> |
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91 </element> |
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92 </output_collection> |
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93 <output name="meta_out" ftype="yaml" file="test-annotation-data/meta.yml" /> |
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94 </test> |
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95 <test expect_num_outputs="2"> |
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96 <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" /> |
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97 <param name="annotation" value="hotspots.data.test,civic.variants.test" /> |
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98 <param name="retrieve_meta" value="tab" /> |
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99 <output_collection name="list_output" type="list" count="2"> |
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100 <element name="hotspots.data.test" ftype="bed" file="test-annotation-data/hotspots.data.test"> |
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101 <metadata name="dbkey" value="hg19" /> |
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102 </element> |
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103 <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test"> |
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104 <metadata name="dbkey" value="hg19" /> |
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105 </element> |
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106 </output_collection> |
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107 <output name="meta_out" ftype="tabular" file="anno-version.tsv"/> |
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108 </test> |
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109 <test expect_num_outputs="2"> |
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110 <param name="packaged_data" value="Cancer_variant_data__hg19__1__2021-12-16" /> |
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111 <param name="annotation" value="civic.variants.test" /> |
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112 <param name="retrieve_meta" value="tab" /> |
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113 <output_collection name="list_output" type="list" count="1"> |
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114 <element name="civic.variants.test" ftype="bed" file="test-annotation-data/civic.variants.test"> |
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115 <metadata name="dbkey" value="hg19" /> |
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116 </element> |
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117 </output_collection> |
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118 <output name="meta_out" ftype="tabular"> |
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119 <assert_contents> |
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120 <has_n_lines n="2" /> |
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121 <has_line line="Annotation	Version" /> |
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122 <has_line line="CIViC variants	01-Feb-2019" /> |
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123 </assert_contents> |
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124 </output> |
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125 </test> |
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126 </tests> |
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127 <help><![CDATA[ |
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128 This tool can be used to make genome annotation data installed via the |
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129 `data manager for packaged_annotation data |
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130 <https://toolshed.g2.bx.psu.edu/view/wolma/data_manager_packaged_annotation_data>`__ |
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131 accessible as a list of datasets collection. |
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132 ]]></help> |
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133 </tool> |