Mercurial > repos > iuc > qiime_extract_viz

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
author iuc
date Mon, 13 May 2024 09:25:59 +0000
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f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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1 <tool id="qiime_extract_viz" name="QIIME vizualisation extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT">
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2 <description></description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.1.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <edam_topics>
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8 <edam_topic>topic_3174</edam_topic><!-- metagenomics -->
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9 </edam_topics>
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10 <edam_operations>
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11 <edam_operation>operation_2422</edam_operation> <!-- Data retrieval -->
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12 </edam_operations>
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13 <requirements>
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14 <requirement type="package" version="6.0">unzip</requirement>
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15 </requirements>
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16 <command detect_errors="exit_code"><![CDATA[
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17 unzip '$infile' "*/data/*" &&
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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18 mkdir -p '${viz.extra_files_path}' &&
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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19 mv '$infile.metadata.uuid'/data/* '${viz.extra_files_path}' &&
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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20
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21 ## the html file use <script src="./data.jsonp" charset="utf-8"></script>
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22 ## Galaxy sets application/octet-stream as mime type for which browsers
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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23 ## refuse to include the file. Therefore we replace the extensions by js
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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24 ## for which Galaxy sets the appropriate mime type
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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25 for nonjs in \$(cat '${viz.extra_files_path}'/*.html | grep '<script src="' | sed 's/^\s*<script src="//; s/".*//' | grep -v "\.js\$"); do
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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26 js=\$(echo "\$nonjs" | sed 's/\.[^.]\+$//').js &&
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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27 mv '${viz.extra_files_path}'"/\$nonjs" '${viz.extra_files_path}'"/\$js" &&
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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28 sed -i -e "s@\"\${nonjs}\"@\"\${js}\"@" '${viz.extra_files_path}'/*.html;
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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29 done &&
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30
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31 mv '${viz.extra_files_path}'/index.html '$viz'
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32 ]]></command>
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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33 <inputs>
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34 <param name="infile" type="data" format="qzv" label="QIIME visualization artifact" />
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35 </inputs>
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36 <outputs>
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37 <data name="viz" format="html"/>
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38 </outputs>
f1605d46cb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
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39 <tests>
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40 <!-- the first test use the test data from the galaxy datatypes module
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41 where the html file just contains 43 -->
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42 <test>
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43 <param name="infile" value="qiime2.qzv" ftype="qzv"/>
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44 <output name="viz">
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45 <assert_contents>
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46 <has_text text="43"/>
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47 </assert_contents>
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48 </output>
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49 </test>
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50 <test>
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51 <param name="infile" value="demux-summ.qzv" ftype="qzv"/>
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52 <output name="viz">
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53 <assert_contents>
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54 <has_text text="html"/>
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55 </assert_contents>
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56 </output>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60
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61 .. class:: infomark
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62
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63 **What it does**
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64
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65 The tool extracts visualisation from QIIME visualisation artifact datasets (qzv).
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66
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67 QIIME visualisation artifact files are zip files that contain visualisations of the data
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68 which is extracted by this tool.
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69
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70 Note that Galaxy contains a Display application that uses
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71 https://view.qiime2.org/ to show this data. For non-public Galaxy instances this
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72 does not work.
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73
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74 ]]></help>
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75 <citations>
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76 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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77 </citations>
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78 </tool>