Mercurial > repos > iuc > data_manager_mapseq

annotate mapseq_db_fetcher.xml @ 4:19ef193d1316 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit abbc840d4383eee1f26abef04b1ce4df1e6e20a2
author iuc
date Fri, 06 Dec 2024 15:43:18 +0000
parents a0d77af1d226
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1 <tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Fetches the DB required for mapseq</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 python '$__tool_directory__/data_manager_fetch_mapseq_db.py'
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11 --out '${out_file}'
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12 --version '${select_version.version}'
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13 --database-type '${database_type}'
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14 $test_data_manager_v5
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15 ]]>
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16 </command>
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17 <inputs>
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18 <!-- <param name="test_data_manager" type="hidden" /> -->
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19 <param name="test_data_manager_v5" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry for v5." />
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20 <conditional name="select_version">
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21 <param argument="--version" type="select" label="Select MGnify version">
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22 <option value="5.0">v5.0</option>
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23 <option value="6.0">v6.0</option>
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24 </param>
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25 <when value="5.0">
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26 <param name="database_type" type="select" multiple="false" label="Database Type">
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27 <option value="mgnify_v5_lsu">MGnify LSU (v5.0.7)</option>
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28 <option value="mgnify_v5_ssu">MGnify SSU (v5.0.7)</option>
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29 <option value="mgnify_v5_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
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30 <option value="mgnify_v5_its_unite">MGnify ITS UNITE (v5.0.7)</option>
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31 </param>
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32 </when>
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33 <when value="6.0">
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34 <param name="database_type" type="select" multiple="false" label="Database Type">
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35 <option value="mgnify_v6_lsu">MGnify LSU (v6.0)</option>
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36 <option value="mgnify_v6_ssu">MGnify SSU (v6.0)</option>
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37 <option value="mgnify_v6_its_itsonedb">MGnify ITS ITSonedb (v6.0)</option>
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38 <option value="mgnify_v6_its_unite">MGnify ITS UNITE (v6.0)</option>
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39 <option value="mgnify_v6_pr2">MGnify PR2 (v6.0)</option>
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40 </param>
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41 </when>
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42 </conditional>
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43 </inputs>
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44 <outputs>
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45 <data format="data_manager_json" name="out_file" />
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46 </outputs>
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47 <tests>
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48 <test expect_num_outputs="1">
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49 <param name="test_data_manager_v5" value="--test"/>
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50 <param name="version" value="5.0.7"/>
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51 <param name="database_type" value="mgnify_v5_lsu"/>
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52 <output name="out_file">
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53 <assert_contents>
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54 <has_text text="mgnify_v5_lsu"/>
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55 <has_text text="5.0.7"/>
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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60 <help>
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61 Downloads preformatted DBs form MGnify that can be used for mapseq.
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62 The download paths were taken from: https://github.com/EBI-Metagenomics/pipeline-v5/
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63 </help>
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64 <expand macro="citations" />
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65 <expand macro="creator" />
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66 </tool>