Mercurial > repos > iuc > data_manager_mapseq

comparison mapseq_db_fetcher.xml @ 2:23511530b8fd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
author iuc
date Mon, 30 Sep 2024 10:08:03 +0000
parents dbf2735e8480
children
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1:4cd97cc67061 2:23511530b8fd
1 <?xml version="1.0"?>
2 <tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>Fetches the DB required for mapseq</description> 2 <description>Fetches the DB required for mapseq</description>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
10 <![CDATA[ 9 <![CDATA[
11 python '$__tool_directory__/data_manager_fetch_mapseq_db.py' 10 python '$__tool_directory__/data_manager_fetch_mapseq_db.py'
12 --out '${out_file}' 11 --out '${out_file}'
13 --version '${version}' 12 --version '${version}'
14 --database-type '${database_type}' 13 --database-type '${database_type}'
15 $test_data_manager 14 $test_data_manager_v5
15 $test_data_manager_v6
16 ]]> 16 ]]>
17 </command> 17 </command>
18 <inputs> 18 <inputs>
19 <!-- <param name="test_data_manager" type="hidden" /> --> 19 <!-- <param name="test_data_manager" type="hidden" /> -->
20 <param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." /> 20 <param name="test_data_manager_v5" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." />
21 21 <param name="test_data_manager_v6" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." />
22 <param name="database_type" type="select" multiple="false" label="Database Type"> 22
23 <option value="mgnify_lsu">MGnify LSU (v5.0.7)</option> 23 <param name="database_type" type="select" multiple="false" label="Database Type">
24 <option value="mgnify_ssu">MGnify SSU (v5.0.7)</option> 24 <option value="mgnify_v6_lsu">MGnify LSU (v6.0)</option>
25 <option value="mgnify_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option> 25 <option value="mgnify_v6_ssu">MGnify SSU (v6.0)</option>
26 <option value="mgnify_its_unite">MGnify ITS UNITE (v5.0.7)</option> 26 <option value="mgnify_v6_its_itsonedb">MGnify ITS ITSonedb (v6.0)</option>
27 </param> 27 <option value="mgnify_v6_its_unite">MGnify ITS UNITE (v6.0)</option>
28 28 <option value="mgnify_v6_pr2">MGnify PR2 (v6.0)</option>
29 <!-- <param name="test_data_manager" type="text" value=""/> --> 29 <option value="mgnify_v5_lsu">MGnify LSU (v5.0.7)</option>
30 <param argument="--version" type="text" value="5.0.7" help="Check MGnify GitHub (https://github.com/EBI-Metagenomics/pipeline-v5/releases) for the version."/> 30 <option value="mgnify_v5_ssu">MGnify SSU (v5.0.7)</option>
31 <option value="mgnify_v5_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
32 <option value="mgnify_v5_its_unite">MGnify ITS UNITE (v5.0.7)</option>
33 </param>
34
35 <!-- <param name="test_data_manager" type="text" value=""/> -->
36 <param argument="--version" type="text" value="6.0" help="Check MGnify GitHub (https://github.com/EBI-Metagenomics/amplicon-pipeline) for the version."/>
31 </inputs> 37 </inputs>
32 <outputs> 38 <outputs>
33 <data format="data_manager_json" name="out_file" /> 39 <data format="data_manager_json" name="out_file" />
34 </outputs> 40 </outputs>
35 <tests> 41 <tests>
36 <test expect_num_outputs="1"> 42 <test expect_num_outputs="1">
37 <param name="test_data_manager" value="--test"/> 43 <param name="test_data_manager_v5" value="--test"/>
38 <param name="version" value="5.0.7"/> 44 <param name="version" value="5.0.7"/>
39 <param name="database_type" value="mgnify_lsu"/> 45 <param name="database_type" value="mgnify_v5_lsu"/>
40 <output name="out_file"> 46 <output name="out_file">
41 <assert_contents> 47 <assert_contents>
42 <has_text text="mgnify_lsu"/> 48 <has_text text="mgnify_v5_lsu"/>
43 <has_text text="5.0.7"/> 49 <has_text text="5.0.7"/>
44 </assert_contents> 50 </assert_contents>
51 </output>
52 </test>
53 <test expect_num_outputs="1">
54 <param name="test_data_manager_v6" value="--test"/>
55 <param name="version" value="6.0"/>
56 <param name="database_type" value="mgnify_v6_pr2"/>
57 <output name="out_file">
58 <assert_contents>
59 <has_text text="mgnify_v6_pr2"/>
60 <has_text text="6.0"/>
61 </assert_contents>
45 </output> 62 </output>
46 </test> 63 </test>
47 </tests> 64 </tests>
48 <help> 65 <help>
49 Downloads preformatted DBs form MGnify that can be used for mapseq. 66 Downloads preformatted DBs form MGnify that can be used for mapseq.