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planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
author ufz
date Wed, 16 Apr 2025 09:43:42 +0000
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daaab891f936 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 3c8e23e1dea22f625fb6f77ae61e1f4b605aaae2
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1 <tool id="phabox_tree" name="PhaBOX tree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
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2 <description>Build phylogenetic trees based on marker genes</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 <xrefs>
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7 <xref type="bio.tools">phabox</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">phabox</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 phabox2 --task tree
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14 @GENERAL@
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15 @TREE@
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16 ]]></command>
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17 <inputs>
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18 <expand macro="general"/>
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19 <expand macro="tree"/>
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20 </inputs>
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21 <outputs>
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22 <collection name="marker_genes" format="fasta" type="list">
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23 <discover_datasets pattern="found_marker_(?P&lt;designation&gt;.+)_combined_db.fa" directory="output/final_prediction/tree_supplementary"/>
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24 </collection>
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25 </outputs>
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26 <tests>
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27 <test expect_num_outputs="1">
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28 <param name="dbdir" value="phaboxdb"/>
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29 <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
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30 <output_collection name="marker_genes" count="2">
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31 <element name="portal">
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32 <assert_contents>
1
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33 <has_text text=">" n="4281"/>
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34 </assert_contents>
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35 </element>
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36 <element name="terl">
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37 <assert_contents>
1
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38 <has_text text=">" n="4672"/>
0
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39 </assert_contents>
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40 </element>
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41 </output_collection>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 Get sequences of specific marker genes that can be used for phylogentic tree construction.
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46
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47 @COMMON_INPUT_DOC@
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48
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49 ]]></help>
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50 <expand macro="citations"/>
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51 </tool>