Mercurial > repos > ufz > phabox_phamer

comparison phamer.xml @ 0:21ed0e3791c5 draft default tip

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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 09:42:38 +0000
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1 <tool id="phabox_phamer" name="PhaBOX phamer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
2 <description>Virus identification</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <xrefs>
7 <xref type="bio.tools">phabox</xref>
8 </xrefs>
9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">phabox</requirement>
11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[
13 phabox2 --task phamer
14 @GENERAL@
15 @PHAMER@
16 ]]></command>
17 <inputs>
18 <expand macro="general"/>
19 <expand macro="phamer"/>
20 </inputs>
21 <outputs>
22 <data name="phamer_out" format="tabular" from_work_dir="output/final_prediction/phamer_prediction.tsv"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="dbdir" value="phaboxdb"/>
27 <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
28 <output name="phamer_out">
29 <assert_contents>
30 <has_line line="Accession&#9;Length&#9;Pred&#9;Proportion&#9;PhaMerScore&#9;PhaMerConfidence"/>
31 <has_n_lines n="391"/> <!-- 1 per input sequence-->
32 <has_n_columns n="6"/>
33 </assert_contents>
34 </output>
35 </test>
36 </tests>
37 <help><![CDATA[
38
39 Identify phage contigs from metagenomics data.
40
41 @COMMON_INPUT_DOC@
42
43 **Output**:
44
45 @COMMON_OUTPUT_DOC@
46 @PHAMER_OUTPUT_DOC@
47 ]]></help>
48 <expand macro="citations">
49 <citation type="doi">10.1093/bib/bbac258</citation>
50 </expand>
51 </tool>