Mercurial > repos > ufz > phabox_contamination

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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 09:42:58 +0000
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6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
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1 <tool id="phabox_contamination" name="PhaBOX contamination" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
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2 <description>Contamination/provirus detection</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 contamination
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14 @GENERAL@
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15 @CONTAMINATION@
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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="contamination"/>
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20 </inputs>
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21 <outputs>
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22 <data name="out" format="tabular" from_work_dir="output/final_prediction/contamination_prediction.tsv"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="dbdir" value="phaboxdb"/>
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27 <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
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28 <output name="out">
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29 <assert_contents>
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30 <has_line line="Accession&#9;Length&#9;Total_genes&#9;Viral_genes&#9;Prokaryotic_genes&#9;Kmer_freq&#9;Contamination&#9;Provirus&#9;Pure_viral"/>
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31 <has_n_lines n="391"/>
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32 <has_n_columns n="9"/>
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33 </assert_contents>
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34 </output>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38
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39 Check for contaminations / proviruses.
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41
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42 @COMMON_INPUT_DOC@
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43
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44 **Output**:
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45
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46 @COMMON_OUTPUT_DOC@
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47 - Total_genes: number of genes in the contigs (predicted by prodigal-gv)
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48 - Viral_genes: number of viral marker genes
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49 - Prokaryotic_genes: number of prokaryotic marker genes
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50 - Kmer_freq: average frequency of 20-mer. This is a value to estimate the copy number of the genes; usually, the Kmer_freq of 99.9% virus is less than 1.25.
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51 - Contamination:
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52 - Provirus: Whether the sequence is a provirus
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53 - Pure_viral: High quality or Medium quality or Low quality
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54
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55
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56 ]]></help>
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57 <expand macro="citations"/>
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58 </tool>