Mercurial > repos > ufz > phabox_contamination
comparison contamination.xml @ 0:6c7718bc9849 draft default tip
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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| children |
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| -1:000000000000 | 0:6c7718bc9849 |
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| 1 <tool id="phabox_contamination" name="PhaBOX contamination" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT"> | |
| 2 <description>Contamination/provirus detection</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 contamination | |
| 14 @GENERAL@ | |
| 15 @CONTAMINATION@ | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 <expand macro="general"/> | |
| 19 <expand macro="contamination"/> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data name="out" format="tabular" from_work_dir="output/final_prediction/contamination_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="out"> | |
| 29 <assert_contents> | |
| 30 <has_line line="Accession	Length	Total_genes	Viral_genes	Prokaryotic_genes	Kmer_freq	Contamination	Provirus	Pure_viral"/> | |
| 31 <has_n_lines n="391"/> | |
| 32 <has_n_columns n="9"/> | |
| 33 </assert_contents> | |
| 34 </output> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help><![CDATA[ | |
| 38 | |
| 39 Check for contaminations / proviruses. | |
| 40 | |
| 41 | |
| 42 @COMMON_INPUT_DOC@ | |
| 43 | |
| 44 **Output**: | |
| 45 | |
| 46 @COMMON_OUTPUT_DOC@ | |
| 47 - Total_genes: number of genes in the contigs (predicted by prodigal-gv) | |
| 48 - Viral_genes: number of viral marker genes | |
| 49 - Prokaryotic_genes: number of prokaryotic marker genes | |
| 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. | |
| 51 - Contamination: | |
| 52 - Provirus: Whether the sequence is a provirus | |
| 53 - Pure_viral: High quality or Medium quality or Low quality | |
| 54 | |
| 55 | |
| 56 ]]></help> | |
| 57 <expand macro="citations"/> | |
| 58 </tool> |