Mercurial > repos > ufz > phabox_end_to_end
view end_to_end.xml @ 0:14307de7bbab draft default tip
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 3c8e23e1dea22f625fb6f77ae61e1f4b605aaae2
author | ufz |
---|---|
date | Tue, 12 Nov 2024 09:31:26 +0000 |
parents | |
children |
line wrap: on
line source
<tool id="phabox_end_to_end" name="PhaBOX end to end" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT"> <description></description> <macros> <import>macros.xml</import> </macros> <xrefs> <xref type="bio.tools">phabox</xref> </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">phabox</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @CRISPR_PRE@ phabox2 --task end_to_end @GENERAL@ @PHAMER@ @NETWORK@ @CRISPR@ ]]></command> <inputs> <expand macro="general"/> <expand macro="phamer"/> <expand macro="network"/> <expand macro="crispr"/> <param name="supplements" type="select" optional="true" multiple="true" label="Output supplementary collections"> <option value="phamer">phamer</option> <option value="phagcn">phagcn</option> <option value="cherry">cherry</option> </param> </inputs> <outputs> <data name="end_to_end_out" format="tabular" from_work_dir="output/final_prediction/final_prediction_summary.tsv"/> <expand macro="supp_out" task="phamer"/> <expand macro="supp_out" task="phagcn"/> <expand macro="supp_out" task="cherry"/> </outputs> <tests> <test expect_num_outputs="1"> <param name="dbdir" value="phaboxdb"/> <param name="contigs" value="example_contigs.fa"/> <output name="end_to_end_out"> <assert_contents> <has_n_lines n="11"/> <has_n_columns n="17"/> <has_text text="Accession	Length	Pred	Proportion	PhaMerScore	PhaMerConfidence	Lineage	PhaGCNScore	Genus	GenusCluster	TYPE	PhaTYPScore	Host	CHERRYScore	Method	Host_NCBI_lineage	Host_GTDB_lineage"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Runs the phabox2 pipeline, i.e. it runs - phamer: Virus identification - phagcn: Taxonomic classification - phatyp: Lifestyle prediction - cherry: Host prediction The outputs of the separate tools are joined into one big table. @COMMON_INPUT_DOC@ **Output** @COMMON_OUTPUT_DOC@ @PHAMER_OUTPUT_DOC@ @PHAGCN_OUTPUT_DOC@ @PHATYP_OUTPUT_DOC@ @CHERRY_OUTPUT_DOC@ ]]></help> <expand macro="citations"/> </tool>