Mercurial > repos > iuc > plasclass
diff plasclass.xml @ 0:8a97b4648968 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass commit 8cec6b221914a96102b6d09b51e95626d43a9f8c
author | iuc |
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date | Thu, 31 Jul 2025 13:21:38 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plasclass.xml Thu Jul 31 13:21:38 2025 +0000 @@ -0,0 +1,59 @@ +<tool id="plasclass" name="PlasClass" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description>for plasmid/chromosome classification</description> + <macros> + <token name="@TOOL_VERSION@">0.1.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">24.1</token> + </macros> + <xrefs> + <xref type="bio.tools">PlasClass</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">plasclass</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +classify_fasta.py + --fasta '$fasta' + --outfile '$outfile' + --num_processes "\${GALAXY_SLOTS:-1}" + ]]></command> + <inputs> + <param argument="--fasta" type="data" format="fasta" label="Sequences to be classified"/> + </inputs> + <outputs> + <data name="outfile" format="tabular"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="fasta" value="test.fa"/> + <output name="outfile" ftype="tabular"> + <assert_contents> + <has_text text="EDGE_1998488_length_236_cov_0.817680"/> + <has_n_lines n="62"/> + <has_n_columns n="2"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +**What it does** + +PlasClass is a cutting-edge plasmid classifier designed to address the challenges of distinguishing between +plasmid and bacterial genome sequences in metagenomic and isolate assemblies. Many bacteria contain plasmids, +but identifying contigs that originate from plasmids can be particularly difficult in metagenomic assembly, +where the origin of contigs is often unknown. + +**Input** + +- FASTA file with sequences to classify + +**Output** + +- A tabular separated file with each line containing a sequence header and the corresponding score. The sequences are in the same order as in the input FASTA file. + + ]]></help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1007781</citation> + </citations> +</tool>