Mercurial > repos > iuc > plasclass
comparison 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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| -1:000000000000 | 0:8a97b4648968 |
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| 1 <tool id="plasclass" name="PlasClass" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> | |
| 2 <description>for plasmid/chromosome classification</description> | |
| 3 <macros> | |
| 4 <token name="@TOOL_VERSION@">0.1.1</token> | |
| 5 <token name="@VERSION_SUFFIX@">0</token> | |
| 6 <token name="@PROFILE@">24.1</token> | |
| 7 </macros> | |
| 8 <xrefs> | |
| 9 <xref type="bio.tools">PlasClass</xref> | |
| 10 </xrefs> | |
| 11 <requirements> | |
| 12 <requirement type="package" version="@TOOL_VERSION@">plasclass</requirement> | |
| 13 </requirements> | |
| 14 <command detect_errors="exit_code"><![CDATA[ | |
| 15 classify_fasta.py | |
| 16 --fasta '$fasta' | |
| 17 --outfile '$outfile' | |
| 18 --num_processes "\${GALAXY_SLOTS:-1}" | |
| 19 ]]></command> | |
| 20 <inputs> | |
| 21 <param argument="--fasta" type="data" format="fasta" label="Sequences to be classified"/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data name="outfile" format="tabular"/> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test expect_num_outputs="1"> | |
| 28 <param name="fasta" value="test.fa"/> | |
| 29 <output name="outfile" ftype="tabular"> | |
| 30 <assert_contents> | |
| 31 <has_text text="EDGE_1998488_length_236_cov_0.817680"/> | |
| 32 <has_n_lines n="62"/> | |
| 33 <has_n_columns n="2"/> | |
| 34 </assert_contents> | |
| 35 </output> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help><![CDATA[ | |
| 39 | |
| 40 **What it does** | |
| 41 | |
| 42 PlasClass is a cutting-edge plasmid classifier designed to address the challenges of distinguishing between | |
| 43 plasmid and bacterial genome sequences in metagenomic and isolate assemblies. Many bacteria contain plasmids, | |
| 44 but identifying contigs that originate from plasmids can be particularly difficult in metagenomic assembly, | |
| 45 where the origin of contigs is often unknown. | |
| 46 | |
| 47 **Input** | |
| 48 | |
| 49 - FASTA file with sequences to classify | |
| 50 | |
| 51 **Output** | |
| 52 | |
| 53 - 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. | |
| 54 | |
| 55 ]]></help> | |
| 56 <citations> | |
| 57 <citation type="doi">10.1371/journal.pcbi.1007781</citation> | |
| 58 </citations> | |
| 59 </tool> |