Mercurial > repos > iuc > samtools_faidx
comparison samtools_faidx.xml @ 0:baa79754a17e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_faidx commit da2aa10802e960a69f3858f86b858807442ca7c7
| author | iuc |
|---|---|
| date | Mon, 12 May 2025 18:06:17 +0000 |
| parents | |
| children | 76c27c4861bd |
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| -1:000000000000 | 0:baa79754a17e |
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| 1 <tool id="samtools_faidx" name="Samtools faidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| 2 <description>Index a FASTA file</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <expand macro="stdio"/> | |
| 8 <expand macro="version_command"/> | |
| 9 <command><![CDATA[ | |
| 10 samtools | |
| 11 faidx | |
| 12 '$in_fasta' | |
| 13 --fai-idx '$output' | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param name="in_fasta" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="dataset with sequences" /> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data name="output" format="tabular"/> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test expect_num_outputs="1"> | |
| 23 <param name="in_fasta" value="samtools_fastx-out1-2.fasta" /> | |
| 24 <output name="output" file="out.tabular" /> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help><![CDATA[ | |
| 28 **What it does** | |
| 29 | |
| 30 Runs the ``samtools faidx`` command to index reference sequence in the FASTA format reference sequence. | |
| 31 | |
| 32 Full `documentation <https://www.htslib.org/doc/samtools-faidx.html>`_ for the faidx command. | |
| 33 ]]></help> | |
| 34 <expand macro="citations"/> | |
| 35 </tool> |