Mercurial > repos > iuc > samtools_faidx

diff samtools_faidx.xml @ 0:baa79754a17e draft

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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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_faidx.xml	Mon May 12 18:06:17 2025 +0000
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+<tool id="samtools_faidx" name="Samtools faidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Index a FASTA file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+    samtools
+        faidx
+        '$in_fasta'
+        --fai-idx '$output'
+    ]]></command>
+    <inputs>
+        <param name="in_fasta" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="dataset with sequences" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="in_fasta" value="samtools_fastx-out1-2.fasta" />
+            <output name="output" file="out.tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Runs the ``samtools faidx`` command to index reference sequence in the FASTA format reference sequence.
+
+Full `documentation <https://www.htslib.org/doc/samtools-faidx.html>`_ for the faidx command.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>