# HG changeset patch
# User iuc
# Date 1663590580 0
# Node ID bd3dc3b5aea543f240c7c3434754b44443db0cc2

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e

diff -r 000000000000 -r bd3dc3b5aea5 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Sep 19 12:29:40 2022 +0000
@@ -0,0 +1,3 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.2</token>
+</macros>
diff -r 000000000000 -r bd3dc3b5aea5 miniprot_index.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/miniprot_index.xml	Mon Sep 19 12:29:40 2022 +0000
@@ -0,0 +1,34 @@
+<tool id="miniprot_index" name="Miniprot index" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+    <description>build a genome index for miniprot</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">miniprot</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        miniprot -d '$output_index' '$input_genome'
+    ]]></command>
+    <inputs>
+        <param name="input_genome" type="data" format="fasta,fasta.gz" label="Genomic sequence (FASTA)" help="Genomic contigs / scaffolds in FASTA format" />
+    </inputs>
+    <outputs>
+        <!-- refine this when miniprot index format is in Galaxy datatypes -->
+        <data name="output_index" format="binary" label="Miniprot index on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_genome" value="input_genome.fasta.gz" ftype="fasta" />
+            <output name="output_index" ftype="binary">
+                <assert_contents>
+                    <has_size value="135707709" delta="1000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Pre-index genomic sequences (contigs, scaffolds or chromosomes) for use in the miniprot_ protein to genome alignment tool.
+
+        .. _miniprot: https://github.com/lh3/miniprot
+    ]]></help>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r bd3dc3b5aea5 test-data/input_genome.fasta.gz
Binary file test-data/input_genome.fasta.gz has changed
diff -r 000000000000 -r bd3dc3b5aea5 test-data/input_query.fasta.gz
Binary file test-data/input_query.fasta.gz has changed