diff minimap2.xml @ 15:7db8d4bc1eea draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"

--- a/minimap2.xml	Fri Jun 25 17:45:36 2021 +0000
+++ b/minimap2.xml	Fri Oct 08 09:48:01 2021 +0000
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
-<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
+<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
+    <xrefs>
+        <xref type="bio.tools">minimap2</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -384,7 +387,7 @@
                 </conditional>
             </actions>
             <change_format>
-                <when input="io_options.output_format" value="paf" format="tabular" />
+                <when input="io_options.output_format" value="paf" format="paf" />
                 <when input="io_options.output_format" value="CRAM" format="cram" />
             </change_format>
         </data>
@@ -485,7 +488,7 @@
             <param name="fastq_input1" ftype="fastqsanger"  value="mini_reads.fq" />
             <param name="analysis_type_selector" value="ava-ont"/>
             <param name="output_format" value="paf"/>
-            <output name="alignment_output" ftype="tabular" file="mini_reads.paf" />
+            <output name="alignment_output" ftype="paf" file="mini_reads.paf" />
         </test>
         <test>
             <!-- test self-homology mode -->
@@ -518,6 +521,15 @@
             <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" />
         </test>
         <test>
+            <!-- test map-hifi uncompressed reference-->
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/>
+            <param name="fastq_input_selector" value="single"/>
+            <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
+            <param name="analysis_type_selector" value="map-hifi"/>
+            <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" />
+        </test>
+        <test>
             <!-- test kmer ocurrence interval option -->
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>