# HG changeset patch
# User iuc
# Date 1623447601 0
# Node ID 1f06dccdc5d1503b9c76887a82f6648553fd885f
# Parent  037c6e54df11f225e1711330da5ec4956a672d44
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"

diff -r 037c6e54df11 -r 1f06dccdc5d1 macros.xml
--- a/macros.xml	Fri May 28 21:09:55 2021 +0000
+++ b/macros.xml	Fri Jun 11 21:40:01 2021 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.20</token>
-    <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
+    <token name="@GALAXY_TOOL_VERSION@">galaxy1</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0102</edam_topic>
@@ -24,17 +24,15 @@
     </xml>
     <xml name="citations">
         <citations>
-            <citations>
-                <citation type="doi">10.1093/bioinformatics/btp324</citation>
-                <citation type="doi">10.1093/bioinformatics/btp698</citation>
-                <citation type="bibtex">@misc{1303.3997,
-                    Author = {Heng Li},
-                    Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},
-                    Year = {2017},
-                    Eprint = {arXiv:1708.01492},
-                    url = {https://arxiv.org/abs/1708.01492},
-                    }</citation>
-            </citations>
+            <citation type="doi">10.1093/bioinformatics/btp324</citation>
+            <citation type="doi">10.1093/bioinformatics/btp698</citation>
+            <citation type="bibtex">@misc{1303.3997,
+                Author = {Heng Li},
+                Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},
+                Year = {2017},
+                Eprint = {arXiv:1708.01492},
+                url = {https://arxiv.org/abs/1708.01492},
+                }</citation>
         </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r 037c6e54df11 -r 1f06dccdc5d1 minimap2.xml
--- a/minimap2.xml	Fri May 28 21:09:55 2021 +0000
+++ b/minimap2.xml	Fri Jun 11 21:40:01 2021 +0000
@@ -6,7 +6,6 @@
     </macros>
     <expand macro="edam_ontology"/>
     <expand macro="requirements"/>
-    <expand macro="pe_anaylsis_fixed_selector"/>
     <stdio>
         <exit_code range="1:" level="fatal" />
         <regex match="\[ERROR\]" source="stderr" level="fatal" />
@@ -147,15 +146,16 @@
     #else if $fastq_input.fastq_input_selector == 'paired_collection':
          '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
     #end if
+    #if str($io_options.output_format) in ('BAM', 'CRAM'):
+        -a | samtools view --no-PG -hT reference.fa
+    #end if
     #if $io_options.output_format == 'BAM':
-        -a
         | samtools sort
         -@\${GALAXY_SLOTS:-2}
         -T "\${TMPDIR:-.}"
         -O $io_options.output_format
         -o '$alignment_output'
     #else if $io_options.output_format == 'CRAM':
-        -a
         | samtools sort
         -T "\${TMPDIR:-.}"
         -@\${GALAXY_SLOTS:-2}
@@ -397,7 +397,7 @@
             <param name="fastq_input_selector" value="single"/>
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
             <param name="analysis_type_selector" value="sr"/>
-            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
         </test>
         <test>
             <!-- test cram output -->
@@ -416,7 +416,7 @@
             <param name="fastq_input_selector" value="paired"/>
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
-            <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
         </test>
         <test>
             <!-- test paired input with one pair compressed -->
@@ -425,7 +425,7 @@
             <param name="fastq_input_selector" value="paired"/>
             <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
             <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
-            <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
         </test>
         <test>
             <!-- test collection input -->
@@ -438,7 +438,7 @@
                     <element name="reverse" value="bwa-mem-fastq2.fq" />
                 </collection>
             </param>
-            <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" />
         </test>
         <test>
             <!-- test data table reference -->
@@ -447,7 +447,7 @@
             <param name="fastq_input_selector" value="single"/>
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
             <param name="analysis_type_selector" value="sr"/>
-            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
         </test>
         <test>
             <!-- test alignment options -->
@@ -470,7 +470,7 @@
                 <param name="z" value="400" />
                 <param name="s" value="40" />
             </section>
-            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
         </test>        
         <test>
             <!-- test paf output -->
@@ -489,7 +489,7 @@
             <param name="fastq_input_selector" value="single" />
             <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
             <param name="analysis_type_selector" value="self-homology" />
-            <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" />
         </test>
         <test>
             <!-- test mask-len option -->
@@ -501,7 +501,7 @@
             <section name="mapping_options">
                 <param name="mask_len" value="100"/>
             </section>
-            <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" />
         </test>
         <test>
             <!-- test map-hifi -->
@@ -510,7 +510,7 @@
             <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-fasta.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" />
         </test>
         <test>
             <!-- test kmer ocurrence interval option -->
@@ -524,7 +524,7 @@
                 <param name="lower_limit" value="10"/>
                 <param name="upper_limit" value="30"/>
             </conditional>
-            <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="4" />
         </test>
     </tests>
     <help>