changeset 2:35ea4a8b1ea6 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f12e139eb362fea66360aefbbc678197e2440139"

--- a/test-data/all_fasta.loc	Mon May 10 19:28:32 2021 +0000
+++ b/test-data/all_fasta.loc	Tue Jul 13 12:16:19 2021 +0000
@@ -1,1 +1,1 @@
-bwa-mem-mt-genome	bwa-mem-mt-genome	bwa-mem-mt-genome	${__HERE__}/bwa-mem-mt-genome.fa
\ No newline at end of file
+bwa-mem-mt-genome	bwa-mem-mt-genome-dbkey	bwa-mem-mt-genome-display	${__HERE__}/bwa-mem-mt-genome.fa
\ No newline at end of file

Binary file test-data/winnowmap-self-homology.bam has changed

Binary file test-data/winnowmap-test1-fasta.bam has changed

Binary file test-data/winnowmap-test1-fasta.cram has changed

Binary file test-data/winnowmap-test1.bam has changed

Binary file test-data/winnowmap-test2-fasta.bam has changed

Binary file test-data/winnowmap-test2.bam has changed

--- a/winnowmap.xml	Mon May 10 19:28:32 2021 +0000
+++ b/winnowmap.xml	Tue Jul 13 12:16:19 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="winnowmap" name="Winnowmap" version="@TOOL_VERSION@+galaxy0" profile="20.01">
+<tool id="winnowmap" name="Winnowmap" version="@TOOL_VERSION@+galaxy1" profile="20.05">
     <description>a mapping tool optimized for repetitive sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -145,6 +145,7 @@
     #if $io_options.output_format == 'BAM':
         -a
         | samtools sort
+        --no-PG
         -@\${GALAXY_SLOTS:-2}
         -T "\${TMPDIR:-.}"
         -O $io_options.output_format
@@ -152,6 +153,7 @@
     #else if $io_options.output_format == 'CRAM':
         -a
         | samtools sort
+        --no-PG
         -T "\${TMPDIR:-.}"
         -@\${GALAXY_SLOTS:-2}
         -O $io_options.output_format
@@ -229,7 +231,7 @@
             <param argument="-I" type="integer" min="1" optional="true"  label="Split index for every N input gigabases" help=""/>
         </section>
         <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, --sv-off and --min-occ-floor options." expanded="False">
-            <param name="sv_off" argument="--sv-off" type="boolean" truevalue="--sv-off" falsevalue=""  checked="False" label="Turn off SV-aware mode" help="SV aware k-mer search allows to find approximate mapping locations for a read"/>
+            <param argument="--sv-off" type="boolean" truevalue="--sv-off" falsevalue=""  checked="False" label="Turn off SV-aware mode" help="SV aware k-mer search allows to find approximate mapping locations for a read"/>
             <param argument="-F" type="integer" min="0" value="" optional="true"
             label="Max fragment length for PE alignment"
             help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" />
@@ -361,7 +363,7 @@
                 </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>
@@ -375,18 +377,34 @@
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
             <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
             <param name="analysis_type_selector" value="map-ont"/>
-            <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" />
+            <param name="min_occ_floor" value="1000"/>
+            <section name="alignment_options">
+                <param name="min_occ_floor" value="1000"/>
+                <param name="A" value="2"/>
+                <param name="B" value="8"/>
+                <param name="O" value="12"/>
+                <param name="O2" value="32"/>
+                <param name="E" value="2"/>
+                <param name="E2" value="1"/>
+                <param name="z" value="400"/>
+                <param name="s" value="40"/>
+            </section>
+            <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" >
+                <metadata name="dbkey" value="?" />
+            </output>
         </test>
         <test>
             <!-- test cram output -->
             <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa" dbkey="hg19"/>
             <param name="fastq_input_selector" value="single"/>
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
             <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
             <param name="analysis_type_selector" value="map-ont"/>
             <param name="output_format" value="CRAM"/>
-            <output name="alignment_output" ftype="cram" file="winnowmap-test1-fasta.cram" compare="sim_size" />
+            <output name="alignment_output" ftype="cram" file="winnowmap-test1-fasta.cram" lines_diff="2">
+                <metadata name="dbkey" value="hg19" />
+            </output>
         </test>
         <test>
             <!-- test paired input -->
@@ -422,17 +440,30 @@
                 </collection>
             </param>
             <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
-            <output name="alignment_output" ftype="bam" file="winnowmap-test2.bam" lines_diff="2" />
+            <output name="alignment_output" ftype="bam" file="winnowmap-test2.bam" lines_diff="2"/>
         </test>
         <test>
             <!-- test data table reference -->
             <param name="reference_source_selector" value="cached" />
-            <param name="ref_file" value="bwa-mem-mt-genome"/>
+            <param name="ref_file" value="bwa-mem-mt-genome" dbkey="hg19"/>
             <param name="fastq_input_selector" value="single"/>
             <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
             <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
             <param name="analysis_type_selector" value="map-ont"/>
-            <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" />
+            <section name="alignment_options">
+                <param name="min_occ_floor" value="1000"/>
+                <param name="A" value="2"/>
+                <param name="B" value="8"/>
+                <param name="O" value="12"/>
+                <param name="O2" value="32"/>
+                <param name="E" value="2"/>
+                <param name="E2" value="1"/>
+                <param name="z" value="400"/>
+                <param name="s" value="40"/>
+            </section>
+            <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" >
+                <metadata name="dbkey" value="bwa-mem-mt-genome-dbkey" />
+            </output>
         </test>
         <test>
             <!-- test alignment options -->
@@ -457,6 +488,14 @@
                 <param name="s" value="40" />
             </section>
             <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" />
+            <assert_command>
+                <has_text text="-A 2"/>
+                <has_text text="-B 8"/>
+                <has_text text="-O 12,32"/>
+                <has_text text="-E 2,1"/>
+                <has_text text="-z 400"/>
+                <has_text text="-s 40"/>
+            </assert_command>
         </test>        
         <test>
             <!-- test paf output -->
@@ -467,7 +506,7 @@
             <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
             <param name="analysis_type_selector" value="map-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 -->