diff minimap2.xml @ 7:b3eab4b67562 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"

--- a/minimap2.xml	Mon May 06 09:34:30 2019 -0400
+++ b/minimap2.xml	Fri Oct 11 13:27:18 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@" profile="17.01">
+<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy0" profile="17.01">
     <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
     <macros>
         <token name="@TOOL_VERSION@">2.17</token>
@@ -17,7 +17,11 @@
         ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
     #end if
     minimap2
-    -x $analysis_type_selector
+    #if str($analysis_type_selector) == 'self-homology':
+        -DP -k19 -w19 -m200
+    #else
+        -x $analysis_type_selector
+    #end if
     ## indexing options
     $indexing_options.H
     #if $indexing_options.k:
@@ -113,11 +117,13 @@
         -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}
         -O $io_options.output_format
         $io_options.eqx
@@ -186,6 +192,7 @@
             <option value="asm20">Long assembly to reference mapping (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence.</option>
             <option value="splice">Long-read spliced alignment (-k15 -w5 --splice -g2000 -G200k  -A1 -B2  -O2,32  -E1,0  -C9  -z200  -ub  --splice-flank=yes). In the splice mode, 1) long deletions are taken as  introns  and  represented as the `N' CIGAR operator 2) long insertions are disabled 3) deletion and insertion gap costs are different during chaining 4) the computation of the `ms' tag ignores introns to demote hits to pseudogenes.</option>
             <option value="sr">Short single-end reads without splicing (-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no)</option>
+            <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200)</option>
         </param>
         <section name="mapping_options" title="Set advanced mapping options" help="Sets -f, -g, -G, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False">
             <param argument="-f" type="float" value="" optional="true" label="filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
@@ -331,6 +338,15 @@
             <param name="output_format" value="paf"/>
             <output name="alignment_output" ftype="tabular" file="mini_reads.paf" />
         </test>
+        <test>
+            <!-- test self-homology mode -->
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
+            <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" />
+        </test>
     </tests>
     <help>
 
@@ -448,6 +464,13 @@
 For cross-species full-genome alignment, the scoring system needs to be
 tuned according to the sequence divergence.
 
+Self-homology map creation
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A self-homology map is created by mapping a genome (e.g. that of E. coli)
+against itself. When this option is used the same FASTA file should
+be used for reference and for the (single ended mode) query.
+
 Advanced features
 ~~~~~~~~~~~~~~~~~