Skip to content

Commit a3f6014

Browse files
bgrueningbgruening
authored
Merge pull request #7783 from SaimMomin12/tools/pbmm2
Update tools/pbmm2 to 26.1.99
2 parents 225ce35 + 1aef480 commit a3f6014

File tree

2 files changed

+40
-20
lines changed

2 files changed

+40
-20
lines changed

‎tools/pbmm2/macros.xml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
<macros>
2-
<token name="@TOOL_VERSION@">26.1.0</token>
3-
<token name="@VERSION_SUFFIX@">1</token>
4-
<token name="@PROFILE@">24.2</token>
2+
<token name="@TOOL_VERSION@">26.1.99</token>
3+
<token name="@VERSION_SUFFIX@">0</token>
4+
<token name="@PROFILE@">25.0</token>
55
<xml name="requirements">
66
<requirements>
77
<requirement type="package" version="@TOOL_VERSION@">pbmm2</requirement>

‎tools/pbmm2/pbmm2.xml‎

Lines changed: 37 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -20,11 +20,13 @@
2020
## run pbmm2
2121
pbmm2 align
2222
-j \${GALAXY_SLOTS:-4}
23-
#if str($output_options.l):
24-
-l $output_options.l
25-
#end if
26-
#if str($output_options.N):
27-
-N $output_options.N
23+
-l $output_options.l
24+
-N $output_options.N
25+
#if $output_options.secondary:
26+
--secondary
27+
#if $output_options.max_secondary_alns:
28+
--max-secondary-alns $output_options.max_secondary_alns
29+
#end if
2830
#end if
2931
--preset $preset
3032
'$reads_fn'
@@ -42,19 +44,18 @@
4244
<when value="cached">
4345
<param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
4446
<options from_data_table="all_fasta">
45-
<filter type="sort_by" column="2" />
46-
<validator type="no_options" message="No reference genomes are available" />
47+
<filter type="sort_by" column="2"/>
48+
<validator type="no_options" message="No reference genomes are available"/>
4749
</options>
4850
<validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
4951
</param>
5052
</when>
5153
<when value="history">
52-
<param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
54+
<param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference"/>
5355
</when>
5456
</conditional>
5557
<param type="data" name="reads" format="fastq,fastq.gz,fasta,fasta.gz,bam" label="reads" help="PacBio reads in BAM or [gzipped] fasta or fastq format"/>
56-
<param argument="--preset" type="select"
57-
label="Set alignment mode">
58+
<param argument="--preset" type="select" label="Set alignment mode">
5859
<option value="CCS">PacBio CCS or HiFi reads</option>
5960
<option value="SUBREAD">PacBio CLR or raw subreads</option>
6061
<option value="ISOSEQ">PacBio IsoSeq transcripts</option>
@@ -63,49 +64,68 @@
6364
<section name="output_options" title="Output Options" help="Sets -l, -N, --strip, --split-by-sample, --unmapped, --short-sa-cigar" expanded="False">
6465
<param argument="-l" type="integer" min="0" label="Minimum mapped read length in basepairs" value="50" optional="true"/>
6566
<param argument="-N" type="integer" min="0" label="Output at maximum N alignments for each read, 0 means no maximum" value="0" optional="true"/>
67+
<param argument="--secondary" type="boolean" truevalue="--secondary" falsevalue="" label="Include secondary alignments in output" help="enable secondary alignment output."/>
68+
<param argument="--max-secondary-alns" type="integer" min="0" label="Maximum number of secondary alignments to output per read. Should be used along with --secondary argument" value="" optional="true"/>
6669
</section>
6770
</inputs>
6871
<outputs>
69-
<data name="bam" format="bam" from_work_dir="out.aligned.bam" label="${tool.name} on ${on_string} (BAM file)"/>
72+
<data name="bam" format="bam" from_work_dir="out.aligned.bam" label="${tool.name} on ${on_string}: BAM file"/>
7073
</outputs>
7174
<tests>
7275
<!-- test1: basic test -->
7376
<test expect_num_outputs="1">
7477
<conditional name="reference_source">
75-
<param name="reference_source_selector" value="history" />
78+
<param name="reference_source_selector" value="history"/>
7679
<param name="ref_file" ftype="fasta" value="bnd-ref.fasta"/>
7780
</conditional>
7881
<param name="reads" value="bnd.bam"/>
7982
<output name="bam">
8083
<assert_contents>
81-
<has_size value="2778" delta="200" />
84+
<has_size value="2778" delta="200"/>
8285
</assert_contents>
8386
</output>
8487
</test>
8588
<!-- test2: map some reads for use with pbgcpp -->
8689
<test expect_num_outputs="1">
8790
<conditional name="reference_source">
88-
<param name="reference_source_selector" value="history" />
91+
<param name="reference_source_selector" value="history"/>
8992
<param name="ref_file" ftype="fasta" value="All4mer.V2.01_Insert.fa"/>
9093
</conditional>
9194
<param name="reads" value="out.aligned_subreads.bam"/>
9295
<param name="preset" value="SUBREAD"/>
9396
<output name="bam">
9497
<assert_contents>
95-
<has_size value="538329" delta="50000" />
98+
<has_size value="538329" delta="50000"/>
9699
</assert_contents>
97100
</output>
98101
</test>
99102
<!-- test3: cached genome -->
100103
<test>
101104
<conditional name="reference_source">
102-
<param name="reference_source_selector" value="cached" />
105+
<param name="reference_source_selector" value="cached"/>
106+
<param name="ref_file" value="bnd-ref"/>
107+
</conditional>
108+
<param name="reads" value="bnd.bam"/>
109+
<output name="bam">
110+
<assert_contents>
111+
<has_size value="2778" delta="200"/>
112+
</assert_contents>
113+
</output>
114+
</test>
115+
<!-- test4: secondary alignments -->
116+
<test>
117+
<conditional name="reference_source">
118+
<param name="reference_source_selector" value="cached"/>
103119
<param name="ref_file" value="bnd-ref"/>
104120
</conditional>
105121
<param name="reads" value="bnd.bam"/>
122+
<section name="output_options">
123+
<param name="secondary" value="true"/>
124+
<param name="max_secondary_alns" value="5"/>
125+
</section>
106126
<output name="bam">
107127
<assert_contents>
108-
<has_size value="2778" delta="200" />
128+
<has_size value="2850" delta="200"/>
109129
</assert_contents>
110130
</output>
111131
</test>

0 commit comments

Comments
 (0)