Mercurial > repos > iuc > pbmm2
comparison pbmm2.xml @ 2:55b7b257e12f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 commit ea74a1d7e62c0c7f878cf0d83f3539dfbb146b64
author | iuc |
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date | Wed, 21 Feb 2024 10:27:49 +0000 |
parents | 29eec6c7bab2 |
children |
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1:f4ec47f1a8da | 2:55b7b257e12f |
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18 #end if | 18 #end if |
19 | 19 |
20 ## run pbmm2 | 20 ## run pbmm2 |
21 pbmm2 align | 21 pbmm2 align |
22 -j \${GALAXY_SLOTS:-4} | 22 -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 | |
28 #end if | |
29 --preset $preset | |
23 '$reads_fn' | 30 '$reads_fn' |
24 '$ref_fn' | 31 '$ref_fn' |
25 out.aligned.bam | 32 out.aligned.bam |
26 --sort | 33 --sort |
27 ]]></command> | 34 ]]></command> |
43 </when> | 50 </when> |
44 <when value="history"> | 51 <when value="history"> |
45 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> | 52 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> |
46 </when> | 53 </when> |
47 </conditional> | 54 </conditional> |
48 <param type="data" name="reads" format="fastq,fastq.gz,fasta,fasta.gz,bam" label="reads" help="PacBio reads in BAM or [gzipped] fasta or fastq format." /> | 55 <param type="data" name="reads" format="fastq,fastq.gz,fasta,fasta.gz,bam" label="reads" help="PacBio reads in BAM or [gzipped] fasta or fastq format"/> |
56 <param argument="--preset" type="select" | |
57 label="Set alignment mode"> | |
58 <option value="CCS">PacBio CCS or HiFi reads</option> | |
59 <option value="SUBREAD">PacBio CLR or raw subreads</option> | |
60 <option value="ISOSEQ">PacBio IsoSeq transcripts</option> | |
61 <option value="UNROLLED">Align entire raw ZMW</option> | |
62 </param> | |
63 <section name="output_options" title="Output Options" help="Sets -l, -N, --strip, --split-by-sample, --unmapped, --short-sa-cigar" expanded="False"> | |
64 <param argument="-l" type="integer" min="0" label="Minimum mapped read length in basepairs" value="50" optional="true"/> | |
65 <param argument="-N" type="integer" min="0" label="Output at maximum N alignments for each read, 0 means no maximum" value="0" optional="true"/> | |
66 </section> | |
49 </inputs> | 67 </inputs> |
50 <outputs> | 68 <outputs> |
51 <data name="bam" format="bam" from_work_dir="out.aligned.bam" label="${tool.name} on ${on_string} (BAM file)" /> | 69 <data name="bam" format="bam" from_work_dir="out.aligned.bam" label="${tool.name} on ${on_string} (BAM file)"/> |
52 </outputs> | 70 </outputs> |
53 <tests> | 71 <tests> |
54 <!-- test1: basic test --> | 72 <!-- test1: basic test --> |
55 <test expect_num_outputs="1"> | 73 <test expect_num_outputs="1"> |
56 <param name="reference_source_selector" value="history" /> | 74 <param name="reference_source_selector" value="history" /> |
65 <!-- test2: map some reads for use with pbgcpp --> | 83 <!-- test2: map some reads for use with pbgcpp --> |
66 <test expect_num_outputs="1"> | 84 <test expect_num_outputs="1"> |
67 <param name="reference_source_selector" value="history" /> | 85 <param name="reference_source_selector" value="history" /> |
68 <param name="ref_file" ftype="fasta" value="All4mer.V2.01_Insert.fa"/> | 86 <param name="ref_file" ftype="fasta" value="All4mer.V2.01_Insert.fa"/> |
69 <param name="reads" value="out.aligned_subreads.bam"/> | 87 <param name="reads" value="out.aligned_subreads.bam"/> |
88 <param name="preset" value="SUBREAD"/> | |
70 <output name="bam"> | 89 <output name="bam"> |
71 <assert_contents> | 90 <assert_contents> |
72 <has_size value="539464" delta="50000" /> | 91 <has_size value="538329" delta="50000" /> |
73 </assert_contents> | 92 </assert_contents> |
74 </output> | 93 </output> |
75 </test> | 94 </test> |
76 <!-- test3: cached genome --> | 95 <!-- test3: cached genome --> |
77 <test> | 96 <test> |
106 | 125 |
107 **Output**: A **sorted** PacBio BAM file, suitable for use with | 126 **Output**: A **sorted** PacBio BAM file, suitable for use with |
108 pbgcpp (previously known as GenomicConsensus). | 127 pbgcpp (previously known as GenomicConsensus). |
109 | 128 |
110 ]]></help> | 129 ]]></help> |
130 <citations> | |
131 <citation type="bibtex"> | |
132 @misc{githubpbmm2, | |
133 author = {PacBio}, | |
134 year = {2023}, | |
135 title = {pbmm2}, | |
136 publisher = {GitHub}, | |
137 journal = {GitHub repository}, | |
138 url = {https://github.com/PacificBiosciences/pbmm2}, | |
139 }</citation> | |
140 </citations> | |
111 <expand macro="creator"/> | 141 <expand macro="creator"/> |
112 </tool> | 142 </tool> |