Mercurial > repos > iuc > bam2fastx
comparison bam2fastx.xml @ 0:61a6b93ee6e1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit cd34bba7aafb92ea993d4ef17a3669957de7c537
author | iuc |
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date | Tue, 12 Mar 2024 15:42:13 +0000 |
parents | |
children | 7f7f2ee03430 |
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-1:000000000000 | 0:61a6b93ee6e1 |
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1 <tool id="bam2fastx" name="PacBio bam2fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> | |
2 <description>PacBio BAM to Fastx</description> | |
3 <macros> | |
4 <token name="@TOOL_VERSION@">3.1.1</token> | |
5 <token name="@VERSION_SUFFIX@">0</token> | |
6 </macros> | |
7 <requirements> | |
8 <requirement type="package" version="@TOOL_VERSION@">pbtk</requirement> | |
9 </requirements> | |
10 <command><![CDATA[ | |
11 mkdir -p output_files/ && | |
12 ln -s '$input_bam' input.bam && | |
13 pbindex input.bam && | |
14 #if $output_format == "fasta_gz": | |
15 bam2fasta -o output | |
16 #elif $output_format == "fastq_gz": | |
17 bam2fastq -o output | |
18 #end if | |
19 input.bam | |
20 --num-threads "\${GALAXY_SLOTS:-1}" && | |
21 #if $output_format == "fasta": | |
22 mv output.fasta.gz '$output_fasta_gz' | |
23 #elif $output_format == "fastq": | |
24 mv output.fastq.gz '$output_fastq_gz' | |
25 #end if | |
26 ]]></command> | |
27 <inputs> | |
28 <param name="input_bam" type="data" format="unsorted.bam" label="PacBio Bam file "/> | |
29 <param name="output_format" type="select" label="Output Format" help="Output a fasta.gz or fastq.gz"> | |
30 <option value="fastq_gz">fastq.gz</option> | |
31 <option value="fasta_gz">fasta.gz</option> | |
32 </param> | |
33 </inputs> | |
34 <outputs> | |
35 <data name="output_fasta_gz" format="fasta.gz" label="${tool.name} on ${on_string}: Fasta"> | |
36 <filter>output_format == "fasta"</filter> | |
37 </data> | |
38 <data name="output_fastq_gz" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Fastq"> | |
39 <filter>output_format == "fastq"</filter> | |
40 </data> | |
41 </outputs> | |
42 <tests> | |
43 <test expect_num_outputs="1"> | |
44 <param name="input_bam" ftype="unsorted.bam" value="sample.bam"/> | |
45 <param name="output_format" value="fastq_gz" /> | |
46 <output name="output_fastq_gz"> | |
47 <assert_contents> | |
48 <has_size min="9000" /> | |
49 </assert_contents> | |
50 </output> | |
51 </test> | |
52 <test expect_num_outputs="1" > | |
53 <param name="input_bam" ftype="bam" value="sample.bam"/> | |
54 <param name="output_format" value="fasta_gz" /> | |
55 <output name="output_fasta_gz" > | |
56 <assert_contents> | |
57 <has_size min="9000" /> | |
58 </assert_contents> | |
59 </output> | |
60 </test> | |
61 </tests> | |
62 <help><![CDATA[ | |
63 Convert a PacBio BAM file to Fastq or Fasta file. | |
64 ]]></help> | |
65 <citations> | |
66 <citation type="bibtex"> | |
67 @misc{githubpbtk, | |
68 author = {}, | |
69 year = {2024}, | |
70 title = {pbtk}, | |
71 publisher = {GitHub}, | |
72 journal = {GitHub repository}, | |
73 url = {https://github.com/PacificBiosciences/pbtk}, | |
74 } | |
75 </citation> | |
76 </citations> | |
77 </tool> |