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comparison bam2fastx.xml @ 1:7f7f2ee03430 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit c2e67f103e2b83fd0fb9757ea6b75984d4fd9b64
author iuc
date Mon, 25 Mar 2024 17:50:00 +0000
parents 61a6b93ee6e1
children 0bfdf46e5e31
comparison
equal deleted inserted replaced
0:61a6b93ee6e1 1:7f7f2ee03430
1 <tool id="bam2fastx" name="PacBio bam2fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> 1 <tool id="bam2fastx" name="PacBio bam2fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
2 <description>PacBio BAM to Fastx</description> 2 <description>PacBio BAM to Fastx</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">3.1.1</token> 4 <token name="@TOOL_VERSION@">3.1.1</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">pbtk</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">pbtk</requirement>
9 </requirements> 9 </requirements>
10 <command><![CDATA[ 10 <command><![CDATA[
16 #elif $output_format == "fastq_gz": 16 #elif $output_format == "fastq_gz":
17 bam2fastq -o output 17 bam2fastq -o output
18 #end if 18 #end if
19 input.bam 19 input.bam
20 --num-threads "\${GALAXY_SLOTS:-1}" && 20 --num-threads "\${GALAXY_SLOTS:-1}" &&
21 #if $output_format == "fasta": 21 #if $output_format == "fasta_gz":
22 mv output.fasta.gz '$output_fasta_gz' 22 mv output.fasta.gz '$output_fasta_gz'
23 #elif $output_format == "fastq": 23 #elif $output_format == "fastq_gz":
24 mv output.fastq.gz '$output_fastq_gz' 24 mv output.fastq.gz '$output_fastq_gz'
25 #end if 25 #end if
26 ]]></command> 26 ]]></command>
27 <inputs> 27 <inputs>
28 <param name="input_bam" type="data" format="unsorted.bam" label="PacBio Bam file "/> 28 <param name="input_bam" type="data" format="unsorted.bam" label="PacBio Bam file "/>
31 <option value="fasta_gz">fasta.gz</option> 31 <option value="fasta_gz">fasta.gz</option>
32 </param> 32 </param>
33 </inputs> 33 </inputs>
34 <outputs> 34 <outputs>
35 <data name="output_fasta_gz" format="fasta.gz" label="${tool.name} on ${on_string}: Fasta"> 35 <data name="output_fasta_gz" format="fasta.gz" label="${tool.name} on ${on_string}: Fasta">
36 <filter>output_format == "fasta"</filter> 36 <filter>output_format == "fasta_gz"</filter>
37 </data> 37 </data>
38 <data name="output_fastq_gz" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Fastq"> 38 <data name="output_fastq_gz" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Fastq">
39 <filter>output_format == "fastq"</filter> 39 <filter>output_format == "fastq_gz"</filter>
40 </data> 40 </data>
41 </outputs> 41 </outputs>
42 <tests> 42 <tests>
43 <test expect_num_outputs="1"> 43 <test expect_num_outputs="1">
44 <param name="input_bam" ftype="unsorted.bam" value="sample.bam"/> 44 <param name="input_bam" ftype="unsorted.bam" value="sample.bam"/>
45 <param name="output_format" value="fastq_gz" /> 45 <param name="output_format" value="fastq.gz" />
46 <output name="output_fastq_gz"> 46 <output name="output_fastq_gz" decompress="true">
47 <assert_contents> 47 <assert_contents>
48 <has_size min="9000" /> 48 <has_text text="AATGCCTTATTAAGTTAAGAAATGGTTTTTTTTAAACTTACAGATGGAA" />
49 </assert_contents> 49 </assert_contents>
50 </output> 50 </output>
51 </test> 51 </test>
52 <test expect_num_outputs="1" > 52 <test expect_num_outputs="1" >
53 <param name="input_bam" ftype="bam" value="sample.bam"/> 53 <param name="input_bam" ftype="bam" value="sample.bam"/>
54 <param name="output_format" value="fasta_gz" /> 54 <param name="output_format" value="fasta.gz" />
55 <output name="output_fasta_gz" > 55 <output name="output_fasta_gz" decompress="true">
56 <assert_contents> 56 <assert_contents>
57 <has_size min="9000" /> 57 <has_text text="AATGCCTTATTAAGTTAAGAAATGGTTTTTTTTAAACTTACAGATGGAA" />
58 </assert_contents> 58 </assert_contents>
59 </output> 59 </output>
60 </test> 60 </test>
61 </tests> 61 </tests>
62 <help><![CDATA[ 62 <help><![CDATA[