Mercurial > repos > iuc > bwameth
changeset 11:b6b87635cf29 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit a8808d30f9293ff09e3eed63a42db13a7c4eaad2
| author | iuc |
|---|---|
| date | Wed, 06 Aug 2025 15:23:59 +0000 |
| parents | cf1322aeb137 |
| children | b7ce99273d62 |
| files | bwameth.xml test-data/output.bam |
| diffstat | 2 files changed, 34 insertions(+), 28 deletions(-) [+] |
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--- a/bwameth.xml Sun Jun 02 16:38:23 2024 +0000 +++ b/bwameth.xml Wed Aug 06 15:23:59 2025 +0000 @@ -1,7 +1,9 @@ -<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy0" profile="20.05"> - <description>Fast and accurate aligner of BS-Seq reads.</description> +<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Fast and accurate aligner of BS-Seq reads</description> <macros> - <token name="@TOOL_VERSION@">0.2.7</token> + <token name="@TOOL_VERSION@">0.2.8</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.05</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement> @@ -88,7 +90,7 @@ <option value="indexed">Use a built-in index</option> </param> <when value="history"> - <param name="reference" type="data" format="fasta" label="Select a genome" help="in FASTA format" /> + <param name="reference" type="data" format="fasta" label="Select a genome" help="in FASTA format"/> </when> <when value="indexed"> <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin"> @@ -107,14 +109,14 @@ <option value="paired_collection">Paired-end Dataset Collection</option> </param> <when value="single"> - <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ" help="FASTQ file." /> + <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ" help="FASTQ file."/> </when> <when value="paired"> - <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="First read in pair" help="FASTQ file." /> - <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Second read in pair" help="FASTQ file." /> + <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="First read in pair" help="FASTQ file."/> + <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Second read in pair" help="FASTQ file."/> </when> <when value="paired_collection"> - <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." /> + <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ paired dataset" help="Must have a fastqsanger datatype."/> </when> </conditional> <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'"> @@ -122,32 +124,36 @@ </param> </inputs> <outputs> - <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" /> + <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}"/> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <conditional name="referenceSource"> - <param name="source" value="history" /> + <param name="source" value="history"/> + <param name="reference" value="ref.fa.gz"/> </conditional> - <param name="reference" value="ref.fa.gz" /> - <param name="single_or_paired_opts" value="paired" /> - <param name="input_mate1" value="t_R1.fastq.gz"/> - <param name="input_mate2" value="t_R2.fastq.gz"/> - <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff--> + <conditional name="single_or_paired"> + <param name="single_or_paired_opts" value="paired"/> + <param name="input_mate1" value="t_R1.fastq.gz"/> + <param name="input_mate2" value="t_R2.fastq.gz"/> + </conditional> + <output file="output.bam" ftype="bam" name="output" lines_diff="7"/> </test> - <test> + <test expect_num_outputs="1"> <conditional name="referenceSource"> - <param name="source" value="history" /> + <param name="source" value="history"/> + <param name="reference" value="ref.fa.gz"/> </conditional> - <param name="reference" value="ref.fa.gz" /> - <param name="single_or_paired_opts" value="paired_collection" /> - <param name="input_mate1"> - <collection type="paired"> - <element name="forward" value="t_R1.fastq.gz"/> - <element name="reverse" value="t_R2.fastq.gz"/> - </collection> - </param> - <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff--> + <conditional name="single_or_paired"> + <param name="single_or_paired_opts" value="paired_collection"/> + <param name="input_mate1"> + <collection type="paired"> + <element name="forward" value="t_R1.fastq.gz"/> + <element name="reverse" value="t_R2.fastq.gz"/> + </collection> + </param> + </conditional> + <output file="output.bam" ftype="bam" name="output" lines_diff="7"/> </test> </tests> <help><![CDATA[ @@ -164,4 +170,4 @@ Eprint = {arXiv:1401.1129}, }</citation> </citations> -</tool> +</tool> \ No newline at end of file