Mercurial > repos > artbio > lumpy_smoove
diff macros.xml @ 11:5a326a6fa105 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
author | artbio |
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date | Fri, 17 Oct 2025 17:21:17 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Oct 17 17:21:17 2025 +0000 @@ -0,0 +1,57 @@ +<macros> + <token name="@TOOL_VERSION@">0.2.8</token> + <token name="@GALAXY_VERSION@">4</token> + + <!-- Requirements for lumpy_smoove (Python 2.7 environment) --> + <xml name="lumpy_smoove_requirements"> + <requirements> + <requirement type="package" version="0.2.8">smoove</requirement> + <requirement type="package" version="0.7.1">svtyper</requirement> + <requirement type="package" version="2.7">python</requirement> + </requirements> + </xml> + + <!-- Requirements for vcf2hrdetect (Python 3.9 environment) --> + <xml name="vcf2hrdetect_requirements"> + <requirements> + <requirement type="package" version="3.9">python</requirement> + </requirements> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + </xml> + <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> + <token name="@set_fasta_index@"><![CDATA[ + #if str( $reference_source.reference_source_selector ) == "history": + ln -s '${reference_source.ref_file}' reference.fa && + samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 && + #else: + ln -s '${reference_source.index.fields.path}' reference.fa && + ln -s '${reference_source.index.fields.path}.fai' reference.fa.fai && + #end if + ]]></token> + <macro name="reference_source_conditional"> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options."> + <option value="cached">Use a built-in genome index</option> + <option value="history">Use a genome from history and build index</option> + </param> + <when value="cached"> + <param name="index" type="select" label="Using built-in genome" help="Select genome from the list"> + <options from_data_table="fasta_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" /> + </when> + </conditional> + </macro> +</macros> + +