Mercurial > repos > artbio > lumpy_smoove
diff macro_lumpy_smoove.xml @ 0:ee8fc44b1655 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
author | artbio |
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date | Tue, 25 Aug 2020 11:35:02 -0400 |
parents | |
children | 49a8a327cc72 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macro_lumpy_smoove.xml Tue Aug 25 11:35:02 2020 -0400 @@ -0,0 +1,35 @@ +<macros> + <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 '${source.index.fields.path}' reference.fa && + ln -s '${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. See `Indexes` section of help below"> + <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> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <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" /> + </when> + </conditional> + </macro> +</macros>