Mercurial > repos > artbio > lumpy_smoove
comparison 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 |
|---|---|
| date | Tue, 25 Aug 2020 11:35:02 -0400 |
| parents | |
| children | 49a8a327cc72 |
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| -1:000000000000 | 0:ee8fc44b1655 |
|---|---|
| 1 <macros> | |
| 2 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> | |
| 3 | |
| 4 <token name="@set_fasta_index@"><![CDATA[ | |
| 5 #if str( $reference_source.reference_source_selector ) == "history": | |
| 6 ln -s '${reference_source.ref_file}' reference.fa && | |
| 7 samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 && | |
| 8 #else: | |
| 9 ln -s '${source.index.fields.path}' reference.fa && | |
| 10 ln -s '${source.index.fields.path}.fai' reference.fa.fai && | |
| 11 #end if | |
| 12 ]]></token> | |
| 13 | |
| 14 <macro name="reference_source_conditional"> | |
| 15 <conditional name="reference_source"> | |
| 16 <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"> | |
| 17 <option value="cached">Use a built-in genome index</option> | |
| 18 <option value="history">Use a genome from history and build index</option> | |
| 19 </param> | |
| 20 <when value="cached"> | |
| 21 <param name="index" type="select" label="Using built-in genome" help="Select genome from the list"> | |
| 22 <options from_data_table="fasta_indexes"> | |
| 23 <filter type="sort_by" column="2" /> | |
| 24 <validator type="no_options" message="No indexes are available" /> | |
| 25 </options> | |
| 26 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 27 </param> | |
| 28 </when> | |
| 29 <when value="history"> | |
| 30 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" | |
| 31 help="You can upload a FASTA sequence to the history and use it as reference" /> | |
| 32 </when> | |
| 33 </conditional> | |
| 34 </macro> | |
| 35 </macros> |