Mercurial > repos > artbio > snvtocnv
comparison macro.xml @ 0:b77d7a0a45e8 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
| author | artbio |
|---|---|
| date | Sun, 07 Mar 2021 23:19:59 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:b77d7a0a45e8 |
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| 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( $reference_source.reference_source_selector ) == "history": | |
| 6 cp '${reference_source.ref_file}' reference.fa && | |
| 7 #else: | |
| 8 cp '${reference_source.index.fields.path}' reference.fa && | |
| 9 #end if | |
| 10 ]]></token> | |
| 11 | |
| 12 <macro name="reference_source_conditional"> | |
| 13 <conditional name="reference_source"> | |
| 14 <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"> | |
| 15 <option value="cached">Use a built-in genome index</option> | |
| 16 <option value="history">Use a genome from history and build index</option> | |
| 17 </param> | |
| 18 <when value="cached"> | |
| 19 <param name="index" type="select" label="Using built-in genome" help="Select genome sorted and with chr prefix (chr1, chr2, ...)"> | |
| 20 <options from_data_table="fasta_indexes"> | |
| 21 <filter type="sort_by" column="2" /> | |
| 22 <validator type="no_options" message="No indexes are available" /> | |
| 23 </options> | |
| 24 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 25 </param> | |
| 26 </when> | |
| 27 <when value="history"> | |
| 28 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" | |
| 29 help="You can upload a FASTA sequence to the history and use it as reference" /> | |
| 30 </when> | |
| 31 </conditional> | |
| 32 </macro> | |
| 33 </macros> |