Mercurial > repos > artbio > lumpy_smoove
annotate macro_lumpy_smoove.xml @ 10:8711df965d4b draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223
author | artbio |
---|---|
date | Wed, 24 Jan 2024 19:26:57 +0000 |
parents | 49a8a327cc72 |
children |
rev | line source |
---|---|
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
1 <macros> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
2 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
3 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
4 <token name="@set_fasta_index@"><![CDATA[ |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
5 #if str( $reference_source.reference_source_selector ) == "history": |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
6 ln -s '${reference_source.ref_file}' reference.fa && |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
7 samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 && |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
8 #else: |
2
49a8a327cc72
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit fa6b4f90ce05c65155b727e0eebaa27549621170"
artbio
parents:
0
diff
changeset
|
9 ln -s '${reference_source.index.fields.path}' reference.fa && |
49a8a327cc72
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit fa6b4f90ce05c65155b727e0eebaa27549621170"
artbio
parents:
0
diff
changeset
|
10 ln -s '${reference_source.index.fields.path}.fai' reference.fa.fai && |
0
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
11 #end if |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
12 ]]></token> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
13 |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
14 <macro name="reference_source_conditional"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
15 <conditional name="reference_source"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
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"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
17 <option value="cached">Use a built-in genome index</option> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
18 <option value="history">Use a genome from history and build index</option> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
19 </param> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
20 <when value="cached"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
21 <param name="index" type="select" label="Using built-in genome" help="Select genome from the list"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
22 <options from_data_table="fasta_indexes"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
23 <filter type="sort_by" column="2" /> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
24 <validator type="no_options" message="No indexes are available" /> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
25 </options> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
26 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
27 </param> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
28 </when> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
29 <when value="history"> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
30 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
31 help="You can upload a FASTA sequence to the history and use it as reference" /> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
32 </when> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
33 </conditional> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
34 </macro> |
ee8fc44b1655
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
parents:
diff
changeset
|
35 </macros> |