Skip to content

Commit f6929e2

Browse files
pvanheuspvanheus
committed
Update tool versions and switch the https for EDAM
1 parent 6d2f2f9 commit f6929e2

16 files changed

Lines changed: 233 additions & 222 deletions

‎conda/meta.yaml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
{% set name = "lukasa" %}
2-
{% set version = "0.0.5" %}
3-
{% set sha256 = "095de485faea6bdf0e19f30ca6e7cdc037309499b24b4266c9d7013e9ad021f6" %}
2+
{% set version = "0.0.6" %}
3+
{% set sha256 = "1e6f311114a0fffd53398a2c8e5f3f735213c07c2fb5f7e8f72b1cd4dd7e98d7" %}
44

55
package:
66
name: {{ name|lower }}

‎galaxy/lukasa.xml‎

Lines changed: 14 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
11
<tool id="lukasa" name="Lukasa" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
22
<description>Align protein evidence against genomic contigs using metaeuk and spaln</description>
33
<macros>
4-
<token name="@TOOL_VERSION@">0.0.6</token>
4+
<token name="@TOOL_VERSION@">0.0.8</token>
55
<!-- note that this DOI is for lukasa 0.0.6 - update as needed -->
6-
<token name="@DOI@">10.5281/zenodo.4084863</token>
6+
<token name="@DOI@">10.5281/zenodo.4084863</token>
77
</macros>
88
<requirements>
99
<requirement type="package" version="@TOOL_VERSION@">lukasa</requirement>
@@ -16,24 +16,24 @@
1616
--output_filename '$output_gff' '$contigs_fasta' '$proteins_fasta'
1717
]]></command>
1818
<inputs>
19-
<param name='contigs_fasta' type='data' format='fasta' label='Genomic contigs (FASTA)' />
20-
<param name='proteins_fasta' type='data' format='fasta' label='Proteins (FASTA)' />
21-
<param name='species_table' type='text' label='Spaln species table to use (optional)' />
19+
<param name="contigs_fasta" type="data" format="fasta" label="Genomic contigs (FASTA)"/>
20+
<param name="proteins_fasta" type="data" format="fasta" label="Proteins (FASTA)"/>
21+
<param name="species_table" type="text" label="Spaln species table to use (optional)"/>
2222
</inputs>
2323
<outputs>
24-
<data name="output_gff" format='gff3' label='Map proteins to genome ${on_string}' />
24+
<data name="output_gff" format="gff3" label="Map proteins to genome ${on_string}"/>
2525
</outputs>
2626
<tests>
2727
<test>
28-
<param name="contigs_fasta" ftype="fasta" value="contig.fasta" />
29-
<param name="proteins_fasta" ftype="fasta" value="proteins.fasta" />
30-
<param name="species_table" value="cynosemi" />
31-
<output name="output_gff" value="spaln_out.gff3" />
28+
<param name="contigs_fasta" ftype="fasta" value="contig.fasta"/>
29+
<param name="proteins_fasta" ftype="fasta" value="proteins.fasta"/>
30+
<param name="species_table" value="cynosemi"/>
31+
<output name="output_gff" value="spaln_out.gff3"/>
3232
</test>
3333
<test>
34-
<param name="contigs_fasta" ftype="fasta" value="contig.fasta" />
35-
<param name="proteins_fasta" ftype="fasta" value="proteins.fasta" />
36-
<output name="output_gff" value="spaln_out_no_st.gff3" />
34+
<param name="contigs_fasta" ftype="fasta" value="contig.fasta"/>
35+
<param name="proteins_fasta" ftype="fasta" value="proteins.fasta"/>
36+
<output name="output_gff" value="spaln_out_no_st.gff3"/>
3737
</test>
3838
</tests>
3939
<help><![CDATA[
@@ -50,4 +50,4 @@
5050
<citations>
5151
<citation type="doi">@DOI@</citation>
5252
</citations>
53-
</tool>
53+
</tool>

‎inputs/extract_regions.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ region_file:
88
path: /home/pvh/Documents/code/Masters/protein_evidence_mapping/data/proteins1.txt
99

1010
$namespaces:
11-
edam: http://edamontology.org/
11+
edam: https://edamontology.org/
1212
iana: https://www.iana.org/assignments/media-types/
1313
$schemas:
14-
- http://edamontology.org/EDAM_1.18.owl
14+
- https://edamontology.org/EDAM_1.18.owl

‎inputs/metaeuk_inputs.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,6 @@ query:
99
output_name: test.fasta
1010

1111
$namespaces:
12-
edam: http://edamontology.org/
12+
edam: https://edamontology.org/
1313
$schemas:
14-
- http://edamontology.org/EDAM_1.18.owl
14+
- https://edamontology.org/EDAM_1.18.owl

‎inputs/metaeuk_to_regions_inputs.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,6 @@ metaeuk_fasta:
44
format: edam:format_1929
55

66
$namespaces:
7-
edam: http://edamontology.org/
7+
edam: https://edamontology.org/
88
$schemas:
9-
- http://edamontology.org/EDAM_1.18.owl
9+
- https://edamontology.org/EDAM_1.18.owl

‎inputs/queue_workflow_inputs.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,6 @@ proteins_fasta:
99
species_table: cynosemi
1010

1111
$namespaces:
12-
edam: http://edamontology.org/
12+
edam: https://edamontology.org/
1313
$schemas:
14-
- http://edamontology.org/EDAM_1.18.owl
14+
- https://edamontology.org/EDAM_1.18.owl

‎inputs/spaln_input.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -10,6 +10,6 @@ species: cynosemi
1010
output_format: 0
1111

1212
$namespaces:
13-
edam: http://edamontology.org/
13+
edam: https://edamontology.org/
1414
$schemas:
15-
- http://edamontology.org/EDAM_1.18.owl
15+
- https://edamontology.org/EDAM_1.18.owl

‎inputs/workflow1_inputs.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,6 @@ metaeuk_output:
1313
species_table: cynosemi
1414

1515
$namespaces:
16-
edam: http://edamontology.org/
16+
edam: https://edamontology.org/
1717
$schemas:
18-
- http://edamontology.org/EDAM_1.18.owl
18+
- https://edamontology.org/EDAM_1.18.owl

‎lukasa.py‎

100644100755
Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -20,9 +20,9 @@
2020
{}
2121
2222
$namespaces:
23-
edam: http://edamontology.org/
23+
edam: https://edamontology.org/
2424
$schemas:
25-
- http://edamontology.org/EDAM_1.18.owl
25+
- https://edamontology.org/EDAM_1.18.owl
2626
"""
2727

2828

‎tools/extract_regions.py‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,5 @@
1+
#!/usr/bin/env python3
2+
13
from __future__ import print_function, division
24
import sys
35

0 commit comments

Comments
 (0)