Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

update version Miniprot v0.13 #5918

Merged
merged 4 commits into from
Mar 28, 2024
Merged

update version Miniprot v0.13 #5918

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
9419bd6
update version
rlibouba Mar 28, 2024
8b58b53
Update tools/miniprot/miniprot.xml
bgruening Mar 28, 2024
34fbc87
fix spacing
bgruening Mar 28, 2024
605c2f2
Update miniprot.xml
bgruening Mar 28, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion tools/miniprot/macros.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">0.12</token>
<token name="@TOOL_VERSION@">0.13</token>
<token name="@VERSION_SUFFIX@">0</token>
<xml name="citation">
<citations>
<citation type="doi">10.1093/bioinformatics/btad014</citation>
Expand Down
23 changes: 17 additions & 6 deletions tools/miniprot/miniprot.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="miniprot" name="Miniprot align" version="@TOOL_VERSION@+galaxy0" profile="21.05">
<tool id="miniprot" name="Miniprot align" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
<description>align a protein sequence against a genome with affine gap penalty, splicing and frameshift</description>
<macros>
<import>macros.xml</import>
Expand All @@ -25,7 +25,10 @@
-C $adv.alignment.non_canonical_splice
-F $adv.alignment.frameshift
-B $adv.alignment.end_bonus
-j $adv.alignment.splice_model
-j $adv.alignment.splice_model
#if str($adv.ncbi_table) !=""
-T '$adv.ncbi_table'
#end if
#if str($adv.mapping.intron_size.mode) == 'manual'
-G $adv.mapping.intron_size.max_intron
#elif str($adv.mapping.intron_size.mode) == 'auto'
Expand Down Expand Up @@ -71,7 +74,7 @@
<param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size for genome-wide indexing"/>
<param argument="-b" name="bits_per_block" type="integer" min="1" value="8" label="Number of bits per bin" help="Miniprot splits the genome into non-overlapping bins of 2^8 bp in size"/>
<param argument="-M" name="modimisers" type="integer" value="1" label="Sample k-mers at a rate 1/2**INT" help="Increasing this option reduces peak memory but decreases sensitivity"/>
<param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index"/>
<param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index"/>
</when>
<when value="preindexed">
<!-- refine the datatype here once Miniprot index data type is in Galaxy -->
Expand Down Expand Up @@ -142,10 +145,17 @@
<param argument="--no-cs" name="output_no_cs" type="boolean" truevalue="--no-cs" falsevalue="" checked="false" label="Disable the cs tag"/>
</section>
<param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
<param argument="-T" name="ncbi_table" type="text" optional="true" label="Enter NCBI translation table" help="1 through 33 except 7-8 and 17-20">
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

We could use a select field here.

<sanitizer invalid_char="">
<valid initial="string.digits"></valid>
</sanitizer>
<validator type="regex">[0-9]+</validator>
</param>
bgruening marked this conversation as resolved.
Show resolved Hide resolved
</when>
<when value="no">
</when>
</conditional>

</inputs>
<outputs>
<data name="output_alignment" format="gff3" label="Miniprot on ${on_string}">
Expand Down Expand Up @@ -235,7 +245,7 @@
<assert_contents>
<has_text text="tr|I6YGH7|I6YGH7_MYCTU" />
<has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
<has_n_lines n="1633"/>
<has_n_lines n="1647"/>
</assert_contents>
</output>
</test>
Expand All @@ -257,7 +267,7 @@
<has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
<has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
<has_text text="NC_000962.3"/>
<has_n_lines n="2172"/>
<has_n_lines n="2196"/>
</assert_contents>
</output>
</test>
Expand All @@ -279,7 +289,7 @@
<has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
<has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
<has_text text="sp|O05779|FTSE_MYCTU"/>
<has_n_lines n="650"/>
<has_n_lines n="654"/>
</assert_contents>
</output>
</test>
Expand Down Expand Up @@ -332,6 +342,7 @@
</conditional>
<param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
<param name="output_format" value="gtf"></param>
<param name="ncbi_table" value="1"></param>
<conditional name="adv">
<param name="options" value="yes"></param>
<section name="output">
Expand Down