Skip to content

ncbi_datasets: Update taxonomy help text #7901

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

Open
SaimMomin12 wants to merge 18 commits into
base: main
Choose a base branch
from
Open

ncbi_datasets: Update taxonomy help text #7901

Show file tree
Hide file tree
Changes from 10 commits
Commits
Show all changes
18 commits
Select commit Hold shift + click to select a range
988ca82
Update taxonomy help text
SaimMomin12 Apr 17, 2026
d0ee882
Update help
SaimMomin12 Apr 22, 2026
ab512d3
Add tests for taxon and taxon_positional given as taxID
bernt-matthias Apr 22, 2026
096dbeb
Allow digits for taxon
bernt-matthias Apr 22, 2026
748b0db
Try to re-enable tests
bernt-matthias Apr 22, 2026
c79e79a
fix linter error
bernt-matthias Apr 23, 2026
3e4abc1
fix sanitizers
bernt-matthias Apr 23, 2026
4f0b372
document sanitizers in help
bernt-matthias Apr 23, 2026
13344b2
debug
bernt-matthias Apr 23, 2026
298ca02
Revert "debug"
bernt-matthias Apr 24, 2026
47476ab
Bump to latest version
SaimMomin12 Apr 27, 2026
4e78461
Merge branch 'main' into ncbi-fix-1
bernt-matthias Apr 27, 2026
d671cc9
add NCBI API key
bernt-matthias Apr 28, 2026
5c7285a
Merge branch 'ncbi-fix-1' of https://github.com/SaimMomin12/tools-iuc…
bernt-matthias Apr 28, 2026
a6468ae
Fix credentials XML
bernt-matthias Apr 29, 2026
5efd8c3
make credentials optional
bernt-matthias Apr 29, 2026
2966e1e
bump
bernt-matthias Apr 29, 2026
0be7a2c
bump
bernt-matthias Apr 30, 2026
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
42 changes: 15 additions & 27 deletions tools/ncbi_datasets/datasets_gene.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,30 +95,16 @@ dataformat
<when value="symbol">
<expand macro="text_or_file" what="Gene Symbol" what_extended="NCBI Gene Symbol" help=""/>
<expand macro="ortholog"/>
<param argument="--taxon" type="text" value="human" label="Species for gene symbol" help="NCBI taxid, common or scientific name">
<sanitizer invalid_char="">
<valid initial="string.letters">
<add value=" "/>
<add value="-"/>
</valid>
</sanitizer>
</param>
<expand macro="taxon_parameter" argument="--taxon" value="human" label="Species for gene symbol" help="NCBI Taxon ID, common or scientific name"/>
</when>
<when value="accession">
<expand macro="text_or_file" what="Gene Accession" what_extended="NCBI Gene Accession" help=""/>
<expand macro="ortholog"/>
<param argument="--taxon-filter" type="text" value="" label="Limit gene sequences and annotation report file to specified taxon" help="any rank, only available for WP accessions">
<sanitizer invalid_char="">
<valid initial="string.letters">
<add value=" "/>
<add value="-"/>
</valid>
</sanitizer>
</param>
<expand macro="taxon_parameter" argument="--taxon-filter" value="" label="Limit gene sequences and annotation report file to specified taxon" help="any rank, only available for WP accessions"/>
<param argument="--include-flanks-bp" type="integer" optional="true" min="0" value="" label="Length of flanking nucleotides" help="WP accessions only"/>
</when>
<when value="taxon">
<expand macro="taxon_positional"/>
<expand macro="taxon_parameter" argument="taxon_positional" value="" label="Enter taxon" help="e.g. human, house mouse, bos taurus, etc. or use Taxonomy ID from NCBI for greater accuracy, use species-level only not genera or larger taxa"/>
</when>
</conditional>
</section>
Expand All @@ -131,10 +117,12 @@ dataformat
</param>
<when value=""/>
<when value="text">
<param argument="--fasta-filter" type="text" label="RefSeq nucleotide and protein accessions" help="Comma separated">
<param argument="--fasta-filter" type="text" label="RefSeq nucleotide and protein accessions" help="Comma separated, Charcters other than A-Z, a-z, 0-9, _, and . will be stripped from the input.">
<sanitizer invalid_char="">
<valid initial="string.letters,string.digits">
<add value=","/>
<add value="_"/>
<add value="."/>
</valid>
</sanitizer>
</param>
Expand Down Expand Up @@ -510,7 +498,7 @@ dataformat
<param name="text_or_file" value="text"/>
<param name="accession" value="brca1,tp53"/>
</conditional>
<param name="taxon" value="human"/>
<param name="taxon" value="9606"/>
</conditional>
<section name="file_choices">
<conditional name="kingdom_cond">
Expand Down Expand Up @@ -576,15 +564,15 @@ dataformat
</assert_command>
</test>

<!-- 10: datasets download gene taxon human -->
<!-- <test expect_num_outputs="1">
<!-- 13: datasets download gene taxon human -->
<test expect_num_outputs="1">
<conditional name="query|subcommand">
<param name="download_by" value="taxon"/>
<param name="taxon_positional" value="human"/>
</conditional>
<section name="file_choices">
<conditional name="kingdom_cond">
<param name="include" value=""/>
<param name="include" value_json="null"/>
</conditional>
</section>
<output name="gene_data_report">
Expand All @@ -594,12 +582,12 @@ dataformat
<has_n_columns n="8"/>
</assert_contents>
</output>
</test> -->
<!-- 11: datasets download gene taxon human + \-\-fasta-filter -->
<!-- <test expect_num_outputs="2">
</test>
<!-- 14: datasets download gene taxon human (given as taxID) + \-\-fasta-filter -->
<test expect_num_outputs="2">
<conditional name="query|subcommand">
<param name="download_by" value="taxon"/>
<param name="taxon_positional" value="human"/>
<param name="taxon_positional" value="9606"/>
</conditional>
<section name="file_choices">
<conditional name="kingdom_cond">
Expand All @@ -624,7 +612,7 @@ dataformat
<has_text text=">" n="1" />
</assert_contents>
</output>
</test> -->
</test>
</tests>
<help><![CDATA[
.. class:: infomark
Expand Down
2 changes: 1 addition & 1 deletion tools/ncbi_datasets/datasets_genome.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@ $filters.exclude_atypical
<expand macro="text_or_file"/>
</when>
<when value="taxon">
<expand macro="taxon_positional"/>
<expand macro="taxon_parameter" argument="taxon_positional" value="" label="Enter taxon" help="e.g. human, house mouse, bos taurus, etc. or use Taxonomy ID from NCBI for greater accuracy, use species-level only not genera or larger taxa"/>
<param argument="--tax-exact-match" type="boolean" truevalue="--tax-exact-match" falsevalue="" label="Exclude sub-species when a species-level taxon is specified"/>
</when>
</conditional>
Expand Down
15 changes: 11 additions & 4 deletions tools/ncbi_datasets/macros.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">18.23.0</token>
Comment thread
SaimMomin12 marked this conversation as resolved.
Outdated
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">25.0</token>
<token name="@LICENSE@">MIT</token>
<token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
Expand Down Expand Up @@ -45,7 +45,7 @@
<conditional name="text_or_file" label="How do you want to specify the @WHAT@(s) to download">
<param name="text_or_file" type="select" label="Enter @WHAT@ or read from file ?">
<option value="text">Enter @WHAT@s</option>
<option value="file">Read a list of @WHAT_EXTENDED@s from a dataset</option>
<option value="file">Read a list of @WHAT_EXTENDED@s from a dataset, one per line</option>
</param>
<when value="text">
<!-- command section also allows spaces as separator for backward compatibility
Expand All @@ -71,8 +71,15 @@
</param>
</xml>

<xml name="taxon_positional">
<param name="taxon_positional" type="text" label="Enter taxon" help="e.g. human, house mouse, bos taurus, etc. or use Taxonomy ID from NCBI for greater accuracy, use species-level only not genera or larger taxa"/>
<xml name="taxon_parameter" tokens="argument,value,label,help">
<param argument="@ARGUMENT@" type="text" value="@VALUE@" label="@LABEL@" help="@HELP@. Charcters other than A-Z, a-z, 0-9, dash and space will be stripped from the input.">
<sanitizer invalid_char="">
<valid initial="string.letters,string.digits">
<add value=" "/>
<add value="-"/>
</valid>
</sanitizer>
</param>
</xml>

<xml name="ortholog">
Expand Down
Loading
⚡