Skip to content

small fixes for integron finder #7668

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

Merged
bernt-matthias merged 1 commit into from
Feb 10, 2026
Merged

small fixes for integron finder #7668

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
2 changes: 0 additions & 2 deletions tools/integron_finder/.lint_skip
View file
Open in desktop

This file was deleted.

14 changes: 7 additions & 7 deletions tools/integron_finder/integron_finder.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,16 +65,16 @@
<param name="no_logfile" type="boolean" truevalue="true" falsevalue="false" label="Remove log file"/>
</inputs>
<outputs>
<collection type="list" label="Genbank files from [$tool.name] on $[on_string]" name="genbank_out">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.gbk" format="gbk" visible="false" directory="Results_Integron_Finder/" />
<collection type="list" label="${tool.name} on ${on_string}: Genbank " name="genbank_out">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.gbk" format="genbank" visible="false" directory="Results_Integron_Finder/" />
<filter>gbk</filter>
</collection>
<data format="txt" name="integron_log" from_work_dir="Results_Integron_Finder/integron_finder.out" label="Log from [$tool.name] on $[on_string]">
<data format="txt" name="integron_log" from_work_dir="Results_Integron_Finder/integron_finder.out" label="${tool.name} on ${on_string}: Log">
<filter> no_logfile == False</filter>
</data>
<data format="tsv" name="integrons_table" from_work_dir="Results_Integron_Finder/*.integrons" label="Integrons annotations from [$tool.name] on $[on_string]"/>
<data format="tsv" name="summary" from_work_dir="Results_Integron_Finder/*.summary" label="Summary from [$tool.name] on $[on_string]"/>
<collection type="list" label="Graphic from [$tool.name] on $[on_string]" name="pdf_out">
<data format="tsv" name="integrons_table" from_work_dir="Results_Integron_Finder/*.integrons" label="${tool.name} on ${on_string}: Integron annotations"/>
<data format="tsv" name="summary" from_work_dir="Results_Integron_Finder/*.summary" label="${tool.name} on ${on_string}: Summary"/>
<collection name="pdf_out" type="list" label="${tool.name} on ${on_string}: Graphic">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" visible="false" directory="Results_Integron_Finder/" />
<filter>pdf</filter>
</collection>
Expand Down Expand Up @@ -146,7 +146,7 @@
<param name="calin_threshold" value="3"/>
<param name="max_attc_size" value="188"/>
<param name="min_attc_size" value="30"/>
<param name="keep_palindromes" value=""/>
<param name="keep_palindromes" value="false"/>
</section>
</section>
<output name="integrons_table" value="test7_integrons_table.tsv" lines_diff="3" />
Expand Down
4 changes: 2 additions & 2 deletions tools/integron_finder/macro.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<macros>
<token name="@TOOL_VERSION@">2.0.5</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">22.05</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">24.2</token>
<token name="@THREADS@">\${GALAXY_SLOTS:-2}</token>
<xml name="requirements">
<requirements>
Expand Down