Skip to content

fixed optional rendering of the plasmid report in MOB-Typer with this new small patch #274

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
kbessonov1984 merged 5 commits into from
Feb 26, 2025
Merged

fixed optional rendering of the plasmid report in MOB-Typer with this new small patch #274

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
b163bb4
fixed optional rendering of the plasmid report
kbessonov1984 Feb 25, 2025
ebfc22d
fixed optional rendering of the plasmid report
kbessonov1984 Feb 25, 2025
37211ae
fixed optional rendering of the plasmid report
kbessonov1984 Feb 25, 2025
9137349
release galaxy1 fixed optional rendering of the plasmid report and im…
kbessonov1984 Feb 25, 2025
7c72cfb
Merge branch 'master' into mob-suite
kbessonov1984 Feb 25, 2025
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: 1 addition & 1 deletion tools/mob_suite/mob_recon.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -138,7 +138,7 @@
</collection>
</outputs>
<tests>
<test>
<test expect_num_outputs="4">
<param name="input" value="Ecoli_strain_KV7_complete_LT795502.fasta" ftype="fasta"/>
<section name="adv_param">
<param name="unicycler_contigs" value="True"/>
Expand Down
16 changes: 8 additions & 8 deletions tools/mob_suite/mob_typer.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="mob_typer" name="MOB-Typer" version="@VERSION@+galaxy0">
<tool id="mob_typer" name="MOB-Typer" version="@VERSION@+galaxy1">
<description>Get the plasmid type and mobility given its sequence</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -65,18 +65,16 @@
#if $adv_param.biomarker_report_file
--biomarker_report_file biomarker_report.txt
#end if



--out_file plasmid_report.txt;

]]>
</command>
<inputs>
<param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
<section name="adv_param" title="Advanced parameters" expanded="False">
<param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independent plasmid?" help="Treat each sequence in the FASTA file as a separate input (--multi)" />
<param name="biomarker_report_file" type="boolean" truevalue="true" falsevalue="" checked="false" label="Output BLAST biomarker report?" help="The report will report all biomarkers identified in a given query plasmid (--biomarker_report_file)" />

<param name="multi" type="boolean" checked="false" label="Treat each input sequence as an independent plasmid?" help="Treat each sequence in the FASTA file as a separate input (--multi)" />
<param name="biomarker_report_file" type="boolean" checked="true" label="Output BLAST biomarker report?" help="The report will report all biomarkers identified in a given query plasmid (--biomarker_report_file)" />
<param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn" help="(--min_rep_evalue)"/>
<param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn" help="(--min_mob_evalue)"/>
<param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn" help="(--min_con_evalue)"/>
Expand All @@ -101,10 +99,12 @@
</inputs>
<outputs>
<data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" />
<data name="biomarker_report" from_work_dir="biomarker_report.txt" label="${tool.name}: Biomarker report on ${input.element_identifier}" format="tabular" />
<data name="biomarker_report" from_work_dir="biomarker_report.txt" label="${tool.name}: Biomarker report on ${input.element_identifier}" format="tabular">
<filter>adv_param["biomarker_report_file"]</filter>
</data>
</outputs>
<tests>
<test>
<test expect_num_outputs="2">
<param name="input" value="plasmid_476.fasta" ftype="fasta"/>
<output name="plasmid_report">
<assert_contents>
Expand Down