Comments (4)
Hello @pimarin
Do you mean like this option?
Or do you mean you'd like to see the options in that drop-down renamed to their species name (e.g., escherichia_coli
named Escherichia coli
) so that they will correspond to the species output of another tool?
from staramr.
Hello @apetkau , I apologize the time to answer you, I was very busy...
I wan to link the species name given by another tool (from user metadata or from kraken taxonomic asssignation) to choose the good species parameter in pointfinder option of staramr.
In this tutorial, we can see that galaxy can extract from an output text information for example to give as input to another tool, So if it's possible to modify the galawy wrapper for staramr by adding a free text option for pointfinder choice it could be great !
from staramr.
From you wrapper xlm file for example, it could be possible to modify the '${pointfinder_db.use_pointfinder}'
#if str($pointfinder_db.use_pointfinder) != 'disabled'
--output-pointfinder '$pointfinder'
#if str($pointfinder_db.use_pointfinder) == 'custom'
--pointfinder-organism '${pointfinder_db.pointfinder_custom}'
#else
--pointfinder-organism '${pointfinder_db.use_pointfinder}'
#end if
#end if
When you are in the input choice for the species name, change the last options, non_valid
for the species list of non validated pointfinder species, and a text option custom
<conditional name="pointfinder_db">
<param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
<option value="disabled" selected="true">Disable PointFinder</option>
<option value="campylobacter">Campylobacter</option>
<option value="enterococcus_faecalis">enterococcus_faecalis</option>
<option value="enterococcus_faecium">enterococcus_faecium</option>
<option value="escherichia_coli">escherichia_coli</option>
<option value="helicobacter_pylori">helicobacter_pylori</option>
<option value="salmonella">Salmonella</option>
<option value="non_valid">Unvalidated</option>
<option value="custom">Free text for species choice</option>
</param>
<when value="custom">
<param name="pointfinder_species" type="text" optional="true" label="manually add the specie name from the staramr available list" help="...">
<validator type="regex">^[a-zA-Z]+$</validator>
</param>
</when>
from staramr.
Okay, thanks so much for the response and clarification. It shouldn't be too difficult to add this to the Galaxy wrapper (you've already pretty much posted the XML changes here 😄). However, I'm wondering if this will work with your tool, since the exact species name may not exactly match what something like Kraken would output (e.g., helicobacter_pylori
vs. Helicobacter pylori
). Though with some regex substitutions this could be fixed.
from staramr.
Related Issues (20)
- The plasmidfinder.tsv shows that there is no plasmid present HOT 4
- Duplicated resfinder hits with update to database HOT 5
- cant run staramr HOT 3
- an unexpected keyword argument "inplace" and can't out the "results.xlxs" HOT 3
- Update Plasmidfinder DB HOT 1
- Update StarAMR documentation HOT 1
- Add PointFinder "Required_mut" column to pointfinder.tsv results HOT 1
- Add option to specify database path HOT 4
- different percent identity/alignment length for identical sequences on opposite strands HOT 5
- ERROR: the local id is too long or OSError: [Errno 39] Directory not empty: 'input-genomes' HOT 3
- Update MLST references in README
- docker image v0.8.0 does not accept --user HOT 3
- conda install gets an old version which does not run well HOT 4
- AttributeError: type object 'object' has no attribute 'dtype' HOT 4
- Dashes in updated pointfinder db cause crash
- A Full Set of pbp5 Ampicillin Mutations are on the Threshold of the Default Percent Identity
- Adding more databases HOT 1
- CGE phenotype not populated for E. faecium pbp5 when all essential mutations are present HOT 1
- Add to GRDI-AMR.com HOT 2
- `np.unicode_` was removed in the NumPy 2.0 release
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from staramr.