biocodz

Parameter 'strand_separation_type' with value '--sout' here https://github.com/biocodz/galaxytools/blob/sortmerna-4/tools/rna_tools/sortmerna/sortmerna.xml#L212 should disable (gray out) the parameter 'paired_output_type' and all its values like '--paired_in' and '--paired_out' here https://github.com/biocodz/galaxytools/blob/sortmerna-4/tools/rna_tools/sortmerna/sortmerna.xml#L214 Example valid/invalid combinations: ` '--out2' AND...

I'm good for now, just very busy with my other duties. I try spending time on Galaxy on a regular basis, so be prepared for new questions like loading pre-indexed...

I need to get the location of the pre-built indices. The reference [$databases_type.input_databases.fields.path](https://github.com/biocodz/galaxytools/blob/sortmerna-4/tools/rna_tools/sortmerna/sortmerna.xml#L74) apparently returns the path from the data table e.g. `/home/biocodz/galaxy/tool-data/rRNA_databases/silva-arc-16s-id95/silva-arc-16s-id95.fasta`, but I need to get this path...

Thank you for the input. We'll fix the min/max readlen error in the next release.

@schwarl Hi, `%id` currently cannot be filtered using a convenient option. However, if you generate the Blast report using e.g. `--blast 1` option, you can review the `%id` (3rd column...

Agree. This needs improvement.

we'll fix this in the next release

@PhoebeCc Hi, you can either download the [source distro v4.2.0.tar.gz](https://github.com/biocore/sortmerna/archive/v4.2.0.tar.gz) or clone the git repo e.g.: ``` pushd $HOME git clone https://github.com/biocore/sortmerna.git ``` the databases are in folder `sortmerna/data/rRNA_databases`

[modified](https://github.com/biocore/sortmerna/blob/master/include/options.hpp#L186) as suggested. Thank you

Indeed! Fixed - [added default 2](https://github.com/biocore/sortmerna/blob/master/include/options.hpp#L176) to show up in the next release. Thanks for the input.