Mercurial > repos > oinizan > frogs
diff normalisation.xml @ 21:74a9b83110a7 draft
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
| author | oinizan |
|---|---|
| date | Thu, 30 Mar 2023 06:09:01 +0000 |
| parents | 4dd70eba5941 |
| children | 57824202c333 |
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--- a/normalisation.xml Fri Mar 10 14:03:08 2023 +0000 +++ b/normalisation.xml Thu Mar 30 06:09:01 2023 +0000 @@ -16,7 +16,7 @@ # along with this program. If not, see <http://www.gnu.org/licenses/>. --> <tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>Normalise OTU abundance.</description> + <description>Normalise ASV abundance.</description> <macros> <import>macros.xml</import> @@ -36,8 +36,8 @@ #if $sampling_method.sampling_by_min == "yes" --sampling-by-min #else - --num-reads $sampling_method.num_reads - #if $sampling_method.delete_samples + --num-reads '$sampling_method.num_reads' + #if $sampling_method.delete_samples == "true" --delete-samples #end if #end if @@ -46,16 +46,20 @@ --summary-file '$summary_file' </command> <inputs> - <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." /> - <param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." /> + <param format="fasta" argument="--input-fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." /> + <param format="biom1" argument="--input-biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." /> <conditional name="sampling_method"> - <param name="sampling_by_min" type="select" label="Sampling method" help='Sampling by the number of sequences of the smallest sample, or select a number manually' display='radio'> + <param argument="--sampling-by-min" type="select" label="Sampling method" help="Sampling by the number of sequences of the smallest sample, or select a number manually" display="radio"> <option value="yes" selected="true">Sampling by the number of sequences of the smallest sample</option> <option value="no">Select a number of sequences</option> </param> + <when value="yes"/> <when value="no"> - <param name="num_reads" type="integer" optional="true" min="1" value="" label="Number of reads" help="The final number of reads per sample." /> - <param name="delete_samples" type="boolean" label="Remove samples that have an initial number of reads below the number of reads to sample ?" /> + <param argument="--num-reads" type="integer" optional="true" min="1" value="" label="Number of reads" help="The final number of reads per sample." /> + <param argument="--delete-samples" type="select" label="Remove samples that have an initial number of reads below the number of reads to sample ?" display="radio"> + <option value="false">No, subsampling threshold need to at most equal to the smallest sample</option> + <option value="true">Yes, subsampling threshold may be greater than the smallest sample</option> + </param> </when> </conditional> </inputs> @@ -101,7 +105,7 @@ **Abundance file**: -The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_). +The abundance of each ASV in each sample (format `BIOM <http://biom-format.org/>`_). **Sampling method**: