Mercurial > repos > genouest > helixer
changeset 5:c2fc4ac35199 draft default tip
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/helixer commit 54445b041f46b8b3a8e25e90e84f034cdddd2ab1
| author | genouest |
|---|---|
| date | Tue, 09 Jul 2024 13:09:23 +0000 |
| parents | ec1a90b97047 |
| children | |
| files | helixer.xml macros.xml test-data/test.h5 |
| diffstat | 2 files changed, 43 insertions(+), 19 deletions(-) [+] |
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--- a/helixer.xml Thu Mar 28 09:41:23 2024 +0000 +++ b/helixer.xml Tue Jul 09 13:09:23 2024 +0000 @@ -12,14 +12,11 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ - /usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '$input' --species '$species' - --lineage '$lineages' --gff-output-path '$output' - --temporary-dir ./ #set default_subsequence_length = {"fungi": 21384, "land_plant": 106920, "invertebrate": 213840, "vertebrate": 213840} @@ -29,23 +26,30 @@ #set default_overlap_core_length = {"fungi": 16038, "land_plant": 80190, "invertebrate": 160380, "vertebrate": 160380} #set overlap_core_len = default_overlap_core_length.get(str($lineages)) - #if str($subsequence_length) == "": - --subsequence-length '$subsequence_len' - #else: + #if str($input_model) != "" and str($input_model) != "None": + --model-filepath '$input_model' --subsequence-length '$subsequence_length' - #end if - - #if str($option_overlap.use_overlap) == "true": - #if str($option_overlap.overlap_offset) == "": - --overlap-offset '$overlap_off' + + #else: + --lineage '$lineages' + #if str($subsequence_length) == "": + --subsequence-length '$subsequence_len' #else: - --overlap-offset '$overlap_offset' + --subsequence-length '$subsequence_length' #end if - #if str($option_overlap.overlap_core_length) == "": - --overlap-core-length '$overlap_core_len' - #else: - --overlap-core-length '$overlap_core_length' + #if str($option_overlap.use_overlap) == "true": + #if str($option_overlap.overlap_offset) == "": + --overlap-offset '$overlap_off' + #else: + --overlap-offset '$overlap_offset' + #end if + + #if str($option_overlap.overlap_core_length) == "": + --overlap-core-length '$overlap_core_len' + #else: + --overlap-core-length '$overlap_core_length' + #end if #end if #end if @@ -59,7 +63,7 @@ <inputs> <param argument="--fasta-path" name="input" type="data" format="fasta,fasta.gz" label="Genomic sequence"></param> - + <param argument="--model-filepath" optional="true" name="input_model" type="data" format="h5" label="Lineage model" help="Import your lineage model to replace the default lineage. Please enter a value for the --subsequence_length parameter."></param> <param argument="--lineage" name="lineages" type="select" label="Available lineages" help="Choose the model to use for the annotation"> <option value="land_plant">land plant</option> <option value="vertebrate">vertebrate</option> @@ -125,7 +129,7 @@ </test> <test expect_num_outputs="1"> - <!-- Test for vertebrates--> + <!-- Test for vertebrates --> <param name="input" value="sequence.fasta"/> <param name="lineages" value="vertebrate"/> <param name="size" value="8"/> @@ -144,6 +148,26 @@ </conditional> <output name="output" value="vertebrate.gff3" ftype="gff3" lines_diff="2"/> </test> + + <test expect_failure="true"> + <!-- Test for model-filepath --> + <param name="input" value="sequence.fasta"/> + <param name="input_model" value="test.h5"/> + <param name="size" value="8"/> + <param name="size" value="8"/> + <param name="subsequence_length" value="1000"/> + <section name="post_processing"> + <param name="window_size" value="100"/> + <param name="edge_threshold" value="0.1"/> + <param name="peak_threshold" value="0.8"/> + <param name="min_coding_length" value="100"/> + </section> + <conditional name="option_overlap"> + <param name="use_overlap" value="true"/> + <param name="overlap_offset" value=""/> + <param name="overlap_core_length" value=""/> + </conditional> + </test> </tests> <help><![CDATA[