Mercurial > repos > petr-novak > repeat_annotation_pipeline3
changeset 8:2557cad81607 draft
Uploaded
| author | petr-novak |
|---|---|
| date | Wed, 03 May 2023 11:12:41 +0000 |
| parents | acf12f2e8355 |
| children | 4a068d23fda6 |
| files | repeat_annotate_custom.xml |
| diffstat | 1 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/repeat_annotate_custom.xml Thu May 19 08:37:22 2022 +0000 +++ b/repeat_annotate_custom.xml Wed May 03 11:12:41 2023 +0000 @@ -1,14 +1,14 @@ <tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.3" python_template_version="3.5"> <requirements> - <requirement type="package">repeatmasker</requirement> + <requirement type="package">repeatmasker=4.1.2.p1</requirement> <requirement type="package">bioconductor-rtracklayer</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if $sensitivity.value == 'default': - RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall -nolow -no_is -e ncbi + RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi #else: - RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall -nolow -no_is -e ncbi $sensitivity + RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi $sensitivity #end if && ls -l * >&2 && @@ -27,6 +27,7 @@ <option value="-s">Slow search, more sensitive </option> <option value="-q">Quick search, less sensitive </option> </param> + <param argument="-nolow" type="boolean" truevalue="-nolow" falsevalue="" checked="true" label="Perform masking of low complexity and simple repeats" /> </inputs> <outputs> <data name="output1" format="gff3" label="Repeat Annotation (GFF3) on ${on_string}"/>