Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison repeat_annotate_custom.xml @ 11:5366d5ea04bc draft
planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
| author | petr-novak |
|---|---|
| date | Fri, 04 Aug 2023 12:35:32 +0000 |
| parents | 276efc4cb17f |
| children | 755a4d643184 |
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| 10:276efc4cb17f | 11:5366d5ea04bc |
|---|---|
| 1 <tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.5" python_template_version="3.5"> | 1 <tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.6" python_template_version="3.5"> |
| 2 <requirements> | 2 <requirements> |
| 3 <requirement type="package" version="4.1.2.p1">repeatmasker</requirement> | 3 <requirement type="package" version="4.1.2.p1">repeatmasker</requirement> |
| 4 <requirement type="package">bioconductor-rtracklayer</requirement> | 4 <requirement type="package">bioconductor-rtracklayer</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <required_files> | |
| 7 <include type="literal" path="clean_rm_output.R"/> | |
| 8 </required_files> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
| 7 | 10 |
| 8 #if $sensitivity.value == 'default': | 11 #if $sensitivity.value == 'default': |
| 9 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi | 12 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi |
| 10 #else: | 13 #else: |
| 25 <param type="select" label="sensitivity" name="sensitivity" > | 28 <param type="select" label="sensitivity" name="sensitivity" > |
| 26 <option value="default" selected="true" >Default sensitivity </option> | 29 <option value="default" selected="true" >Default sensitivity </option> |
| 27 <option value="-s">Slow search, more sensitive </option> | 30 <option value="-s">Slow search, more sensitive </option> |
| 28 <option value="-q">Quick search, less sensitive </option> | 31 <option value="-q">Quick search, less sensitive </option> |
| 29 </param> | 32 </param> |
| 30 <param argument="-nolow" type="boolean" truevalue="-nolow" falsevalue="" checked="false" label="Perform masking of low complexity and simple repeats" /> | 33 <param argument="-nolow" type="boolean" truevalue="" falsevalue="-nolow" checked="false" label="Perform masking of low complexity and simple repeats" /> |
| 31 </inputs> | 34 </inputs> |
| 32 <outputs> | 35 <outputs> |
| 33 <data name="output1" format="gff3" label="Repeat Annotation (GFF3) on ${on_string}"/> | 36 <data name="output1" format="gff3" label="Repeat Annotation (GFF3) on ${on_string}"/> |
| 34 <data name="output2" format="tabular" label="Raw output from RepeatMasker on ${on_string}" /> | 37 <data name="output2" format="tabular" label="Raw output from RepeatMasker on ${on_string}" /> |
| 35 </outputs> | 38 </outputs> |