Mercurial > repos > petr-novak > repeat_annotation_pipeline3

comparison repeat_annotate_custom.xml @ 10:276efc4cb17f draft

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author petr-novak
date Thu, 04 May 2023 09:27:43 +0000
parents 4a068d23fda6
children 5366d5ea04bc
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9:4a068d23fda6 10:276efc4cb17f
1 <tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.3" python_template_version="3.5"> 1 <tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.5" 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 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
25 <param type="select" label="sensitivity" name="sensitivity" > 25 <param type="select" label="sensitivity" name="sensitivity" >
26 <option value="default" selected="true" >Default sensitivity </option> 26 <option value="default" selected="true" >Default sensitivity </option>
27 <option value="-s">Slow search, more sensitive </option> 27 <option value="-s">Slow search, more sensitive </option>
28 <option value="-q">Quick search, less sensitive </option> 28 <option value="-q">Quick search, less sensitive </option>
29 </param> 29 </param>
30 <param argument="-nolow" type="boolean" truevalue="-nolow" falsevalue="" checked="true" label="Perform masking of low complexity and simple repeats" /> 30 <param argument="-nolow" type="boolean" truevalue="-nolow" falsevalue="" checked="false" label="Perform masking of low complexity and simple repeats" />
31 </inputs> 31 </inputs>
32 <outputs> 32 <outputs>
33 <data name="output1" format="gff3" label="Repeat Annotation (GFF3) on ${on_string}"/> 33 <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}" /> 34 <data name="output2" format="tabular" label="Raw output from RepeatMasker on ${on_string}" />
35 </outputs> 35 </outputs>