Mercurial > repos > petr-novak > repeat_annotation_pipeline3

comparison repeat_annotate_custom.xml @ 11:5366d5ea04bc draft

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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>