Mercurial > repos > petr-novak > repeat_annotation_pipeline3

comparison repeat_annotate_custom.xml @ 8:2557cad81607 draft

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author petr-novak
date Wed, 03 May 2023 11:12:41 +0000
parents acf12f2e8355
children 4a068d23fda6
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7:acf12f2e8355 8:2557cad81607
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="0.1.3" python_template_version="3.5">
2 <requirements> 2 <requirements>
3 <requirement type="package">repeatmasker</requirement> 3 <requirement type="package">repeatmasker=4.1.2.p1</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[
7 7
8 #if $sensitivity.value == 'default': 8 #if $sensitivity.value == 'default':
9 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall -nolow -no_is -e ncbi 9 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi
10 #else: 10 #else:
11 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall -nolow -no_is -e ncbi $sensitivity 11 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi $sensitivity
12 #end if 12 #end if
13 && 13 &&
14 ls -l * >&2 && 14 ls -l * >&2 &&
15 cp `basename $input`.out $output2 15 cp `basename $input`.out $output2
16 && 16 &&
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 </inputs> 31 </inputs>
31 <outputs> 32 <outputs>
32 <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}"/>
33 <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}" />
34 </outputs> 35 </outputs>