Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison repeat_annotate_custom.xml @ 8:2557cad81607 draft
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author | petr-novak |
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date | Wed, 03 May 2023 11:12:41 +0000 |
parents | acf12f2e8355 |
children | 4a068d23fda6 |
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7:acf12f2e8355 | 8:2557cad81607 |
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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> |