Mercurial > repos > petr-novak > dante_ltr

comparison dante_ltr_search.xml @ 14:3b3a87915ef6 draft

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"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
author petr-novak
date Mon, 30 Jan 2023 10:05:47 +0000
parents 559940c04c44
children 0ea5d893a057
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13:559940c04c44 14:3b3a87915ef6
1 <tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.1.8.0" python_template_version="3.5"> 1 <tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.2.2.0" python_template_version="3.5">
2 <requirements> 2 <requirements>
3 <requirement type="package">blast</requirement> 3 <requirement type="package">dante_ltr=0.2.2.0</requirement>
4 <requirement type="package">r-optparse</requirement> 4 </requirements>
5 <requirement type="package">bioconductor-bsgenome</requirement>
6 <requirement type="package">bioconductor-biostrings</requirement>
7 <requirement type="package">bioconductor-rtracklayer</requirement>
8 <requirement type="package" version="3.7.12">python</requirement>
9
10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
12 python ${__tool_directory__}/detect_putative_ltr_wrapper.py --gff3 '$dante' 6 echo \$PATH
13 --reference_sequence '$reference' -M $max_missing --output output --cpu 32 7 &&
8 dante_ltr --gff3 '$dante'
9 --reference_sequence '$reference' -M $max_missing --output output --cpu \${GALAXY_SLOTS:-1}
14 && 10 &&
15 mv output.gff3 $te_ltr_gff 11 mv output.gff3 $te_ltr_gff
16 && 12 &&
17 mv output_statistics.csv $statistics 13 mv output_statistics.csv $statistics
18 ]]></command> 14 ]]></command>
19 <inputs> 15 <inputs>
20 <param type="data" name="dante" format="gff3" label="Filtered GFF3 output from DANTE pipeline"/> 16 <param type="data" name="dante" format="gff3" label="GFF3 output from DANTE pipeline - full output"/>
21 <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" /> 17 <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" />
22 <param type="integer" name="max_missing" min="0" max="3" value="1" label="Maximum number of missing protein domains to tolerate in full length retrotransposon" /> 18 <param type="integer" name="max_missing" min="0" max="3" value="1" label="Maximum number of missing protein domains to tolerate in full length retrotransposon" />
23 </inputs> 19 </inputs>
24 <outputs> 20 <outputs>
25 <data name="te_ltr_gff" format="gff3" label="LTR retrotransposons annotation (GFF3) 21 <data name="te_ltr_gff" format="gff3" label="LTR retrotransposons annotation (GFF3)