Mercurial > repos > petr-novak > dante_ltr

comparison dante_ltr_search.xml @ 22:d5508ce50c49 draft

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planemo upload commit 398baa926d7864efeb2c349c52827fd6988e60e6-dirty
author petr-novak
date Tue, 28 Nov 2023 14:32:03 +0000
parents d1c3b29b1478
children
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21:08b5e23859ed 22:d5508ce50c49
10 --reference_sequence '$reference' -M $max_missing --output output --cpu \${GALAXY_SLOTS:-1} 10 --reference_sequence '$reference' -M $max_missing --output output --cpu \${GALAXY_SLOTS:-1}
11 && 11 &&
12 mv output.gff3 $te_ltr_gff 12 mv output.gff3 $te_ltr_gff
13 && 13 &&
14 mv output_statistics.csv $statistics 14 mv output_statistics.csv $statistics
15 &&
16 if [ -f output_summary.html ]; then cp output_summary.html $html_report; fi
17 &&
18 mkdir -p ${html_report.extra_files_path}
19 &&
20 if [ -d output_summary_plots ]; then cp -r output_summary_plots ${html_report.extra_files_path}/; fi
15 ]]></command> 21 ]]></command>
16 <inputs> 22 <inputs>
17 <param type="data" name="dante" format="gff3" label="GFF3 output from DANTE pipeline - full output"/> 23 <param type="data" name="dante" format="gff3" label="GFF3 output from DANTE pipeline - full output"/>
18 <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" /> 24 <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" />
19 <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" /> 25 <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" />
21 <outputs> 27 <outputs>
22 <data name="te_ltr_gff" format="gff3" label="LTR retrotransposons annotation (GFF3) 28 <data name="te_ltr_gff" format="gff3" label="LTR retrotransposons annotation (GFF3)
23 based on DANTE annotation $dante.hid and reference $reference.hid" /> 29 based on DANTE annotation $dante.hid and reference $reference.hid" />
24 <data name="statistics" format="tabular" label="LTR retrotransposons detection 30 <data name="statistics" format="tabular" label="LTR retrotransposons detection
25 summary based on $dante.hid and reference $reference.hid" /> 31 summary based on $dante.hid and reference $reference.hid" />
32 <data name="html_report" format="html" label="LTR retrotransposons detection on $dante.hid and $reference.hid report" />
33
26 </outputs> 34 </outputs>
27 <help><![CDATA[ 35 <help><![CDATA[
28 This tool uses output from DANTE annotation pipeline to identify full length LTR 36 This tool uses output from DANTE annotation pipeline to identify full length LTR
29 transposable elements. Output is in the GFF3 format and include annotation of 37 transposable elements. Output is in the GFF3 format and include annotation of
30 5' and 3' Long Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS). 38 5' and 3' Long Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS).