Mercurial > repos > petr-novak > tidecluster

comparison tidecluster.xml @ 5:af85dfc8676d draft

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planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 06d2db65d620a49e796b90a37c55f89e1e275e5d
author petr-novak
date Tue, 29 Aug 2023 13:06:44 +0000
parents 299f14a6050a
children 971dbc97e607
comparison
equal deleted inserted replaced
4:1cef42f5a11b 5:af85dfc8676d
11 -pr 'tidecluster' 11 -pr 'tidecluster'
12 #if $library: 12 #if $library:
13 -l '$library' 13 -l '$library'
14 #end if 14 #end if
15 -m $min_length 15 -m $min_length
16 -T ' -p $min_period -P $max_period -e $max_diverg' 16 -T ' -p $min_period -P $max_period -e $max_diverg -c $min_copy'
17 -nd $no_dust 17 $no_dust
18 -c \${GALAXY_SLOTS:-1} 18 -c \${GALAXY_SLOTS:-1}
19 -M $min_total_length 19 -M $min_total_length
20 && 20 &&
21 cp tidecluster_tidehunter.gff3 '$gff3_tidehunter' 21 cp tidecluster_tidehunter.gff3 '$gff3_tidehunter'
22 && 22 &&
23 cp tidecluster_clustering.gff3 '$gff3_clustering' 23 cp tidecluster_clustering.gff3 '$gff3_clustering'
24 && 24 &&
25 cp tidecluster_tarean_report.html '$tarean_report' 25 if [ -f tidecluster_tarean_report.html ]; then cp tidecluster_tarean_report.html '$tarean_report'; fi
26 && 26 &&
27 mkdir -p ${tarean_report.extra_files_path} 27 mkdir -p ${tarean_report.extra_files_path}
28 && 28 &&
29 cp -r tidecluster_tarean ${tarean_report.extra_files_path}/ 29 if [ -d tidecluster_tarean ]; then cp -r tidecluster_tarean ${tarean_report.extra_files_path}/; fi
30 && 30 &&
31 cp tidecluster_consensus_dimer_library.fasta ${trc_library} 31 if [ -f tidecluster_consensus_dimer_library.fasta ]; then cp tidecluster_consensus_dimer_library.fasta ${trc_library}; fi
32 && 32 &&
33 zip -r output.zip * 33 zip -r output.zip *
34 #if $library: 34 #if $library:
35 && 35 &&
36 cp tidecluster_annotation.gff3 '$gff3_annotation' 36 cp tidecluster_annotation.gff3 '$gff3_annotation'
53 <param type="integer" name="max_period" value="3000" 53 <param type="integer" name="max_period" value="3000"
54 label="Maximum period size of tandem repeat" max="20000"/> 54 label="Maximum period size of tandem repeat" max="20000"/>
55 <param type="float" name="max_diverg" value="0.25" 55 <param type="float" name="max_diverg" value="0.25"
56 label="Maximum allowed divergence rate between two consecutive repeats" 56 label="Maximum allowed divergence rate between two consecutive repeats"
57 min="0" max="1"/> 57 min="0" max="1"/>
58 <param type="integer" name="min_copy" value="5"
59 label="minimum copy number of tandem repeat" min="2"/>
58 <param type="boolean" name="no_dust" truevalue="--no_dust" falsevalue="" 60 <param type="boolean" name="no_dust" truevalue="--no_dust" falsevalue=""
59 checked="false" label="Do not use dust filter in blastn when clustering"/> 61 checked="false" label="Do not use dust filter in blastn when clustering"/>
60 <param type="integer" name="min_total_length" value="50000" 62 <param type="integer" name="min_total_length" value="50000"
61 label="Minimum combined length of tandem repeat arrays within a single cluster"/> 63 label="Minimum combined length of tandem repeat arrays within a single cluster"
64 help="Minimum combined length of tandem repeat arrays within a single cluster, required for inclusion in TAREAN analysis"
65 />
62 </inputs> 66 </inputs>
63 <outputs> 67 <outputs>
64 <data name="output_archive" format="zip" 68 <data name="output_archive" format="zip"
65 label="${tool.name} on ${on_string}: Archive with complete results"/> 69 label="${tool.name} on ${on_string}: Archive with complete results"/>
66 <data name="gff3_tidehunter" format="gff3" 70 <data name="gff3_tidehunter" format="gff3"