maker: maker.xml annotate

annotate maker.xml @ 4:804af884eef0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b"

author	iuc
date	Thu, 10 Oct 2019 02:55:17 -0400
parents	681e5067048e
children	e06aa22b2e64

rev	line source
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	1 <?xml version="1.0"?>
4 804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	2 <tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy1">
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	3 <description>genome annotation pipeline</description>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	4 <macros>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	5 <import>macros.xml</import>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	6 </macros>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	7 <expand macro="requirements"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	8 <command><![CDATA[
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	9 RM_LIB_PATH=\$(dirname \$(which RepeatMasker))/../share/RepeatMasker/Libraries &&
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	10 mkdir lib &&
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	11 export REPEATMASKER_LIB_DIR=\$(pwd)/lib &&
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	12 for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done &&
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	13 #if $repeat_masking.repeat_source.source_type == "repbase":
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	14 cp '${repeat_masking.repeat_source.repbase_file}' 'lib/${repeat_masking.repeat_source.repbase_file_name}' &&
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	15 #end if
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	16
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	17 maker -CTL
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	18
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	19 &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	20
2 be967733bf81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088 iuc parents: 1 diff changeset	21 cp '$ctl' maker_opts.ctl
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	22
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	23 &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	24
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	25 #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'history'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	26
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	27 ## Using an augustus model from history, we need to unzip it and let augustus find it
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	28
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	29 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	30
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	31 mkdir -p 'augustus_dir/species/' &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	32
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	33 tar -C 'augustus_dir/species/' -xzvf '${abinitio_gene_prediction.aug_prediction.augustus_model}' > /dev/null &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	34
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	35 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	36 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	37
3 681e5067048e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit df4df9980131dcfb7b77de9e625407926fb4d016 iuc parents: 2 diff changeset	38 mpiexec -n \${GALAXY_SLOTS:-4} maker --ignore_nfs_tmp maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	39
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	40 &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	41
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	42 gff3_merge -d .maker.output/_master_datastore_index.log -o '${output_full}'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	43
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	44 &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	45
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	46 awk '{if ($2 == "maker" \|\| $1 ~ /^\#/) {print}}' '${output_full}' \| sed -n '/^\#\#FASTA\$/q;p' > '${output_gff}'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	47
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	48 &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	49
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	50 awk '{if ($2 != "maker") {print}}' '${output_full}' \| sed -n '/^\#\#FASTA\$/q;p' > '${output_evidences}'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	51 ]]></command>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	52 <configfiles>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	53 <!-- Maker doesn't like indentation in its config file... -->
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	54 <configfile name="ctl"><![CDATA[
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	55 #-----Genome (these are always required)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	56 genome=${genome} # genome sequence (fasta file or fasta embeded in GFF3 file)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	57 organism_type=${organism_type} # eukaryotic or prokaryotic. Default is eukaryotic
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	58
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	59 #-----Re-annotation Using MAKER Derived GFF3
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	60 #if $reannotation.reannotate == 'no'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	61 maker_gff= # MAKER derived GFF3 file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	62 est_pass=0 # use ESTs in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	63 altest_pass=0 # use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	64 protein_pass=0 # use protein alignments in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	65 rm_pass=0 # use repeats in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	66 model_pass=0 # use gene models in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	67 pred_pass=0 # use ab-initio predictions in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	68 other_pass=0 # passthrough anything else in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	69 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	70 maker_gff=${reannotation.maker_gff} # MAKER derived GFF3 file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	71 est_pass=${reannotation.est_pass} # use ESTs in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	72 altest_pass=${reannotation.altest_pass} # use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	73 protein_pass=${reannotation.protein_pass} # use protein alignments in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	74 rm_pass=${reannotation.rm_pass} # use repeats in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	75 model_pass=${reannotation.model_pass} # use gene models in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	76 pred_pass=${reannotation.pred_pass} # use ab-initio predictions in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	77 other_pass=${reannotation.other_pass} # passthrough anything else in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	78 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	79
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	80 #-----EST Evidence (for best results provide a file for at least one)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	81 #if $est_evidences.est
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	82 est=${est_evidences.est} # set of ESTs or assembled mRNA-seq in fasta format
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	83 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	84 est= # set of ESTs or assembled mRNA-seq in fasta format
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	85 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	86 #if $est_evidences.altest
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	87 altest=${est_evidences.altest} # EST/cDNA sequence file in fasta format from an alternate organism
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	88 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	89 altest= # EST/cDNA sequence file in fasta format from an alternate organism
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	90 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	91 #if $est_evidences.est_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	92 est_gff=${est_evidences.est_gff} # aligned ESTs or mRNA-seq from an external GFF3 file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	93 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	94 est_gff= # aligned ESTs or mRNA-seq from an external GFF3 file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	95 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	96 #if $est_evidences.altest_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	97 altest_gff=${est_evidences.altest_gff} # aligned ESTs from a closly relate species in GFF3 format
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	98 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	99 altest_gff= # aligned ESTs from a closly relate species in GFF3 format
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	100 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	101
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	102 #-----Protein Homology Evidence (for best results provide a file for at least one)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	103 #if $protein_evidences.protein
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	104 protein=${protein_evidences.protein} # protein sequence file in fasta format (i.e. from mutiple oransisms)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	105 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	106 protein= # protein sequence file in fasta format (i.e. from mutiple oransisms)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	107 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	108 #if $protein_evidences.protein_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	109 protein_gff=${protein_evidences.protein_gff} # aligned protein homology evidence from an external GFF3 file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	110 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	111 protein_gff= # aligned protein homology evidence from an external GFF3 file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	112 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	113
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	114 #-----Repeat Masking (leave values blank to skip repeat masking)
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	115 #if $repeat_masking.repeat_source.source_type == 'repbase'
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	116
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	117 #if $repeat_masking.repeat_source.species_source.species_from_list == 'yes'
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	118 model_org=${repeat_masking.repeat_source.species_source.species_list}
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	119 #else
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	120 model_org=${repeat_masking.repeat_source.species_source.species_name}
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	121 #end if
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	122
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	123 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	124 softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	125
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	126 #else if $repeat_masking.repeat_source.source_type == 'library'
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	127 model_org= # select a model organism for RepBase masking in RepeatMasker
4 804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	128 #if $repeat_masking.repeat_source.rmlib
804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	129 rmlib=${repeat_masking.repeat_source.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	130 #else
804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	131 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	132 #end if
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	133
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	134 #if $repeat_masking.repeat_source.repeat_protein
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	135 repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	136 #else
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	137 repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	138 #end if
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	139 #if $repeat_masking.repeat_source.rm_gff
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	140 rm_gff=${repeat_masking.repeat_source.rm_gff} # pre-identified repeat elements from an external GFF3 file
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	141 #else
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	142 rm_gff= # pre-identified repeat elements from an external GFF3 file
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	143 #end if
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	144
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	145 softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	146
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	147 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	148 model_org= # select a model organism for RepBase masking in RepeatMasker
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	149 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	150 softmask=0 # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	151 #end if
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	152
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	153 prok_rm=0 # forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	154
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	155 #-----Gene Prediction
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	156 #if $abinitio_gene_prediction.snaphmm
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	157 snaphmm=${abinitio_gene_prediction.snaphmm} # SNAP HMM file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	158 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	159 snaphmm= # SNAP HMM file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	160 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	161 gmhmm= # GeneMark HMM file, disabled in galaxy as not free
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	162 #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'builtin'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	163 augustus_species=${abinitio_gene_prediction.aug_prediction.augustus_species} # Augustus gene prediction species model
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	164 #else if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'history'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	165 augustus_species=local # Augustus gene prediction species model
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	166 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	167 augustus_species= # Augustus gene prediction species model
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	168 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	169 fgenesh_par_file= # FGENESH parameter file disabled in galaxy as not free
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	170 #if $gene_prediction.pred_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	171 pred_gff=${gene_prediction.pred_gff} # ab-initio predictions from an external GFF3 file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	172 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	173 pred_gff= # ab-initio predictions from an external GFF3 file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	174 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	175 #if $gene_prediction.model_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	176 model_gff=${gene_prediction.model_gff} # annotated gene models from an external GFF3 file (annotation pass-through)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	177 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	178 model_gff= # annotated gene models from an external GFF3 file (annotation pass-through)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	179 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	180 est2genome=${est_evidences.est2genome} # infer gene predictions directly from ESTs, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	181 protein2genome=${protein_evidences.protein2genome} # infer predictions from protein homology, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	182 trna=${gene_prediction.trna} # find tRNAs with tRNAscan, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	183 #if $gene_prediction.snoscan_rrna
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	184 snoscan_rrna=${gene_prediction.snoscan_rrna} # rRNA file to have Snoscan find snoRNAs
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	185 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	186 snoscan_rrna= # rRNA file to have Snoscan find snoRNAs
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	187 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	188 unmask=${abinitio_gene_prediction.unmask} # also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	189
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	190 #-----Other Annotation Feature Types (features MAKER doesn't recognize)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	191 #if $advanced.other_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	192 other_gff=${advanced.other_gff} # extra features to pass-through to final MAKER generated GFF3 file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	193 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	194 other_gff= # extra features to pass-through to final MAKER generated GFF3 file
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	195 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	196
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	197 #-----External Application Behavior Options
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	198 alt_peptide=${advanced.alt_peptide} # amino acid used to replace non-standard amino acids in BLAST databases
2 be967733bf81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088 iuc parents: 1 diff changeset	199 cpus=1 # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	200
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	201 #-----MAKER Behavior Options
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	202 max_dna_len=${advanced.max_dna_len} # length for dividing up contigs into chunks (increases/decreases memory usage)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	203 min_contig=${advanced.min_contig} # skip genome contigs below this length (under 10kb are often useless)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	204
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	205 pred_flank=${advanced.pred_flank} # flank for extending evidence clusters sent to gene predictors
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	206 pred_stats=${advanced.pred_stats} # report AED and QI statistics for all predictions as well as models
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	207 AED_threshold=${advanced.AED_threshold} # Maximum Annotation Edit Distance allowed (bound by 0 and 1)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	208 min_protein=${advanced.min_protein} # require at least this many amino acids in predicted proteins
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	209 alt_splice=${advanced.alt_splice} # Take extra steps to try and find alternative splicing, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	210 always_complete=${advanced.always_complete} # extra steps to force start and stop codons, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	211 map_forward=${advanced.map_forward} # map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	212 keep_preds=${advanced.keep_preds} # Concordance threshold to add unsupported gene prediction (bound by 0 and 1)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	213
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	214 split_hit=${advanced.split_hit} # length for the splitting of hits (expected max intron size for evidence alignments)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	215 single_exon=${advanced.single_exon.single_exon} # consider single exon EST evidence when generating annotations, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	216 #if $advanced.single_exon.single_exon == '1'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	217 single_length=${advanced.single_length} # min length required for single exon ESTs if 'single_exon is enabled'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	218 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	219 single_length=250 # min length required for single exon ESTs if 'single_exon is enabled'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	220 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	221 correct_est_fusion=${advanced.correct_est_fusion} # limits use of ESTs in annotation to avoid fusion genes
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	222
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	223 tries=2 # number of times to try a contig if there is a failure for some reason
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	224 clean_try=0 # remove all data from previous run before retrying, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	225 clean_up=0 # removes theVoid directory with individual analysis files, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	226 TMP= # specify a directory other than the system default temporary directory for temporary files
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	227 ]]></configfile>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	228 </configfiles>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	229
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	230 <inputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	231 <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	232 <param name="organism_type" type="select" label="Organism type">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	233 <option value="eukaryotic">Eukaryotic</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	234 <option value="prokaryotic">Prokaryotic</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	235 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	236
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	237 <conditional name="reannotation">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	238 <param name="reannotate" type="select" label="Re-annotate using an existing Maker annotation">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	239 <option value="no" selected="true">No</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	240 <option value="yes">Yes</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	241 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	242 <when value="no"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	243 <when value="yes">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	244 <param name="maker_gff" type="data" format="gff" label="Previous Maker annotation"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	245 <param name="est_pass" type="boolean" truevalue="1" falsevalue="0" label="Re-use ESTs"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	246 <param name="altest_pass" type="boolean" truevalue="1" falsevalue="0" label="Re-use alternate organism ESTs"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	247 <param name="protein_pass" type="boolean" truevalue="1" falsevalue="0" label="Re-use protein alignments"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	248 <param name="rm_pass" type="boolean" truevalue="1" falsevalue="0" label="Re-use repeats"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	249 <param name="model_pass" type="boolean" truevalue="1" falsevalue="0" label="Re-use gene models"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	250 <param name="pred_pass" type="boolean" truevalue="1" falsevalue="0" label="Re-use ab-initio predictions"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	251 <param name="other_pass" type="boolean" truevalue="1" falsevalue="0" label="Passthrough anything else"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	252 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	253 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	254
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	255 <section name="est_evidences" title="EST evidences (for best results provide at least one of these)" expanded="True">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	256 <param name="est2genome" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Infer gene predictions directly from all ESTs" help="Maker will blindly trust EST alignments to create gene models. Use this only before training ab-initio predictors."/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	257 <param name="est" type="data" format="fasta" label="ESTs or assembled cDNA" optional="True"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	258 <param name="altest" type="data" format="fasta" label="EST/cDNA from an alternate organism" optional="True"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	259 <param name="est_gff" type="data" format="gff" label="Aligned ESTs or cDNA" optional="True"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	260 <param name="altest_gff" type="data" format="gff" label="Aligned EST/cDNA from an alternate organism" optional="True"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	261 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	262
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	263 <section name="protein_evidences" title="Protein evidences (for best results provide at least one of these)" expanded="True">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	264 <param name="protein2genome" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Infer gene predictions directly from all protein alignments" help="Maker will blindly trust protein alignments to create gene models. Use this only before training ab-initio predictors."/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	265 <param name="protein" type="data" format="fasta" label="Protein sequences" help="From mutiple organisms" optional="True"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	266 <param name="protein_gff" type="data" format="gff" label="Aligned proteins" help="From mutiple organisms" optional="True"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	267 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	268
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	269 <section name="abinitio_gene_prediction" title="Ab-initio gene prediction" expanded="True">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	270 <param name="snaphmm" type="data" format="snaphmm" label="SNAP model" optional="True" help="Leave empty to disable gene prediction by SNAP"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	271
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	272 <conditional name="aug_prediction">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	273 <param name="augustus_mode" type="select" label="Prediction with Augustus">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	274 <option value="no" selected="true">Don't use Augustus to predict genes</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	275 <option value="builtin">Run Augustus with a predefined prediction model</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	276 <option value="history">Run Augustus with a custom prediction model</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	277 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	278 <when value="no"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	279 <when value="history">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	280 <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	281 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	282 <when value="builtin">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	283 <param name="augustus_species" type="select" label="Augustus species model">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	284 <!-- If you update this list, please also update it in augustus and busco tools (../augustus/augustus.xml and ../busco/busco.xml) -->
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	285 <option value="human">Homo sapiens</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	286 <option value="fly">Drosophila melanogaster</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	287 <option value="arabidopsis">Arabidopsis thaliana</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	288 <option value="brugia ">Brugia malayi</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	289 <option value="aedes">Aedes aegypti</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	290 <option value="tribolium2012">Tribolium castaneum</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	291 <option value="schistosoma">Schistosoma mansoni</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	292 <option value="tetrahymena">Tetrahymena thermophila</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	293 <option value="galdieria">Galdieria sulphuraria</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	294 <option value="maize">Zea mays</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	295 <option value="toxoplasma">Toxoplasma gondii</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	296 <option value="caenorhabditis ">Caenorhabditis elegans</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	297 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	298 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	299 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	300 <option value="aspergillus_terreus">Aspergillus terreus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	301 <option value="botrytis_cinerea ">Botrytis cinerea</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	302 <option value="candida_albicans ">Candida albicans</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	303 <option value="candida_guilliermondii ">Candida guilliermondii</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	304 <option value="candida_tropicalis ">Candida tropicalis</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	305 <option value="chaetomium_globosum">Chaetomium globosum</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	306 <option value="coccidioides_immitis">Coccidioides immitis</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	307 <option value="coprinus">Coprinus cinereus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	308 <option value="coprinus_cinereus">Coprinus cinereus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	309 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	310 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	311 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	312 <option value="cryptococcus">Cryptococcus neoformans</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	313 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	314 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	315 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	316 <option value="fusarium_graminearum ">Fusarium graminearum</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	317 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	318 <option value="histoplasma">Histoplasma capsulatum</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	319 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	320 <option value="laccaria_bicolor ">Laccaria bicolor</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	321 <option value="lamprey">Petromyzon marinus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	322 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	323 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	324 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	325 <option value="neurospora_crassa">Neurospora crassa</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	326 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	327 <option value="pichia_stipitis">Pichia stipitis</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	328 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	329 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	330 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	331 <option value="saccharomyces">Saccharomyces cerevisiae</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	332 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	333 <option value="trichinella">Trichinella spiralis</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	334 <option value="ustilago_maydis">Ustilago maydis</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	335 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	336 <option value="nasonia">Nasonia vitripennis</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	337 <option value="tomato">Solanum lycopersicum</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	338 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	339 <option value="amphimedon">Amphimedon queenslandica</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	340 <option value="pneumocystis">Pneumocystis jirovecii</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	341 <option value="chicken">Gallus gallus domesticus (chicken)</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	342 <option value="cacao">Theobroma cacao (cacao)</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	343 <option value="heliconius_melpomene1">Heliconius melpomene</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	344 <option value="xenoturbella">Xenoturbella</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	345 <option value="E_coli_K12">E coli K12</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	346 <option value="c_elegans_trsk">c elegans trsk</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	347 <option value="camponotus_floridanus">Camponotus floridanus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	348 <option value="coyote_tobacco">Coyote tobacco</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	349 <option value="s_aureus">Staphylococcus aureus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	350 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	351 <option value="wheat">wheat</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	352 <option value="zebrafish">Danio rerio</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	353 <option value="anidulans">Aspergillus nidulans</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	354 <option value="bombus_impatiens1">Bombus impatiens1</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	355 <option value="bombus_terrestris2">Bombus terrestris2</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	356 <option value="botrytis_cinerea">Botrytis cinerea</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	357 <option value="brugia_malayi">Brugia malayi</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	358 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	359 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	360 <option value="culex_pipiens">Culex pipiens</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	361 <option value="elephant_shark">Callorhinchus milii</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	362 <option value="honeybee1">Apis mellifera</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	363 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	364 <option value="pea_aphid">Acyrthosiphon pisum</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	365 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	366 <option value="ustilago_maydis">Ustilago maydis</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	367 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	368 <option value="verticillium_longisporum1">Verticillium longisporum1</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	369 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	370 <option value="adorsata">adorsata</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	371 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	372 <option value="maker2_athal1">maker2_athal1</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	373 <option value="maker2_c_elegans1">maker2_c_elegans1</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	374 <option value="maker2_dmel1">maker2_dmel1</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	375 <option value="maker2_spomb1">maker2_spomb1</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	376 <option value="parasteatoda">parasteatoda</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	377 <option value="rice">rice</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	378 <option value="schistosoma2">schistosoma2</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	379 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	380 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	381 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	382 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	383 <param name="unmask" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Run ab-initio prediction programs on unmasked sequence" help="Predictors will look for genes in repeated elements (like transposons). Only useful when you believe that transposons might have been integrated into a real gene structure (rare)."/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	384 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	385
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	386 <section name="repeat_masking" title="Repeat masking" expanded="True">
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	387 <conditional name="repeat_source">
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	388 <param label="Repeat library source" name="source_type" type="select">
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	389 <option selected="true" value="repbase">RepBase</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	390 <option value="library">Custom library of repeats</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	391 <option value="no">Disable repeat masking (not recommended)</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	392 </param>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	393 <when value="repbase">
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	394 <param name="repbase_file" type="data" format="embl" label="RepBase (RMRBSeqs.embl) file" />
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	395 <param name="repbase_file_name" type="hidden" value="RMRBSeqs.embl"/> <!-- This is an ugly hack to allow testing with a fake repbase -->
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	396 <conditional name="species_source">
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	397 <param label="Select species name from a list?" name="species_from_list" type="select">
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	398 <option value="yes" selected="true">Yes</option>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	399 <option value="no">No</option>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	400 </param>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	401 <when value="yes">
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	402 <param name="species_list" type="select" label="Species">
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	403 <option value="anopheles" selected="true">anopheles</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	404 <option value="arabidopsis">arabidopsis</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	405 <option value="artiodactyl">artiodactyl</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	406 <option value="aspergillus">aspergillus</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	407 <option value="carnivore">carnivore</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	408 <option value="cat">cat</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	409 <option value="chicken">chicken</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	410 <option value="ciona intestinalis">ciona intestinalis</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	411 <option value="ciona savignyi">ciona savignyi</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	412 <option value="cow">cow</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	413 <option value="danio">danio</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	414 <option value="diatoaea">diatomea</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	415 <option value="dog">dog</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	416 <option value="drosophila">drosophila</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	417 <option value="elegans">elegans</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	418 <option value="fugu">fugu</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	419 <option value="fungi" selected="true">fungi</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	420 <option value="human">human</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	421 <option value="maize">maize</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	422 <option value="mammal">mammal</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	423 <option value="mouse">mouse</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	424 <option value="pig">pig</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	425 <option value="rat">rat</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	426 <option value="rice">rice</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	427 <option value="rodentia">rodentia</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	428 <option value="ruminantia">ruminantia</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	429 <option value="wheat">wheat</option>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	430 </param>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	431 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	432 <when value="no">
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	433 <param name="species_name" type="text" value="homo sapiens" label="Repeat source species" help="Source species (or clade name) used to select repeats from RepBase" />
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	434 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	435 </conditional>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	436 <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	437 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	438 <when value="library">
4 804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	439 <param name="rmlib" type="data" format="fasta" label="Transposable element sequences for RepeatRunner" optional="True" />
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	440 <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" />
4 804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	441 <param name="rm_gff" type="data" format="gff" label="Pre-identified repeat elements from an external GFF file" optional="True" />
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	442 <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	443 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	444 <when value="no"/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	445 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	446 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	447
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	448 <section name="gene_prediction" title="Other predictions" expanded="True">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	449 <param name="pred_gff" type="data" format="gff" label="Predictions from an external GFF3 file" optional="True"/>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	450 <param name="model_gff" type="data" format="gff" label="Annotated gene models from an external GFF3 file" help="annotation pass-through" optional="True"/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	451 <param name="trna" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Find tRNAs with tRNAscan"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	452 <param name="snoscan_rrna" type="data" format="fasta" label="rRNA file to have Snoscan find snoRNAs" optional="True"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	453 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	454
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	455 <section name="advanced" title="Advanced settings" expanded="False">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	456 <param name="other_gff" type="data" format="gff" label="Extra features to pass-through to final Maker generated GFF3 file" optional="True"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	457 <param name="alt_peptide" type="text" value="C" size="1" label="Amino acid used to replace non-standard amino acids in BLAST databases">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	458 <validator type="regex" message="This must be a single uppercase letter">^[A-Z]$</validator>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	459 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	460 <param name="max_dna_len" type="integer" value="100000" label="Length for dividing up contigs into chunks" help="Increases/decreases memory usage"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	461 <param name="min_contig" type="integer" value="1" label="Skip genome contigs below this length" help="Under 10kb are often useless"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	462 <param name="pred_flank" type="integer" value="200" label="Flank for extending evidence clusters sent to gene predictors"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	463 <param name="pred_stats" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Report AED and QI statistics for all predictions as well as models"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	464 <param name="AED_threshold" type="float" min="0" max="1" value="1" label="Maximum Annotation Edit Distance allowed"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	465 <param name="min_protein" type="integer" value="0" label="Require at least this many amino acids in predicted proteins"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	466 <param name="alt_splice" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Take extra steps to try and find alternative splicing" help="Will try to output gene isoforms when detected instead of a single consensus isoform.Use this if you have good EST evidences allowing to detect isoforms."/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	467 <param name="always_complete" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Take extra steps to force the finding of a start and stop codons" help="Only cannonical gene structures will be reported, but it can lead to biologically incorrect seqences."/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	468 <param name="map_forward" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Map names and attributes forward from old GFF3 genes"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	469 <param name="keep_preds" type="float" min="0" max="1" value="0" label="Concordance threshold to add unsupported gene prediction"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	470 <param name="split_hit" type="integer" value="10000" label="length for the splitting of hits" help="Expected max intron size for evidence alignments"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	471 <param name="correct_est_fusion" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Limit use of ESTs in annotation to avoid fusion genes"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	472 <conditional name="single_exon">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	473 <param name="single_exon" type="select" label="Consider single exon EST evidence when generating annotations">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	474 <option value="0" selected="true">No</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	475 <option value="1">Yes</option>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	476 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	477 <when value="0"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	478 <when value="1">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	479 <param name="single_length" type="integer" value="250" label="min length required for single exon ESTs if"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	480 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	481 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	482 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	483 </inputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	484 <outputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	485 <data format="gff3" name="output_gff" label="${tool.name} on ${on_string}: final annotation"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	486 <data format="gff3" name="output_evidences" label="${tool.name} on ${on_string}: evidences"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	487 <data format="gff3" name="output_full" label="${tool.name} on ${on_string}: full gff (evidences + final annotation)"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	488 </outputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	489 <tests>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	490 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	491 <param name="genome" value="genome.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	492 <param name="est_evidences\|est" value="est.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	493 <param name="est_evidences\|est2genome" value="1"/>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	494 <param name="repeat_masking\|repeat_source\|source_type" value="no"/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	495 <output name="output_gff" file="annot.gff3"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	496 <output name="output_evidences" file="evidences.gff3" compare="sim_size"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	497 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	498 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	499 <param name="genome" value="genome.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	500 <param name="organism_type" value="prokaryotic"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	501 <param name="est_evidences\|est" value="est.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	502 <param name="est_evidences\|est2genome" value="1"/>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	503 <param name="repeat_masking\|repeat_source\|source_type" value="no"/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	504 <output name="output_gff" file="annot_proc.gff3"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	505 <output name="output_evidences" file="evidences_proc.gff3" compare="sim_size"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	506 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	507 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	508 <param name="genome" value="genome.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	509 <param name="reannotation\|reannotate" value="yes"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	510 <param name="reannotation\|maker_gff" value="evidences.gff3"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	511 <param name="reannotation\|est_pass" value="true"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	512 <param name="est_evidences\|est2genome" value="1"/>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	513 <param name="repeat_masking\|repeat_source\|source_type" value="no"/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	514 <output name="output_gff" file="annot_reuse.gff3"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	515 <output name="output_evidences" file="evidences_reuse.gff3" compare="sim_size"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	516 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	517 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	518 <param name="genome" value="genome.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	519 <param name="abinitio_gene_prediction\|snaphmm" value="snap.hmm"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	520 <param name="abinitio_gene_prediction\|aug_prediction\|augustus_mode" value="builtin"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	521 <param name="abinitio_gene_prediction\|aug_prediction\|augustus_species" value="human"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	522 <param name="est_evidences\|est" value="est.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	523 <param name="est_evidences\|est2genome" value="1"/>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	524 <param name="repeat_masking\|repeat_source\|source_type" value="no"/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	525 <output name="output_gff" file="annot_human.gff3" compare="sim_size"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	526 <output name="output_evidences" file="evidences_human.gff3" compare="sim_size"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	527 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	528 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	529 <param name="genome" value="genome.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	530 <param name="abinitio_gene_prediction\|snaphmm" value="snap.hmm"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	531 <param name="abinitio_gene_prediction\|aug_prediction\|augustus_mode" value="history"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	532 <param name="abinitio_gene_prediction\|aug_prediction\|augustus_model" value="local.tar.gz" ftype="augustus"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	533 <param name="est_evidences\|est" value="est.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	534 <param name="est_evidences\|est2genome" value="1"/>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	535 <param name="repeat_masking\|repeat_source\|source_type" value="no"/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	536 <output name="output_gff" file="annot_model.gff3" compare="sim_size"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	537 <output name="output_evidences" file="evidences_model.gff3" compare="sim_size"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	538 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	539 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	540 <param name="genome" value="genome.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	541 <param name="est_evidences\|est" value="est.fasta"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	542 <param name="est_evidences\|est2genome" value="1"/>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	543 <param name="repeat_masking\|repeat_source\|source_type" value="no"/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	544 <output name="output_gff" file="annot_norm.gff3"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	545 <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	546 </test>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	547 <test>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	548 <param name="genome" value="genome.fasta"/>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	549 <param name="est_evidences\|est" value="est.fasta"/>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	550 <param name="est_evidences\|est2genome" value="1"/>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	551 <param name="repeat_masking\|repeat_source\|source_type" value="repbase"/>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	552 <param name="repeat_masking\|repeat_source\|repbase_file" value="fake_repbase.embl" />
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	553 <param name="repeat_masking\|repeat_source\|repbase_file_name" value="fake.embl" />
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	554 <param name="repeat_masking\|repeat_source\|species_list" value="anopheles" />
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	555 <output name="output_gff" file="annot_repbase.gff3"/>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	556 <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	557 </test>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	558 </tests>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	559 <help><![CDATA[
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	560 MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	561
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	562 .. _Maker: http://www.yandell-lab.org/software/maker.html
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	563 ]]></help>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	564 <expand macro="citations"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	565 </tool>

Mercurial > repos > iuc > maker

annotate maker.xml @ 4:804af884eef0 draft