maker: maker.xml annotate

annotate maker.xml @ 2:be967733bf81 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088

author	iuc
date	Fri, 03 May 2019 07:49:50 -0400
parents	c98b3fa910bf
children	681e5067048e

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"?>
2 be967733bf81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088 iuc parents: 1 diff changeset	2 <tool id="maker" name="Maker" profile="16.04" version="@VERSION@">
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
2 be967733bf81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088 iuc parents: 1 diff changeset	38 mpiexec -n \${GALAXY_SLOTS:-4} maker 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 $repeat_masking.repeat_source.source_type == 'library'
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	127 model_org= # select a model organism for RepBase masking in RepeatMasker
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	128 rmlib=${repeat_masking.repeat_source.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	129
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	130 #if $repeat_masking.repeat_source.repeat_protein
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	131 repeat_protein=${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	132 #else
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	133 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	134 #end if
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	135 #if $repeat_masking.repeat_source.rm_gff
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	136 rm_gff=${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	137 #else
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	138 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	139 #end if
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	140
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	141 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	142
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	143 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	144 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	145 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	146 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	147 #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	148
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	149 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	150
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	151 #-----Gene Prediction
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	152 #if $abinitio_gene_prediction.snaphmm
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	153 snaphmm=${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	154 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	155 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	156 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	157 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	158 #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'builtin'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	159 augustus_species=${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	160 #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	161 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	162 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	163 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 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	165 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	166 #if $gene_prediction.pred_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	167 pred_gff=${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	168 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	169 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	170 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	171 #if $gene_prediction.model_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	172 model_gff=${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	173 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	174 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	175 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	176 est2genome=${est_evidences.est2genome} # infer gene predictions directly from ESTs, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	177 protein2genome=${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	178 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	179 #if $gene_prediction.snoscan_rrna
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	180 snoscan_rrna=${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	181 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	182 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	183 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	184 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	185
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	186 #-----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	187 #if $advanced.other_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	188 other_gff=${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	189 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	190 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	191 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	192
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	193 #-----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	194 alt_peptide=${advanced.alt_peptide} # amino acid used to replace non-standard amino acids in BLAST databases
2 be967733bf81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088 iuc parents: 1 diff changeset	195 cpus=1 # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	196
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	197 #-----MAKER Behavior Options
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	198 max_dna_len=${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	199 min_contig=${advanced.min_contig} # skip genome contigs below this length (under 10kb are often useless)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	200
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	201 pred_flank=${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	202 pred_stats=${advanced.pred_stats} # report AED and QI statistics for all predictions as well as models
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	203 AED_threshold=${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	204 min_protein=${advanced.min_protein} # require at least this many amino acids in predicted proteins
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	205 alt_splice=${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	206 always_complete=${advanced.always_complete} # extra steps to force start and stop codons, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	207 map_forward=${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	208 keep_preds=${advanced.keep_preds} # Concordance threshold to add unsupported gene prediction (bound by 0 and 1)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	209
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	210 split_hit=${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	211 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	212 #if $advanced.single_exon.single_exon == '1'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	213 single_length=${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	214 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	215 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	216 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	217 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	218
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	219 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	220 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	221 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	222 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	223 ]]></configfile>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	224 </configfiles>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	225
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	226 <inputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	227 <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	228 <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	229 <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	230 <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	231 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	232
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	233 <conditional name="reannotation">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	234 <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	235 <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	236 <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	237 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	238 <when value="no"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	239 <when value="yes">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	240 <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	241 <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	242 <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	243 <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	244 <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	245 <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	246 <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	247 <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	248 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	249 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	250
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	251 <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	252 <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	253 <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	254 <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	255 <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	256 <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	257 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	258
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	259 <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	260 <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	261 <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	262 <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	263 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	264
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	265 <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	266 <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	267
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	268 <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	269 <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	270 <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	271 <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	272 <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	273 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	274 <when value="no"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	275 <when value="history">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	276 <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	277 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	278 <when value="builtin">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	279 <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	280 <!-- 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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 <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	335 <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	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <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	345 <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	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 <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	373 <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	374 <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	375 <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	376 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	377 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	378 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	379 <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	380 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	381
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	382 <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	383 <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	384 <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	385 <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	386 <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	387 <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	388 </param>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	389 <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	390 <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	391 <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	392 <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	393 <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	394 <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	395 <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	396 </param>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	397 <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	398 <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	399 <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	400 <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	401 <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	402 <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	403 <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	404 <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	405 <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	406 <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	407 <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	408 <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	409 <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	410 <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	411 <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	412 <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	413 <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	414 <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	415 <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	416 <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	417 <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	418 <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	419 <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	420 <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	421 <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	422 <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	423 <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	424 <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	425 <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	426 </param>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	427 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	428 <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	429 <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	430 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	431 </conditional>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	432 <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	433 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	434 <when value="library">
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	435 <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" />
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="rm_gff" type="data" format="fasta" label="Pre-identified repeat elements from an external GFF file" optional="True" />
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	437 <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	438 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	439 <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	440 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	441 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	442
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	443 <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	444 <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	445 <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	446 <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	447 <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	448 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	449
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	450 <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	451 <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	452 <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	453 <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	454 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	455 <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	456 <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	457 <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	458 <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	459 <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	460 <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	461 <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	462 <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	463 <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	464 <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	465 <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	466 <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	467 <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	468 <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	469 <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	470 <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	471 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	472 <when value="0"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	473 <when value="1">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	474 <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	475 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	476 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	477 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	478 </inputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	479 <outputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	480 <data format="gff3" name="output_gff" label="${tool.name} on ${on_string}: final annotation"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	481 <data format="gff3" name="output_evidences" label="${tool.name} on ${on_string}: evidences"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	482 <data format="gff3" name="output_full" label="${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	483 </outputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	484 <tests>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	485 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	486 <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	487 <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	488 <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	489 <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	490 <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	491 <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	492 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	493 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	494 <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	495 <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	496 <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	497 <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	498 <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	499 <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	500 <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	501 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	502 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	503 <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	504 <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	505 <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	506 <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	507 <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	508 <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	509 <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	510 <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	511 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	512 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	513 <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	514 <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	515 <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	516 <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	517 <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	518 <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	519 <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	520 <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	521 <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	522 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	523 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	524 <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	525 <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	526 <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	527 <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	528 <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	529 <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	530 <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	531 <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	532 <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	533 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	534 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	535 <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	536 <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	537 <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	538 <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	539 <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	540 <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	541 </test>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	542 <test>
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="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	544 <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	545 <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	546 <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	547 <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	548 <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	549 <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	550 <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	551 <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	552 </test>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	553 </tests>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	554 <help><![CDATA[
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	555 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	556
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	557 .. _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	558 ]]></help>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	559 <expand macro="citations"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	560 </tool>

Mercurial > repos > iuc > maker

annotate maker.xml @ 2:be967733bf81 draft