maker: maker.xml annotate

annotate maker.xml @ 8:d3b3de98c481 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 90ae29b39b58999e45a8f4e0bfbabc5a59047ba1"

author	iuc
date	Mon, 28 Jun 2021 09:38:50 +0000
parents	10e2edf1e1fb
children	388d33fce1b9

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"?>
7 10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	2 <tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy@SUFFIX_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[
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	9 RM_PATH=\$(which RepeatMasker) &&
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	10 if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	11
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	12 LIBDIR=\$(dirname "\$RM_PATH")/../share/RepeatMasker/Libraries &&
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	13 #if $repeat_masking.repeat_source.source_type == "dfam_up":
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	14 mkdir lib/ &&
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	15 ln -s '${repeat_masking.repeat_source.dfam_lib}' lib/RepeatMaskerLib.h5 &&
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	16 LIBDIR=\$(pwd)/lib &&
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	17 #end if
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	18
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	19 export LIBDIR &&
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	20
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	21 maker -CTL
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
2 be967733bf81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088 iuc parents: 1 diff changeset	25 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	26
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	27 &&
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 #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'history'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	30
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	31 ## Using an augustus model from history, we need to unzip it and let augustus find it
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	32
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	33 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	34
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	35 mkdir -p 'augustus_dir/species/' &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	36
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	37 tar -C 'augustus_dir/species/' -xzvf '${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	38
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	39 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	40 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	41
6 b7ad44afd7b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 6ba137e32243a6de1fb83a7d4b88f9283db5dd01" iuc parents: 5 diff changeset	42 MPI_CMD="" &&
b7ad44afd7b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 6ba137e32243a6de1fb83a7d4b88f9283db5dd01" iuc parents: 5 diff changeset	43 if [ "\$MAKER_MPI" == "1" ]; then
b7ad44afd7b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 6ba137e32243a6de1fb83a7d4b88f9283db5dd01" iuc parents: 5 diff changeset	44 MPI_CMD="mpiexec -n \${GALAXY_SLOTS:-4}";
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	45 fi &&
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	46
7 10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	47 \${MPI_CMD} maker --ignore_nfs_tmp $advanced.fix_nucleotides maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	48
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	49 &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	50
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	51 gff3_merge -d .maker.output/_master_datastore_index.log -o '${output_full}'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	52
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	53 &&
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	54
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	55 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	56
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	57 &&
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 awk '{if ($2 != "maker") {print}}' '${output_full}' \| sed -n '/^\#\#FASTA\$/q;p' > '${output_evidences}'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	60 ]]></command>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	61 <configfiles>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	62 <!-- Maker doesn't like indentation in its config file... -->
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	63 <configfile name="ctl"><![CDATA[
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	64 #-----Genome (these are always required)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	65 genome=${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	66 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	67
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	68 #-----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	69 #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	70 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=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	72 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	73 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	74 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	75 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	76 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	77 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	78 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	79 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	80 est_pass=${reannotation.est_pass} # use ESTs in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	81 altest_pass=${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	82 protein_pass=${reannotation.protein_pass} # use protein alignments in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	83 rm_pass=${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	84 model_pass=${reannotation.model_pass} # use gene models in maker_gff: 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	85 pred_pass=${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	86 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	87 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	88
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	89 #-----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	90 #if $est_evidences.est
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	91 est=${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	92 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	93 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	94 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	95 #if $est_evidences.altest
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	96 altest=${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	97 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	98 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	99 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	100 #if $est_evidences.est_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	101 est_gff=${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	102 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	103 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	104 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	105 #if $est_evidences.altest_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	106 altest_gff=${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	107 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	108 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	109 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	110
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	111 #-----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	112 #if $protein_evidences.protein
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	113 protein=${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	114 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	115 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	116 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	117 #if $protein_evidences.protein_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	118 protein_gff=${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	119 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	120 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	121 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	122
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	123 #-----Repeat Masking (leave values blank to skip repeat masking)
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	124 #if $repeat_masking.repeat_source.source_type == 'dfam'
1 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 #if $repeat_masking.repeat_source.species_source.species_from_list == 'yes'
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	127 model_org=${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	128 #else
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	129 model_org=${repeat_masking.repeat_source.species_source.species_name}
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	130 #end if
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	131
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	132 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	133 softmask=${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	134
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	135 #else if $repeat_masking.repeat_source.source_type == 'dfam_up'
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	136 model_org=${repeat_masking.repeat_source.species_name}
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	137 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	138 softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	139
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	140 #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	141 model_org= # select a model organism for RepBase masking in RepeatMasker
4 804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	142 #if $repeat_masking.repeat_source.rmlib
804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	143 rmlib=${repeat_masking.repeat_source.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	144 #else
804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	145 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	146 #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	147
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	148 #if $repeat_masking.repeat_source.repeat_protein
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	149 repeat_protein=${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	150 #else
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	151 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	152 #end if
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	153 #if $repeat_masking.repeat_source.rm_gff
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	154 rm_gff=${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	155 #else
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	156 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	157 #end if
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	158
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	159 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	160
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	161 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	162 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	163 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	164 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	165 #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	166
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	167 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	168
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	169 #-----Gene Prediction
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	170 #if $abinitio_gene_prediction.snaphmm
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	171 snaphmm=${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	172 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	173 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	174 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	175 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	176 #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'builtin'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	177 augustus_species=${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	178 #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	179 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	180 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	181 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	182 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	183 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	184 #if $gene_prediction.pred_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	185 pred_gff=${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	186 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	187 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	188 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	189 #if $gene_prediction.model_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	190 model_gff=${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	191 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	192 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	193 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	194 est2genome=${est_evidences.est2genome} # infer gene predictions directly from ESTs, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	195 protein2genome=${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	196 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	197 #if $gene_prediction.snoscan_rrna
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	198 snoscan_rrna=${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	199 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	200 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	201 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	202 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	203
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	204 #-----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	205 #if $advanced.other_gff
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	206 other_gff=${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	207 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	208 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	209 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	210
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	211 #-----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	212 alt_peptide=${advanced.alt_peptide} # amino acid used to replace non-standard amino acids in BLAST databases
2 be967733bf81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088 iuc parents: 1 diff changeset	213 cpus=1 # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	214
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	215 #-----MAKER Behavior Options
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	216 max_dna_len=${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	217 min_contig=${advanced.min_contig} # skip genome contigs below this length (under 10kb are often useless)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	218
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	219 pred_flank=${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	220 pred_stats=${advanced.pred_stats} # report AED and QI statistics for all predictions as well as models
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	221 AED_threshold=${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	222 min_protein=${advanced.min_protein} # require at least this many amino acids in predicted proteins
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	223 alt_splice=${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	224 always_complete=${advanced.always_complete} # extra steps to force start and stop codons, 1 = yes, 0 = no
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	225 map_forward=${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	226 keep_preds=${advanced.keep_preds} # Concordance threshold to add unsupported gene prediction (bound by 0 and 1)
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	227
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	228 split_hit=${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	229 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	230 #if $advanced.single_exon.single_exon == '1'
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	231 single_length=${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	232 #else
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	233 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	234 #end if
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	235 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	236
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	237 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	238 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	239 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	240 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	241 ]]></configfile>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	242 </configfiles>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	243
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	244 <inputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	245 <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	246 <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	247 <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	248 <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	249 </param>
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 <conditional name="reannotation">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	252 <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	253 <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	254 <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	255 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	256 <when value="no"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	257 <when value="yes">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	267 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	268
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	269 <section name="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	270 <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	271 <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	272 <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	273 <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	274 <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	275 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	276
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	277 <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	278 <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	279 <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	280 <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	281 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	282
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	283 <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	284 <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	285
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	286 <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	287 <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	288 <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	289 <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	290 <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	291 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	292 <when value="no"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	293 <when value="history">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	294 <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	295 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	296 <when value="builtin">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	297 <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	298 <!-- 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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 <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	335 <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	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <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	345 <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	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 <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	373 <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	374 <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	375 <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	376 <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	377 <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	378 <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	379 <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	380 <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	381 <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	382 <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	383 <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	384 <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	385 <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	386 <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	387 <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	388 <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	389 <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	390 <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	391 <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	392 <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	393 <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	394 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	395 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	396 </conditional>
8 d3b3de98c481 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 90ae29b39b58999e45a8f4e0bfbabc5a59047ba1" iuc parents: 7 diff changeset	397 <param name="unmask" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Run ab-initio prediction programs on both masked and unmasked sequence regions" help="Predictors will look for genes in both masked or unmasked sequence regions (instead of only unmasked). Only useful when you believe that transposons might have been integrated into a real gene structure (rare)."/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	398 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	399
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	400 <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	401 <conditional name="repeat_source">
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	402 <param label="Repeat library source" name="source_type" type="select" help="To use RepBase, choose 'Custom library of repeats' and select a fasta version of this non-free database.">
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	403 <option selected="true" value="dfam">DFam (curated only, bundled with RepeatMasker)</option>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	404 <option value="dfam_up">DFam (full/specific version)</option>
1 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="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	406 <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	407 </param>
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	408 <when value="dfam">
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	409 <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	410 <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	411 <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	412 <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	413 </param>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	414 <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	415 <param name="species_list" type="select" label="Species">
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	416 <option value="vertebrate">Vertebrate (other than below)</option>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	417 <option value="mammal">Mammal (other than below)</option>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	418 <option value="human" selected="true">Human</option>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	419 <option value="rodent">Rodent</option>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	420 <option value="mouse">Mouse</option>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	421 <option value="rat">Rat</option>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	422 <option value="danio">Danio (zebra fish)</option>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	423 <option value="drosophila">Fruit fly (Drosophila melanogaster)</option>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	424 <option value="elegans">Caenorhabditis elegans (nematode)</option>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	425 </param>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	426 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	427 <when value="no">
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	428 <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" />
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	429 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	430 </conditional>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	431 <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	432 </when>
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	433 <when value="dfam_up">
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	434 <param name="dfam_lib" type="data" format="h5" label="DFam library" help="The full DFam library can be downloaded from https://www.dfam.org/releases/current/families/Dfam.h5.gz" />
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	435 <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" />
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	436 <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	437 </when>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	438 <when value="library">
4 804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	439 <param name="rmlib" type="data" format="fasta" label="Transposable element sequences for RepeatRunner" optional="True" />
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	440 <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" />
4 804af884eef0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	441 <param name="rm_gff" type="data" format="gff" label="Pre-identified repeat elements from an external GFF file" optional="True" />
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	442 <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	443 </when>
c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	444 <when value="no"/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	445 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	446 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	447
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	448 <section name="gene_prediction" title="Other predictions" expanded="True">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	449 <param name="pred_gff" type="data" format="gff" label="Predictions from an external GFF3 file" optional="True"/>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	450 <param name="model_gff" type="data" format="gff" label="Annotated gene models from an external GFF3 file" help="annotation pass-through" optional="True"/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	451 <param name="trna" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Find tRNAs with tRNAscan"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	452 <param name="snoscan_rrna" type="data" format="fasta" label="rRNA file to have Snoscan find snoRNAs" optional="True"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	453 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	454
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	455 <section name="advanced" title="Advanced settings" expanded="False">
7 10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	456 <param name="fix_nucleotides" argument="-fix_nucleotides" type="boolean" truevalue="-fix_nucleotides" falsevalue="" checked="false" label="Fix nucleotides" help="This will replace non-IUPAC characters with 'N's."/>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	457 <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	458 <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	459 <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	460 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	461 <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	462 <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	463 <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	464 <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	465 <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	466 <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	467 <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	468 <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	469 <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	470 <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	471 <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	472 <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	473 <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	474 <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	475 <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	476 <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	477 </param>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	478 <when value="0"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	479 <when value="1">
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	480 <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	481 </when>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	482 </conditional>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	483 </section>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	484 </inputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	485 <outputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	486 <data format="gff3" name="output_gff" label="${tool.name} on ${on_string}: final annotation"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	487 <data format="gff3" name="output_evidences" label="${tool.name} on ${on_string}: evidences"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	488 <data format="gff3" name="output_full" label="${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	489 </outputs>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	490 <tests>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	491 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	492 <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	493 <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	494 <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	495 <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	496 <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	497 <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	498 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	499 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	500 <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	501 <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	502 <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	503 <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	504 <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	505 <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	506 <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	507 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	508 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	509 <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	510 <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	511 <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	512 <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	513 <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	514 <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	515 <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	516 <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	517 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	518 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	519 <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	520 <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	521 <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	522 <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	523 <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	524 <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	525 <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	526 <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	527 <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	528 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	529 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	530 <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	531 <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	532 <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	533 <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	534 <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	535 <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	536 <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	537 <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	538 <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	539 </test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	540 <test>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	541 <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	542 <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	543 <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	544 <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	545 <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	546 <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	547 </test>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	548 <test>
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="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	550 <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	551 <param name="est_evidences\|est2genome" value="1"/>
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	552 <param name="repeat_masking\|repeat_source\|source_type" value="dfam"/>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	553 <param name="repeat_masking\|repeat_source\|species_list" value="drosophila" />
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	554 <output name="output_gff" file="annot_dfam.gff3"/>
1 c98b3fa910bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	555 <output name="output_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	556 </test>
5 e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	557 <test>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	558 <param name="genome" value="genome.fasta"/>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	559 <param name="est_evidences\|est" value="est.fasta"/>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	560 <param name="est_evidences\|est2genome" value="1"/>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	561 <param name="repeat_masking\|repeat_source\|source_type" value="dfam_up"/>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	562 <param name="repeat_masking\|repeat_source\|dfam_lib" value="Dfam_partial_test.h5" ftype="h5" />
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	563 <param name="repeat_masking\|repeat_source\|species_name" value="rodent" />
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	564 <output name="output_gff" file="annot_dfam_up.gff3"/>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	565 <output name="output_evidences" file="evidences_norm_dfam_up.gff3" compare="sim_size"/>
e06aa22b2e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	566 </test>
7 10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	567 <test>
10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	568 <param name="genome" value="genome.fasta"/>
10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	569 <param name="est_evidences\|est" value="non_IUPAC.fasta"/>
10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	570 <param name="est_evidences\|est2genome" value="1"/>
10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	571 <param name="repeat_masking\|repeat_source\|source_type" value="no"/>
10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	572 <param name="advanced\|fix_nucleotides" value="true"/>
10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	573 <output name="output_gff" file="annot_fix_nucleotides.gff3"/>
10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	574 <output name="output_evidences" file="evidences_fix_nucletides.gff3" compare="sim_size"/>
10e2edf1e1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	575 </test>
0 0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	576 </tests>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	577 <help><![CDATA[
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	578 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	579
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	580 .. _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	581 ]]></help>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	582 <expand macro="citations"/>
0cb75547ecc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	583 </tool>

Mercurial > repos > iuc > maker

annotate maker.xml @ 8:d3b3de98c481 draft