maker: maker.xml annotate

annotate maker.xml @ 8:3c1a01127868 draft

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

author	iuc
date	Mon, 28 Jun 2021 09:40:12 +0000
parents	7bac6f5fcfa2
children	a444254e9a57

rev	line source
0 16e44ec438c4 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 7bac6f5fcfa2 "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 16e44ec438c4 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>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	4 <macros>
16e44ec438c4 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>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	6 </macros>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	7 <expand macro="requirements"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	8 <command><![CDATA[
5 5201ec38c01f "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) &&
5201ec38c01f "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 &&
5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	11
5201ec38c01f "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 &&
5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	13 #if $repeat_masking.repeat_source.source_type == "dfam_up":
5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	14 mkdir lib/ &&
5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	15 ln -s '${repeat_masking.repeat_source.dfam_lib}' lib/RepeatMaskerLib.h5 &&
5201ec38c01f "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 73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	17 #end if
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	18
5 5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	19 export LIBDIR &&
5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	20
0 16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	21 maker -CTL
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	22
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	23 &&
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	24
2 d3a2072d8745 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 16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	26
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	27 &&
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	28
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	29 #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'history'
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	30
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	31 ## Using an augustus model from history, we need to unzip it and let augustus find it
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	32
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	33 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	34
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	35 mkdir -p 'augustus_dir/species/' &&
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	36
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	37 tar -C 'augustus_dir/species/' -xzvf '${abinitio_gene_prediction.aug_prediction.augustus_model}' > /dev/null &&
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	38
16e44ec438c4 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/ &&
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	40 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	41
6 d46d803ca6cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 6ba137e32243a6de1fb83a7d4b88f9283db5dd01" iuc parents: 5 diff changeset	42 MPI_CMD="" &&
d46d803ca6cc "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
d46d803ca6cc "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 5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	45 fi &&
5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	46
7 7bac6f5fcfa2 "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 $advanced.fix_nucleotides maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
0 16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	48
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	49 &&
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	50
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	51 gff3_merge -d .maker.output/_master_datastore_index.log -o '${output_full}'
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	52
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	53 &&
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	54
16e44ec438c4 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}'
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	56
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	57 &&
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	58
16e44ec438c4 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' > '${output_evidences}'
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	60 ]]></command>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	61 <configfiles>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	62 <!-- Maker doesn't like indentation in its config file... -->
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	63 <configfile name="ctl"><![CDATA[
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	64 #-----Genome (these are always required)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	65 genome=${genome} # genome sequence (fasta file or fasta embeded in GFF3 file)
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	67
16e44ec438c4 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
16e44ec438c4 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'
16e44ec438c4 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
16e44ec438c4 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
16e44ec438c4 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
16e44ec438c4 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
16e44ec438c4 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
16e44ec438c4 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
16e44ec438c4 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
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	78 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	80 est_pass=${reannotation.est_pass} # use ESTs in maker_gff: 1 = yes, 0 = no
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	81 altest_pass=${reannotation.altest_pass} # use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	82 protein_pass=${reannotation.protein_pass} # use protein alignments in maker_gff: 1 = yes, 0 = no
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	83 rm_pass=${reannotation.rm_pass} # use repeats in maker_gff: 1 = yes, 0 = no
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	84 model_pass=${reannotation.model_pass} # use gene models in maker_gff: 1 = yes, 0 = no
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	85 pred_pass=${reannotation.pred_pass} # use ab-initio predictions in maker_gff: 1 = yes, 0 = no
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	87 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	88
16e44ec438c4 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)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	90 #if $est_evidences.est
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	91 est=${est_evidences.est} # set of ESTs or assembled mRNA-seq in fasta format
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	92 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	94 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	95 #if $est_evidences.altest
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	96 altest=${est_evidences.altest} # EST/cDNA sequence file in fasta format from an alternate organism
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	97 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	99 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	100 #if $est_evidences.est_gff
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	101 est_gff=${est_evidences.est_gff} # aligned ESTs or mRNA-seq from an external GFF3 file
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	102 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	104 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	105 #if $est_evidences.altest_gff
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	106 altest_gff=${est_evidences.altest_gff} # aligned ESTs from a closly relate species in GFF3 format
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	107 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	109 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	110
16e44ec438c4 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)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	112 #if $protein_evidences.protein
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	113 protein=${protein_evidences.protein} # protein sequence file in fasta format (i.e. from mutiple oransisms)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	114 #else
16e44ec438c4 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)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	116 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	117 #if $protein_evidences.protein_gff
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	118 protein_gff=${protein_evidences.protein_gff} # aligned protein homology evidence from an external GFF3 file
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	119 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	121 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	122
16e44ec438c4 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 5201ec38c01f "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 73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	125
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	126 #if $repeat_masking.repeat_source.species_source.species_from_list == 'yes'
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	127 model_org=${repeat_masking.repeat_source.species_source.species_list}
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	128 #else
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	129 model_org=${repeat_masking.repeat_source.species_source.species_name}
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	130 #end if
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	131
0 16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	132 rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
1 73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	133 softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	134
5 5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	135 #else if $repeat_masking.repeat_source.source_type == 'dfam_up'
5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	136 model_org=${repeat_masking.repeat_source.species_name}
5201ec38c01f "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
5201ec38c01f "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)
5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	139
1 73a79dec987b 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 16e44ec438c4 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 5e96efe6e6c6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	142 #if $repeat_masking.repeat_source.rmlib
5e96efe6e6c6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	143 rmlib=${repeat_masking.repeat_source.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
5e96efe6e6c6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b" iuc parents: 3 diff changeset	144 #else
5e96efe6e6c6 "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
5e96efe6e6c6 "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 73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	147
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	148 #if $repeat_masking.repeat_source.repeat_protein
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	149 repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	150 #else
73a79dec987b 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
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	152 #end if
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	153 #if $repeat_masking.repeat_source.rm_gff
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	154 rm_gff=${repeat_masking.repeat_source.rm_gff} # pre-identified repeat elements from an external GFF3 file
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	155 #else
73a79dec987b 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
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	157 #end if
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	158
73a79dec987b 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)
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	160
0 16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	161 #else
16e44ec438c4 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
16e44ec438c4 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 73a79dec987b 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 16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	165 #end if
1 73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	166
0 16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	168
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	169 #-----Gene Prediction
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	170 #if $abinitio_gene_prediction.snaphmm
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	171 snaphmm=${abinitio_gene_prediction.snaphmm} # SNAP HMM file
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	172 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	174 #end if
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	176 #if $abinitio_gene_prediction.aug_prediction.augustus_mode == 'builtin'
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	177 augustus_species=${abinitio_gene_prediction.aug_prediction.augustus_species} # Augustus gene prediction species model
16e44ec438c4 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'
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	180 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	182 #end if
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	184 #if $gene_prediction.pred_gff
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	185 pred_gff=${gene_prediction.pred_gff} # ab-initio predictions from an external GFF3 file
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	186 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	188 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	189 #if $gene_prediction.model_gff
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	190 model_gff=${gene_prediction.model_gff} # annotated gene models from an external GFF3 file (annotation pass-through)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	191 #else
16e44ec438c4 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)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	193 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	194 est2genome=${est_evidences.est2genome} # infer gene predictions directly from ESTs, 1 = yes, 0 = no
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	195 protein2genome=${protein_evidences.protein2genome} # infer predictions from protein homology, 1 = yes, 0 = no
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	197 #if $gene_prediction.snoscan_rrna
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	198 snoscan_rrna=${gene_prediction.snoscan_rrna} # rRNA file to have Snoscan find snoRNAs
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	199 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	201 #end if
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	203
16e44ec438c4 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)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	205 #if $advanced.other_gff
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	206 other_gff=${advanced.other_gff} # extra features to pass-through to final MAKER generated GFF3 file
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	207 #else
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	209 #end if
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	210
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	212 alt_peptide=${advanced.alt_peptide} # amino acid used to replace non-standard amino acids in BLAST databases
2 d3a2072d8745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 4141a68e0ce1cf6a24f721dce31b81b56f249088 iuc parents: 1 diff changeset	213 cpus=1 # max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)
0 16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	214
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	215 #-----MAKER Behavior Options
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	216 max_dna_len=${advanced.max_dna_len} # length for dividing up contigs into chunks (increases/decreases memory usage)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	217 min_contig=${advanced.min_contig} # skip genome contigs below this length (under 10kb are often useless)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	218
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	219 pred_flank=${advanced.pred_flank} # flank for extending evidence clusters sent to gene predictors
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	220 pred_stats=${advanced.pred_stats} # report AED and QI statistics for all predictions as well as models
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	221 AED_threshold=${advanced.AED_threshold} # Maximum Annotation Edit Distance allowed (bound by 0 and 1)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	222 min_protein=${advanced.min_protein} # require at least this many amino acids in predicted proteins
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	223 alt_splice=${advanced.alt_splice} # Take extra steps to try and find alternative splicing, 1 = yes, 0 = no
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	224 always_complete=${advanced.always_complete} # extra steps to force start and stop codons, 1 = yes, 0 = no
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	225 map_forward=${advanced.map_forward} # map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	226 keep_preds=${advanced.keep_preds} # Concordance threshold to add unsupported gene prediction (bound by 0 and 1)
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	227
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	228 split_hit=${advanced.split_hit} # length for the splitting of hits (expected max intron size for evidence alignments)
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	230 #if $advanced.single_exon.single_exon == '1'
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	231 single_length=${advanced.single_length} # min length required for single exon ESTs if 'single_exon is enabled'
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	232 #else
16e44ec438c4 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'
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	234 #end if
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	236
16e44ec438c4 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
16e44ec438c4 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
16e44ec438c4 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
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	241 ]]></configfile>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	242 </configfiles>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	243
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	244 <inputs>
16e44ec438c4 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"/>
16e44ec438c4 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">
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	249 </param>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	250
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	251 <conditional name="reannotation">
16e44ec438c4 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">
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	255 </param>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	256 <when value="no"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	257 <when value="yes">
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	266 </when>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	267 </conditional>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	268
16e44ec438c4 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">
16e44ec438c4 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."/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	275 </section>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	276
16e44ec438c4 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">
16e44ec438c4 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."/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	281 </section>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	282
16e44ec438c4 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">
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	285
16e44ec438c4 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">
16e44ec438c4 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">
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	291 </param>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	292 <when value="no"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	293 <when value="history">
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	295 </when>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	296 <when value="builtin">
16e44ec438c4 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">
16e44ec438c4 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) -->
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	394 </param>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	395 </when>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	396 </conditional>
8 3c1a01127868 "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 16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	398 </section>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	399
16e44ec438c4 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 73a79dec987b 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 5201ec38c01f "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.">
5201ec38c01f "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>
5201ec38c01f "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 73a79dec987b 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>
73a79dec987b 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>
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	407 </param>
5 5201ec38c01f "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 73a79dec987b 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">
73a79dec987b 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">
73a79dec987b 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 16e44ec438c4 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 73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	413 </param>
73a79dec987b 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">
73a79dec987b 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 5201ec38c01f "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>
5201ec38c01f "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>
5201ec38c01f "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>
5201ec38c01f "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>
5201ec38c01f "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>
5201ec38c01f "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>
5201ec38c01f "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>
5201ec38c01f "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>
5201ec38c01f "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 73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	425 </param>
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	426 </when>
73a79dec987b 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 5201ec38c01f "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 73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	429 </when>
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	430 </conditional>
73a79dec987b 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"/>
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	432 </when>
5 5201ec38c01f "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">
5201ec38c01f "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" />
5201ec38c01f "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" />
5201ec38c01f "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"/>
5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	437 </when>
1 73a79dec987b 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 5e96efe6e6c6 "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 73a79dec987b 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 5e96efe6e6c6 "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 73a79dec987b 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"/>
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	443 </when>
73a79dec987b 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 16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	445 </conditional>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	446 </section>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	447
16e44ec438c4 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">
16e44ec438c4 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 73a79dec987b 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 16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	453 </section>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	454
16e44ec438c4 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 7bac6f5fcfa2 "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 16e44ec438c4 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"/>
16e44ec438c4 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">
16e44ec438c4 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>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	460 </param>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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."/>
16e44ec438c4 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."/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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">
16e44ec438c4 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">
16e44ec438c4 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>
16e44ec438c4 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>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	477 </param>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	478 <when value="0"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	479 <when value="1">
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	481 </when>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	482 </conditional>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	483 </section>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	484 </inputs>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	485 <outputs>
16e44ec438c4 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 ${on_string}: final annotation"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	487 <data format="gff3" name="output_evidences" label="${tool.name} on ${on_string}: evidences"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	488 <data format="gff3" name="output_full" label="${tool.name} on ${on_string}: full gff (evidences + final annotation)"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	489 </outputs>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	490 <tests>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	491 <test>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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 73a79dec987b 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 16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	498 </test>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	499 <test>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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 73a79dec987b 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 16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	507 </test>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	508 <test>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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 73a79dec987b 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 16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	517 </test>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	518 <test>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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 73a79dec987b 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 16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	528 </test>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	529 <test>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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 73a79dec987b 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 16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	539 </test>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	540 <test>
16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 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 73a79dec987b 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 16e44ec438c4 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"/>
16e44ec438c4 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"/>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	547 </test>
1 73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	548 <test>
73a79dec987b 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"/>
73a79dec987b 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"/>
73a79dec987b 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 5201ec38c01f "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"/>
5201ec38c01f "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" />
5201ec38c01f "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 73a79dec987b 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"/>
73a79dec987b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 iuc parents: 0 diff changeset	556 </test>
5 5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	557 <test>
5201ec38c01f "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"/>
5201ec38c01f "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"/>
5201ec38c01f "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"/>
5201ec38c01f "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"/>
5201ec38c01f "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" />
5201ec38c01f "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" />
5201ec38c01f "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"/>
5201ec38c01f "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"/>
5201ec38c01f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715" iuc parents: 4 diff changeset	566 </test>
7 7bac6f5fcfa2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	567 <test>
7bac6f5fcfa2 "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"/>
7bac6f5fcfa2 "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"/>
7bac6f5fcfa2 "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"/>
7bac6f5fcfa2 "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"/>
7bac6f5fcfa2 "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"/>
7bac6f5fcfa2 "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"/>
7bac6f5fcfa2 "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"/>
7bac6f5fcfa2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9" iuc parents: 6 diff changeset	575 </test>
0 16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	576 </tests>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	577 <help><![CDATA[
16e44ec438c4 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.
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	579
16e44ec438c4 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
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	581 ]]></help>
16e44ec438c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e iuc parents: diff changeset	582 <expand macro="citations"/>
16e44ec438c4 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 @ 8:3c1a01127868 draft