ppanggolin_projection: ppanggolin_projection.xml annotate

annotate ppanggolin_projection.xml @ 2:ded401aa8b09 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin commit 29098ae57dcc42db8f9adf321d31ed37fb999d17

author	iuc
date	Mon, 24 Nov 2025 12:56:19 +0000
parents	a87adcb122b4
children

rev	line source
0 a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	1 <tool id="ppanggolin_projection" name="PPanGGOLiN projection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	2 <description>annotates external genomes using an existing pangenome</description>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	3 <macros>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	4 <import>macros.xml</import>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	5 </macros>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	6 <expand macro="xrefs"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	7 <expand macro="requirements"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	8
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	10 #import re
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	11
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	12 mkdir -p ./tmp_ppanggolin/projection &&
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	13 mkdir -p ./tmp_ppanggolin/tmpdir_projection &&
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	14 mkdir -p ./tmp_ppanggolin/organism_list &&
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	15
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	16 @ORGANISM_LIST@
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	17
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	18 ppanggolin projection
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	19 --pangenome '$pangenome_h5'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	20
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	21 #if $extension_input_files == "fasta":
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	22 --fasta
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	23 #elif $extension_input_files == "genbank":
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	24 --anno
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	25 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	26 ./tmp_ppanggolin/organism_list/organism.list
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	27
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	28 --output ./tmp_ppanggolin/projection
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	29 --tmpdir ./tmp_ppanggolin/tmpdir_projection
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	30 --force
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	31 --cpu "\${GALAXY_SLOTS:-4}"
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	32 --disable_prog_bar
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	33
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	34 --coverage $coverage
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	35 --identity $identity
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	36 --table
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	37
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	38 $do_defrag
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	39
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	40 --soft_core $soft_core
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	41
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	42 #if "output_genome_gff" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	43 --gff
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	44 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	45 #if "output_genome_proksee" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	46 --proksee
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	47 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	48
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	49 #for $counter_input_files, $file in enumerate($genomes):
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	50 #set base_name = re.sub('[^\w\-_\.]', '_', str($file.element_identifier))
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	51
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	52 #if "output_gene_to_gene_family" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	53 && mv './tmp_ppanggolin/projection/${base_name}/gene_to_gene_family.tsv' './tmp_ppanggolin/projection/${base_name}_gene_to_gene_family.tsv'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	54 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	55
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	56 #if "output_input_genome_rgp_to_spot" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	57 && mv './tmp_ppanggolin/projection/${base_name}/input_genome_rgp_to_spot.tsv' './tmp_ppanggolin/projection/${base_name}_input_genome_rgp_to_spot.tsv'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	58 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	59
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	60 #if "output_modules_in_input_genome" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	61 && mv './tmp_ppanggolin/projection/${base_name}/modules_in_input_genome.tsv' './tmp_ppanggolin/projection/${base_name}_modules_in_input_genome.tsv'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	62 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	63
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	64 #if "output_genome_gff" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	65 && mv './tmp_ppanggolin/projection/${base_name}/${base_name}.gff' './tmp_ppanggolin/projection/${base_name}_genome_gff.gff'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	66 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	67
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	68 && mv './tmp_ppanggolin/projection/${base_name}/${base_name}.tsv' './tmp_ppanggolin/projection/${base_name}_genome_tsv.tsv'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	69
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	70 #if "output_genome_proksee" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	71 && mv './tmp_ppanggolin/projection/${base_name}/${base_name}_proksee.json' './tmp_ppanggolin/projection/${base_name}_genome_proksee.json'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	72 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	73
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	74 #if "output_projection_summary" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	75 && mv './tmp_ppanggolin/projection/${base_name}/projection_summary.yaml' './tmp_ppanggolin/projection/${base_name}_projection_summary.yaml'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	76 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	77
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	78 #if "output_regions_of_genomic_plasticity" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	79 && mv './tmp_ppanggolin/projection/${base_name}/regions_of_genomic_plasticity.tsv' './tmp_ppanggolin/projection/${base_name}_regions_of_genomic_plasticity.tsv'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	80 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	81
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	82 #if "output_sequences_partition_projection" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	83 && mv './tmp_ppanggolin/projection/${base_name}/sequences_partition_projection.tsv' './tmp_ppanggolin/projection/${base_name}_sequences_partition_projection.tsv'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	84 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	85
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	86 #if "output_specific_genes" in $advanced_pangenome_optional_files:
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	87 && mv './tmp_ppanggolin/projection/${base_name}/specific_genes.tsv' './tmp_ppanggolin/projection/${base_name}_specific_genes.tsv'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	88 #end if
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	89
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	90 #end for
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	91
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	92 && cat './tmp_ppanggolin/projection/summary_projection.tsv' > '${summary_projection}'
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	93
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	94 ]]></command>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	95
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	96 <inputs>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	97
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	98 <expand macro="inputs_pangenome"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	99
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	100 <expand macro="inputs_genomes" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	101
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	102 <expand macro="inputs_identity_coverage_do_defrag"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	103
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	104 <expand macro="inputs_soft_core"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	105
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	106 <param name="advanced_pangenome_optional_files" type="select" label="Add the following output files in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	107 <option value="output_gene_to_gene_family" selected="true">gene_to_gene_family.tsv: provide the mapping of genes to gene families of the pangenome</option>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	108 <option value="output_input_genome_rgp_to_spot" selected="true">input_genome_rgp_to_spot.tsv: provide information about the association between RGPs and insertion spots in the input genome</option>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	109 <option value="output_modules_in_input_genome" selected="true">modules_in_input_genome.tsv: list the modules that have been found in the input genome</option>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	110 <option value="output_genome_gff" selected="true">genome.gff: generate GFF files with projected pangenome annotations for each input genome</option>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	111 <option value="output_genome_proksee" selected="true">genome_proksee.json: Generate JSON map files for PROKSEE with projected pangenome annotations for each input genome ; PROKSEE (https://proksee.ca) is a user friendly interface to visualize your ppanggolin analysed genome as a circular genome plot</option>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	112 <option value="output_projection_summary" selected="true">projection_summary.yaml: provide an overview of the projection in the input genome</option>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	113 <option value="output_regions_of_genomic_plasticity" selected="true">regions_of_genomic_plasticity.tsv: contain information about RGPs within the input genome</option>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	114 <option value="output_sequences_partition_projection" selected="true">sequences_partition_projection.tsv: map the input genes to its partition (Persistent, Shell or Cloud)</option>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	115 <option value="output_specific_genes" selected="true">specific_genes.tsv: list the gene of the input genomes that do not align to any gene of the pangenome. These genes are assigned to Cloud parititon</option>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	116 </param>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	117
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	118 </inputs>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	119
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	120 <outputs>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	121
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	122 <collection name="gene_to_gene_family" type="list" label="PPanGGOLiN projection on ${on_string}: Gene to gene family">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	123 <discover_datasets pattern="(?P<designation>.+)_gene_to_gene_family.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	124 <filter>advanced_pangenome_optional_files and "output_gene_to_gene_family" in advanced_pangenome_optional_files</filter>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	125 </collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	126 <collection name="input_genome_rgp_to_spot" type="list" label="PPanGGOLiN projection on ${on_string}: Input genome rgp to spot">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	127 <discover_datasets pattern="(?P<designation>.+)_input_genome_rgp_to_spot.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	128 <filter>advanced_pangenome_optional_files and "output_input_genome_rgp_to_spot" in advanced_pangenome_optional_files</filter>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	129 </collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	130 <collection name="modules_in_input_genome" type="list" label="PPanGGOLiN projection on ${on_string}: Modules in input genome">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	131 <discover_datasets pattern="(?P<designation>.+)_modules_in_input_genome.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	132 <filter>advanced_pangenome_optional_files and "output_modules_in_input_genome" in advanced_pangenome_optional_files</filter>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	133 </collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	134 <collection name="genome_gff" type="list" label="PPanGGOLiN projection on ${on_string}: Genome gff">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	135 <discover_datasets pattern="(?P<designation>.+)_genome_gff.gff" format="gff" directory="./tmp_ppanggolin/projection"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	136 <filter>advanced_pangenome_optional_files and "output_genome_gff" in advanced_pangenome_optional_files</filter>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	137 </collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	138 <collection name="genome_tsv" type="list" label="PPanGGOLiN projection on ${on_string}: Genome tsv">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	139 <discover_datasets pattern="(?P<designation>.+)_genome_tsv.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	140 </collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	141 <collection name="genome_proksee" type="list" label="PPanGGOLiN projection on ${on_string}: Genome proksee">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	142 <discover_datasets pattern="(?P<designation>.+)_genome_proksee.json" format="json" directory="./tmp_ppanggolin/projection"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	143 <filter>advanced_pangenome_optional_files and "output_genome_proksee" in advanced_pangenome_optional_files</filter>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	144 </collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	145 <collection name="projection_summary" type="list" label="PPanGGOLiN projection on ${on_string}: Genome projection summary">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	146 <discover_datasets pattern="(?P<designation>.+)_projection_summary.yaml" format="yaml" directory="./tmp_ppanggolin/projection"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	147 <filter>advanced_pangenome_optional_files and "output_projection_summary" in advanced_pangenome_optional_files</filter>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	148 </collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	149 <collection name="regions_of_genomic_plasticity" type="list" label="PPanGGOLiN projection on ${on_string}: Regions of genomic plasticity">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	150 <discover_datasets pattern="(?P<designation>.+)_regions_of_genomic_plasticity.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	151 <filter>advanced_pangenome_optional_files and "output_regions_of_genomic_plasticity" in advanced_pangenome_optional_files</filter>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	152 </collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	153 <collection name="sequences_partition_projection" type="list" label="PPanGGOLiN projection on ${on_string}: Sequences partition projection">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	154 <discover_datasets pattern="(?P<designation>.+)_sequences_partition_projection.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	155 <filter>advanced_pangenome_optional_files and "output_sequences_partition_projection" in advanced_pangenome_optional_files</filter>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	156 </collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	157 <collection name="specific_genes" type="list" label="PPanGGOLiN projection on ${on_string}: Specific genes">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	158 <discover_datasets pattern="(?P<designation>.+)_specific_genes.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	159 <filter>advanced_pangenome_optional_files and "output_specific_genes" in advanced_pangenome_optional_files</filter>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	160 </collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	161
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	162 <data name="summary_projection" format="tabular" label="PPanGGOLiN projection on ${on_string}: Global summary projection" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	163
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	164 </outputs>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	165
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	166 <tests>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	167 <test expect_num_outputs="11">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	168 <param name="pangenome_h5" value="h5/test_data.h5" ftype="h5"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	169 <param name="genomes" value="fasta/PROJECT1_984801_1194801.fasta.gz,fasta/PROJECT5_1290693_1440693.fasta.gz,fasta/PROJECT8_1022972_1232972.fasta.gz" ftype="fasta"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	170 <param name="coverage" value="0.8"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	171 <param name="identity" value="0.8"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	172 <param name="soft_core" value="0.95"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	173 <output_collection name="gene_to_gene_family" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	174 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	175 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	176 <has_text text="CDS_0062" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	177 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	178 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	179 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	180 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	181 <has_text text="CDS_0093" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	182 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	183 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	184 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	185 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	186 <has_text text="CDS_0152" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	187 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	188 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	189 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	190 <output_collection name="input_genome_rgp_to_spot" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	191 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	192 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	193 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	194 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	195 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	196 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	197 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	198 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	199 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	200 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	201 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	202 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	203 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	204 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	205 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	206 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	207 <output_collection name="modules_in_input_genome" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	208 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	209 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	210 <has_text text="module_id" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	211 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	212 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	213 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	214 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	215 <has_text text="module_id" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	216 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	217 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	218 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	219 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	220 <has_text text="module_id" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	221 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	222 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	223 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	224 <output_collection name="genome_gff" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	225 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="gff">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	226 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	227 <has_text text="sequence-region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	228 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	229 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	230 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="gff">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	231 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	232 <has_text text="sequence-region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	233 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	234 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	235 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="gff">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	236 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	237 <has_text text="sequence-region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	238 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	239 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	240 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	241 <output_collection name="genome_tsv" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	242 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	243 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	244 <has_text text="gene" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	245 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	246 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	247 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	248 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	249 <has_text text="gene" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	250 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	251 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	252 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	253 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	254 <has_text text="gene" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	255 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	256 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	257 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	258 <output_collection name="genome_proksee" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	259 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="json">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	260 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	261 <has_text text="cgview" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	262 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	263 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	264 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="json">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	265 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	266 <has_text text="cgview" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	267 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	268 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	269 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="json">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	270 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	271 <has_text text="cgview" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	272 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	273 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	274 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	275 <output_collection name="projection_summary" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	276 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="yaml">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	277 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	278 <has_text text="Projection_summary" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	279 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	280 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	281 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="yaml">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	282 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	283 <has_text text="Projection_summary" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	284 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	285 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	286 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="yaml">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	287 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	288 <has_text text="Projection_summary" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	289 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	290 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	291 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	292 <output_collection name="regions_of_genomic_plasticity" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	293 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	294 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	295 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	296 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	297 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	298 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	299 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	300 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	301 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	302 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	303 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	304 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	305 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	306 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	307 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	308 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	309 <output_collection name="sequences_partition_projection" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	310 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	311 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	312 <has_text text="shell" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	313 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	314 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	315 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	316 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	317 <has_text text="shell" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	318 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	319 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	320 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	321 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	322 <has_text text="shell" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	323 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	324 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	325 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	326 <output_collection name="specific_genes" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	327 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	328 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	329 <has_text text="CDS_0112" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	330 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	331 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	332 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	333 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	334 <has_text text="CDS_0137" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	335 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	336 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	337 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	338 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	339 <has_text text="CDS_0017" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	340 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	341 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	342 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	343 <output name="summary_projection" >
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	344 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	345 <has_text text="Genome_name" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	346 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	347 </output>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	348 </test>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	349 <test expect_num_outputs="11">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	350 <param name="pangenome_h5" value="h5/test_data.h5" ftype="h5"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	351 <param name="genomes" value="genbank/PROJECT1_984801_1194801.gb.gz,genbank/PROJECT5_1290693_1440693.gb.gz,genbank/PROJECT8_1022972_1232972.gb.gz" ftype="genbank"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	352 <param name="coverage" value="0.8"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	353 <param name="identity" value="0.8"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	354 <param name="soft_core" value="0.95"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	355 <output_collection name="gene_to_gene_family" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	356 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	357 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	358 <has_text text="TKY121527_11890" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	359 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	360 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	361 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	362 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	363 <has_text text="OTU47_07365" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	364 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	365 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	366 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	367 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	368 <has_text text="ODS73_05675" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	369 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	370 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	371 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	372 <output_collection name="input_genome_rgp_to_spot" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	373 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	374 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	375 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	376 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	377 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	378 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	379 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	380 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	381 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	382 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	383 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	384 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	385 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	386 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	387 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	388 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	389 <output_collection name="modules_in_input_genome" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	390 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	391 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	392 <has_text text="module_id" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	393 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	394 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	395 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	396 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	397 <has_text text="module_id" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	398 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	399 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	400 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	401 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	402 <has_text text="module_id" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	403 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	404 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	405 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	406 <output_collection name="genome_gff" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	407 <element name="PROJECT1_984801_1194801.gb.gz" ftype="gff">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	408 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	409 <has_text text="sequence-region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	410 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	411 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	412 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="gff">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	413 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	414 <has_text text="sequence-region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	415 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	416 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	417 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="gff">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	418 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	419 <has_text text="sequence-region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	420 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	421 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	422 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	423 <output_collection name="genome_tsv" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	424 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	425 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	426 <has_text text="gene" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	427 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	428 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	429 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	430 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	431 <has_text text="gene" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	432 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	433 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	434 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	435 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	436 <has_text text="gene" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	437 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	438 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	439 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	440 <output_collection name="genome_proksee" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	441 <element name="PROJECT1_984801_1194801.gb.gz" ftype="json">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	442 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	443 <has_text text="cgview" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	444 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	445 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	446 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="json">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	447 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	448 <has_text text="cgview" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	449 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	450 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	451 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="json">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	452 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	453 <has_text text="cgview" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	454 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	455 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	456 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	457 <output_collection name="projection_summary" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	458 <element name="PROJECT1_984801_1194801.gb.gz" ftype="yaml">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	459 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	460 <has_text text="Projection_summary" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	461 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	462 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	463 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="yaml">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	464 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	465 <has_text text="Projection_summary" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	466 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	467 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	468 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="yaml">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	469 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	470 <has_text text="Projection_summary" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	471 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	472 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	473 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	474 <output_collection name="regions_of_genomic_plasticity" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	475 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	476 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	477 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	478 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	479 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	480 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	481 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	482 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	483 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	484 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	485 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	486 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	487 <has_text text="region" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	488 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	489 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	490 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	491 <output_collection name="sequences_partition_projection" type="list" count="3">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	492 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	493 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	494 <has_text text="shell" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	495 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	496 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	497 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	498 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	499 <has_text text="shell" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	500 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	501 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	502 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	503 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	504 <has_text text="shell" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	505 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	506 </element>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	507 </output_collection>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	508 <output name="summary_projection" >
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	509 <assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	510 <has_text text="Genome_name" />
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	511 </assert_contents>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	512 </output>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	513 </test>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	514 </tests>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	515
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	516 <help><![CDATA[
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	517
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	518 PPanGGOLiN_ (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either assembled
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	519 genomic DNA sequences or provided genome annotations. PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	520 families in persistent, shell and cloud genomes. It integrates both information on protein-coding genes and their genomic neighborhood to build a graph
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	521 of gene families where each node is a gene family, and each edge is a relation of genetic contiguity.
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	522
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	523 The `ppanggolin projection` command annotates external genomes using an existing pangenome. This process eliminates the need to recompute all components, streamlining the annotation process. Input genomes are expected to belong to the same species.
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	524
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	525 Genes within the input genome are aligned with genes in the pangenome to determine their gene families and partitions. Genes that do not align with any existing gene in the pangenome are considered specific to the input genome and are assigned to the “Cloud” partition. The number of this specific cloud families are detailed in the summary table.
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	526
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	527 Based on the alignment and partition assignment, Regions of Plasticity (RGPs) within the input genome are predicted. Each RGP that is not located on a contig border is assigned to a spot of insertion. Finally, conserved modules of the pangenome found in the input genome are reported in the output files.
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	528
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	529 .. _PPanGGOLiN: https://github.com/labgem/PPanGGOLiN
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	530 .. _documentation: https://ppanggolin.readthedocs.io/en/latest/user/projection.html#projection
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	531
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	532 ]]></help>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	533
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	534 <expand macro="citation"/>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	535
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	536 </tool>
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	537
a87adcb122b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 iuc parents: diff changeset	538

Mercurial > repos > iuc > ppanggolin_projection

annotate ppanggolin_projection.xml @ 2:ded401aa8b09 draft default tip