ppanggolin_projection: ppanggolin_projection.xml annotate

annotate ppanggolin_projection.xml @ 1:03ab6a22d85c 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 12:55:26 +0000
parents	79e2653684f8
children

rev	line source
0 79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	1 <tool id="ppanggolin_projection" name="PPanGGOLiN projection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	2 <description>annotates external genomes using an existing pangenome</description>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	3 <macros>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	4 <import>macros.xml</import>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	5 </macros>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	6 <expand macro="xrefs"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	7 <expand macro="requirements"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	8
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	10 #import re
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	11
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	12 mkdir -p ./tmp_ppanggolin/projection &&
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	13 mkdir -p ./tmp_ppanggolin/tmpdir_projection &&
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	14 mkdir -p ./tmp_ppanggolin/organism_list &&
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	15
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	16 @ORGANISM_LIST@
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	17
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	18 ppanggolin projection
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	19 --pangenome '$pangenome_h5'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	20
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	21 #if $extension_input_files == "fasta":
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	22 --fasta
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	23 #elif $extension_input_files == "genbank":
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	24 --anno
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	25 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	26 ./tmp_ppanggolin/organism_list/organism.list
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	27
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	28 --output ./tmp_ppanggolin/projection
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	29 --tmpdir ./tmp_ppanggolin/tmpdir_projection
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	30 --force
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	31 --cpu "\${GALAXY_SLOTS:-4}"
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	32 --disable_prog_bar
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	33
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	34 --coverage $coverage
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	35 --identity $identity
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	36 --table
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	37
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	38 $do_defrag
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	39
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	40 --soft_core $soft_core
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	41
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	42 #if "output_genome_gff" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	43 --gff
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	44 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	45 #if "output_genome_proksee" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	46 --proksee
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	47 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	48
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	49 #for $counter_input_files, $file in enumerate($genomes):
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	50 #set base_name = re.sub('[^\w\-_\.]', '_', str($file.element_identifier))
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	51
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	52 #if "output_gene_to_gene_family" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	53 && mv './tmp_ppanggolin/projection/${base_name}/gene_to_gene_family.tsv' './tmp_ppanggolin/projection/${base_name}_gene_to_gene_family.tsv'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	54 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	55
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	56 #if "output_input_genome_rgp_to_spot" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	57 && mv './tmp_ppanggolin/projection/${base_name}/input_genome_rgp_to_spot.tsv' './tmp_ppanggolin/projection/${base_name}_input_genome_rgp_to_spot.tsv'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	58 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	59
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	60 #if "output_modules_in_input_genome" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	61 && mv './tmp_ppanggolin/projection/${base_name}/modules_in_input_genome.tsv' './tmp_ppanggolin/projection/${base_name}_modules_in_input_genome.tsv'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	62 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	63
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	64 #if "output_genome_gff" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	65 && mv './tmp_ppanggolin/projection/${base_name}/${base_name}.gff' './tmp_ppanggolin/projection/${base_name}_genome_gff.gff'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	66 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	67
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	68 && mv './tmp_ppanggolin/projection/${base_name}/${base_name}.tsv' './tmp_ppanggolin/projection/${base_name}_genome_tsv.tsv'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	69
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	70 #if "output_genome_proksee" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	71 && mv './tmp_ppanggolin/projection/${base_name}/${base_name}_proksee.json' './tmp_ppanggolin/projection/${base_name}_genome_proksee.json'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	72 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	73
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	74 #if "output_projection_summary" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	75 && mv './tmp_ppanggolin/projection/${base_name}/projection_summary.yaml' './tmp_ppanggolin/projection/${base_name}_projection_summary.yaml'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	76 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	77
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	78 #if "output_regions_of_genomic_plasticity" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	79 && mv './tmp_ppanggolin/projection/${base_name}/regions_of_genomic_plasticity.tsv' './tmp_ppanggolin/projection/${base_name}_regions_of_genomic_plasticity.tsv'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	80 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	81
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	82 #if "output_sequences_partition_projection" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	83 && mv './tmp_ppanggolin/projection/${base_name}/sequences_partition_projection.tsv' './tmp_ppanggolin/projection/${base_name}_sequences_partition_projection.tsv'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	84 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	85
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	86 #if "output_specific_genes" in $advanced_pangenome_optional_files:
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	87 && mv './tmp_ppanggolin/projection/${base_name}/specific_genes.tsv' './tmp_ppanggolin/projection/${base_name}_specific_genes.tsv'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	88 #end if
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	89
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	90 #end for
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	91
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	92 && cat './tmp_ppanggolin/projection/summary_projection.tsv' > '${summary_projection}'
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	93
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	94 ]]></command>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	95
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	96 <inputs>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	97
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	98 <expand macro="inputs_pangenome"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	99
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	100 <expand macro="inputs_genomes" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	101
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	102 <expand macro="inputs_identity_coverage_do_defrag"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	103
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	104 <expand macro="inputs_soft_core"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	105
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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" >
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	116 </param>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	117
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	118 </inputs>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	119
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	120 <outputs>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	121
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	122 <collection name="gene_to_gene_family" type="list" label="PPanGGOLiN projection on ${on_string}: Gene to gene family">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	123 <discover_datasets pattern="(?P<designation>.+)_gene_to_gene_family.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	124 <filter>advanced_pangenome_optional_files and "output_gene_to_gene_family" in advanced_pangenome_optional_files</filter>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	125 </collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	127 <discover_datasets pattern="(?P<designation>.+)_input_genome_rgp_to_spot.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	128 <filter>advanced_pangenome_optional_files and "output_input_genome_rgp_to_spot" in advanced_pangenome_optional_files</filter>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	129 </collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	130 <collection name="modules_in_input_genome" type="list" label="PPanGGOLiN projection on ${on_string}: Modules in input genome">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	131 <discover_datasets pattern="(?P<designation>.+)_modules_in_input_genome.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	132 <filter>advanced_pangenome_optional_files and "output_modules_in_input_genome" in advanced_pangenome_optional_files</filter>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	133 </collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	134 <collection name="genome_gff" type="list" label="PPanGGOLiN projection on ${on_string}: Genome gff">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	135 <discover_datasets pattern="(?P<designation>.+)_genome_gff.gff" format="gff" directory="./tmp_ppanggolin/projection"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	136 <filter>advanced_pangenome_optional_files and "output_genome_gff" in advanced_pangenome_optional_files</filter>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	137 </collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	138 <collection name="genome_tsv" type="list" label="PPanGGOLiN projection on ${on_string}: Genome tsv">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	139 <discover_datasets pattern="(?P<designation>.+)_genome_tsv.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	140 </collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	141 <collection name="genome_proksee" type="list" label="PPanGGOLiN projection on ${on_string}: Genome proksee">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	142 <discover_datasets pattern="(?P<designation>.+)_genome_proksee.json" format="json" directory="./tmp_ppanggolin/projection"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	143 <filter>advanced_pangenome_optional_files and "output_genome_proksee" in advanced_pangenome_optional_files</filter>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	144 </collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	145 <collection name="projection_summary" type="list" label="PPanGGOLiN projection on ${on_string}: Genome projection summary">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	146 <discover_datasets pattern="(?P<designation>.+)_projection_summary.yaml" format="yaml" directory="./tmp_ppanggolin/projection"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	147 <filter>advanced_pangenome_optional_files and "output_projection_summary" in advanced_pangenome_optional_files</filter>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	148 </collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	149 <collection name="regions_of_genomic_plasticity" type="list" label="PPanGGOLiN projection on ${on_string}: Regions of genomic plasticity">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	150 <discover_datasets pattern="(?P<designation>.+)_regions_of_genomic_plasticity.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	151 <filter>advanced_pangenome_optional_files and "output_regions_of_genomic_plasticity" in advanced_pangenome_optional_files</filter>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	152 </collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	153 <collection name="sequences_partition_projection" type="list" label="PPanGGOLiN projection on ${on_string}: Sequences partition projection">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	154 <discover_datasets pattern="(?P<designation>.+)_sequences_partition_projection.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	155 <filter>advanced_pangenome_optional_files and "output_sequences_partition_projection" in advanced_pangenome_optional_files</filter>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	156 </collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	157 <collection name="specific_genes" type="list" label="PPanGGOLiN projection on ${on_string}: Specific genes">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	158 <discover_datasets pattern="(?P<designation>.+)_specific_genes.tsv" format="tabular" directory="./tmp_ppanggolin/projection"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	159 <filter>advanced_pangenome_optional_files and "output_specific_genes" in advanced_pangenome_optional_files</filter>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	160 </collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	161
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	162 <data name="summary_projection" format="tabular" label="PPanGGOLiN projection on ${on_string}: Global summary projection" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	163
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	164 </outputs>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	165
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	166 <tests>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	167 <test expect_num_outputs="11">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	168 <param name="pangenome_h5" value="h5/test_data.h5" ftype="h5"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	170 <param name="coverage" value="0.8"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	171 <param name="identity" value="0.8"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	172 <param name="soft_core" value="0.95"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	173 <output_collection name="gene_to_gene_family" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	174 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	175 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	176 <has_text text="CDS_0062" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	177 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	178 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	179 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	180 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	181 <has_text text="CDS_0093" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	182 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	183 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	184 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	185 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	186 <has_text text="CDS_0152" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	187 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	188 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	189 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	190 <output_collection name="input_genome_rgp_to_spot" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	191 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	192 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	193 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	194 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	195 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	196 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	197 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	198 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	199 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	200 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	201 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	202 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	203 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	204 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	205 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	206 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	207 <output_collection name="modules_in_input_genome" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	208 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	209 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	210 <has_text text="module_id" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	211 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	212 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	213 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	214 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	215 <has_text text="module_id" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	216 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	217 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	218 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	219 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	220 <has_text text="module_id" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	221 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	222 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	223 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	224 <output_collection name="genome_gff" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	225 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="gff">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	226 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	227 <has_text text="sequence-region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	228 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	229 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	230 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="gff">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	231 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	232 <has_text text="sequence-region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	233 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	234 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	235 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="gff">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	236 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	237 <has_text text="sequence-region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	238 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	239 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	240 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	241 <output_collection name="genome_tsv" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	242 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	243 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	244 <has_text text="gene" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	245 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	246 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	247 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	248 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	249 <has_text text="gene" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	250 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	251 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	252 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	253 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	254 <has_text text="gene" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	255 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	256 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	257 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	258 <output_collection name="genome_proksee" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	259 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="json">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	260 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	261 <has_text text="cgview" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	262 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	263 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	264 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="json">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	265 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	266 <has_text text="cgview" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	267 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	268 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	269 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="json">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	270 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	271 <has_text text="cgview" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	272 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	273 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	274 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	275 <output_collection name="projection_summary" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	276 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="yaml">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	277 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	278 <has_text text="Projection_summary" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	279 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	280 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	281 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="yaml">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	282 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	283 <has_text text="Projection_summary" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	284 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	285 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	286 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="yaml">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	287 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	288 <has_text text="Projection_summary" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	289 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	290 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	291 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	292 <output_collection name="regions_of_genomic_plasticity" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	293 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	294 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	295 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	296 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	297 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	298 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	299 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	300 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	301 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	302 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	303 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	304 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	305 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	306 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	307 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	308 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	309 <output_collection name="sequences_partition_projection" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	310 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	311 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	312 <has_text text="shell" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	313 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	314 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	315 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	316 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	317 <has_text text="shell" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	318 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	319 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	320 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	321 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	322 <has_text text="shell" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	323 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	324 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	325 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	326 <output_collection name="specific_genes" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	327 <element name="PROJECT1_984801_1194801.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	328 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	329 <has_text text="CDS_0112" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	330 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	331 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	332 <element name="PROJECT5_1290693_1440693.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	333 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	334 <has_text text="CDS_0137" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	335 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	336 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	337 <element name="PROJECT8_1022972_1232972.fasta.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	338 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	339 <has_text text="CDS_0017" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	340 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	341 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	342 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	343 <output name="summary_projection" >
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	344 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	345 <has_text text="Genome_name" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	346 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	347 </output>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	348 </test>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	349 <test expect_num_outputs="11">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	350 <param name="pangenome_h5" value="h5/test_data.h5" ftype="h5"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	352 <param name="coverage" value="0.8"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	353 <param name="identity" value="0.8"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	354 <param name="soft_core" value="0.95"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	355 <output_collection name="gene_to_gene_family" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	356 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	357 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	358 <has_text text="TKY121527_11890" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	359 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	360 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	361 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	362 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	363 <has_text text="OTU47_07365" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	364 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	365 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	366 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	367 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	368 <has_text text="ODS73_05675" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	369 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	370 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	371 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	372 <output_collection name="input_genome_rgp_to_spot" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	373 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	374 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	375 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	376 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	377 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	378 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	379 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	380 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	381 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	382 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	383 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	384 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	385 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	386 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	387 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	388 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	389 <output_collection name="modules_in_input_genome" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	390 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	391 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	392 <has_text text="module_id" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	393 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	394 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	395 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	396 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	397 <has_text text="module_id" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	398 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	399 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	400 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	401 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	402 <has_text text="module_id" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	403 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	404 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	405 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	406 <output_collection name="genome_gff" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	407 <element name="PROJECT1_984801_1194801.gb.gz" ftype="gff">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	408 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	409 <has_text text="sequence-region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	410 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	411 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	412 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="gff">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	413 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	414 <has_text text="sequence-region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	415 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	416 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	417 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="gff">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	418 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	419 <has_text text="sequence-region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	420 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	421 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	422 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	423 <output_collection name="genome_tsv" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	424 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	425 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	426 <has_text text="gene" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	427 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	428 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	429 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	430 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	431 <has_text text="gene" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	432 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	433 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	434 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	435 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	436 <has_text text="gene" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	437 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	438 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	439 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	440 <output_collection name="genome_proksee" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	441 <element name="PROJECT1_984801_1194801.gb.gz" ftype="json">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	442 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	443 <has_text text="cgview" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	444 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	445 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	446 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="json">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	447 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	448 <has_text text="cgview" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	449 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	450 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	451 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="json">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	452 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	453 <has_text text="cgview" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	454 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	455 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	456 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	457 <output_collection name="projection_summary" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	458 <element name="PROJECT1_984801_1194801.gb.gz" ftype="yaml">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	459 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	460 <has_text text="Projection_summary" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	461 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	462 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	463 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="yaml">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	464 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	465 <has_text text="Projection_summary" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	466 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	467 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	468 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="yaml">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	469 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	470 <has_text text="Projection_summary" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	471 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	472 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	473 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	474 <output_collection name="regions_of_genomic_plasticity" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	475 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	476 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	477 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	478 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	479 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	480 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	481 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	482 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	483 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	484 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	485 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	486 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	487 <has_text text="region" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	488 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	489 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	490 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	491 <output_collection name="sequences_partition_projection" type="list" count="3">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	492 <element name="PROJECT1_984801_1194801.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	493 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	494 <has_text text="shell" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	495 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	496 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	497 <element name="PROJECT5_1290693_1440693.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	498 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	499 <has_text text="shell" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	500 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	501 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	502 <element name="PROJECT8_1022972_1232972.gb.gz" ftype="tabular">
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	503 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	504 <has_text text="shell" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	505 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	506 </element>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	507 </output_collection>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	508 <output name="summary_projection" >
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	509 <assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	510 <has_text text="Genome_name" />
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	511 </assert_contents>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	512 </output>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	513 </test>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	514 </tests>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	515
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	516 <help><![CDATA[
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	517
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	521 of gene families where each node is a gene family, and each edge is a relation of genetic contiguity.
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	522
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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.
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	524
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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.
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	526
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 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.
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	528
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	529 .. _PPanGGOLiN: https://github.com/labgem/PPanGGOLiN
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	530 .. _documentation: https://ppanggolin.readthedocs.io/en/latest/user/projection.html#projection
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	531
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	532 ]]></help>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	533
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	534 <expand macro="citation"/>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	535
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	536 </tool>
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	537
79e2653684f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247 iuc parents: diff changeset	538

Mercurial > repos > iuc > ppanggolin_projection

annotate ppanggolin_projection.xml @ 1:03ab6a22d85c draft default tip