humann2: humann2.xml annotate

annotate humann2.xml @ 4:019864881779 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 52d835f027b052a0a887be14a55faf9fa9e456ae"

author	iuc
date	Mon, 01 Feb 2021 18:17:35 +0000
parents	b168c0ef3c14
children	bb13650e8115

rev	line source
4 019864881779 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 52d835f027b052a0a887be14a55faf9fa9e456ae" iuc parents: 3 diff changeset	1 <tool id="humann2" name="HUMAnN2" version="@WRAPPER_VERSION@.1">
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	2 <description>to profile presence/absence and abundance of microbial pathways and gene families</description>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	3 <macros>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	4 <import>humann2_macros.xml</import>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	5 </macros>
4 019864881779 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 52d835f027b052a0a887be14a55faf9fa9e456ae" iuc parents: 3 diff changeset	6 <stdio>
019864881779 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 52d835f027b052a0a887be14a55faf9fa9e456ae" iuc parents: 3 diff changeset	7 <regex match="Failed to allocate sufficient memory." source="stderr" level="fatal_oom" description="Out of memory error occurred" />
019864881779 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 52d835f027b052a0a887be14a55faf9fa9e456ae" iuc parents: 3 diff changeset	8 </stdio>
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	9 <expand macro="requirements">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	10 <requirement type="package" version="2.3.0">bowtie2</requirement>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	11 <requirement type="package" version="2.6.0">metaphlan2</requirement>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	12 <requirement type="package" version="0.8.24">diamond</requirement>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	13 <requirement type="package" version="2.24">rapsearch</requirement>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	14 <requirement type="package" version="2.7.10">python</requirement>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	15 </expand>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	16 <expand macro="version"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	17 <command detect_errors="exit_code"><![CDATA[
1 1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	18 #if $nucleotide_db.nucleotide_db_selector == "history"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	19 mkdir nucleotide_db
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	20 &&
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	21 #for $file in $nucleotide_db.nucleotide_database:
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	22 cp '$file' 'nucleotide_db/$file.name' &&
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	23 #end for
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	24 #end if
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	25
1 1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	26 #if $protein_db.protein_db_selector == "history"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	27 mkdir protein_db
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	28 &&
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	29 #if $translated_alignment == "diamond"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	30 diamond makedb
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	31 --in '$protein_db.protein_database'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	32 --db 'protein_db/protein_db'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	33 --threads "\${GALAXY_SLOTS:-4}"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	34 #else
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	35 prerapsearch
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	36 -d '$protein_db.protein_database'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	37 -n 'protein_db/protein_db'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	38 #end if
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	39 &&
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	40 #end if
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	41
1 1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	42 #if $taxo_profile.taxonomic_profile_test == "false"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	43 #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	44 mkdir ref_db
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	45 &&
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	46 bowtie2-build '$taxo_profile.metaphlan2_db_choice.bowtie2db' 'ref_db/ref_db'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	47 &&
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	48 python '$__tool_directory__/transform_json_to_pkl.py'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	49 --json_input '$taxo_profile.metaphlan2_db_choice.mpa_pkl'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	50 --pkl_output 'ref_db/metadata.pkl'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	51 &&
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	52 #end if
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	53 #end if
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	54
1 1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	55 humann2
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	56 --input '$input'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	57 -o 'output'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	58 $bypass.bypass_prescreen
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	59 $bypass.bypass_nucleotide_index
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	60 $bypass.bypass_translated_search
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	61 $bypass.bypass_nucleotide_search
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	62
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	63 #set $metaphlan_option = "-t rel_ab"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	64 #if $taxo_profile.taxonomic_profile_test == "true":
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	65 --taxonomic-profile '$taxo_profile.taxonomic_profile'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	66 #else
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	67 #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	68 #set $metaphlan_option += " --bowtie2db " + 'ref_db/ref_db'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	69 #set $metaphlan_option += " --mpa_pkl " + 'ref_db/metadata.pkl'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	70 #else
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	71 #set $path = $taxo_profile.metaphlan2_db_choice.cached_db.fields.path
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	72 #set $value = $taxo_profile.metaphlan2_db_choice.cached_db.fields.value
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	73 #set $metaphlan_option += " --bowtie2db " + $path + "/" + $value
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	74 #set $metaphlan_option += " --mpa_pkl " + $path + "/" + $value + ".pkl"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	75 #end if
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	76 #end if
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	77 --metaphlan-options="$metaphlan_option"
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	78
1 1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	79 #if $nucleotide_db.nucleotide_db_selector == "cached"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	80 --nucleotide-database '$nucleotide_db.nucleotide_database.fields.path'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	81 #else
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	82 --nucleotide-database nucleotide_db
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	83 #end if
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	84
1 1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	85 --translated-alignment '$translated_alignment'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	86 #if $protein_db.protein_db_selector == "cached"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	87 --protein-database '$protein_db.protein_database.fields.path'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	88 #else
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	89 --protein-database protein_db
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	90 #end if
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	91 --search-mode '$search_mode'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	92 --pathways '$pathways'
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	93
1 1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	94 --annotation-gene-index $adv.annotation_gene_index
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	95 --evalue '$adv.evalue'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	96 --threads "\${GALAXY_SLOTS:-4}"
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	97 --memory-use minimum
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	98 --prescreen-threshold '$adv.prescreen_threshold'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	99 --identity-threshold '$adv.identity_threshold'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	100 --translated-subject-coverage-threshold '$adv.translated_subject_coverage_threshold'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	101 --translated-query-coverage-threshold '$adv.translated_query_coverage_threshold'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	102 #if $adv.id_mapping
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	103 --id-mapping '$adv.id_mapping'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	104 #end if
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	105 --xipe '$adv.xipe'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	106 --minpath '$adv.minpath'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	107 --pick-frames '$adv.pick_frames'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	108 --gap-fill '$adv.gap_fill'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	109 --output-format '$adv.output_format'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	110 --output-max-decimals '$adv.output_max_dec'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	111 --output-basename 'humann2'
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	112 $adv.remove_statified_output
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	113 $adv.remove_column_description_output
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	114 ]]></command>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	115 <inputs>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	116 <param argument="--input" type="data" format="fastq,fasta,sam,bam,biom1" label="Input sequence file"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	117 <section name="bypass" title="Options to bypass some steps" expanded="False">
1 1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	118 <param name="bypass_prescreen" argument="--bypass-prescreen" type="boolean" truevalue="--bypass-prescreen" falsevalue="" checked="false" label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/>
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	119 <param name="bypass_nucleotide_index" argument="--bypass-nucleotide-index" type="boolean" truevalue="--bypass-nucleotide-index" falsevalue="" checked="false" label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/>
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	120 <param name="bypass_translated_search" argument="--bypass-translated-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the translated search step?"/>
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	121 <param name="bypass_nucleotide_search" argument="--bypass-nucleotide-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the nucleotide search steps?"/>
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	122 </section>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	123 <conditional name="taxo_profile">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	124 <param name="taxonomic_profile_test" type="select" label="Use a custom taxonomic profile?" help="The file must have been created by MetaPhlan2">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	125 <option value="true">Yes</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	126 <option value="false" selected="true">No</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	127 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	128 <when value="true">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	129 <param name="taxonomic_profile" argument="--taxonomic-profile" type="data" format="tabular,txt" label="Taxonomic profile file"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	130 </when>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	131 <when value="false">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	132 <conditional name="metaphlan2_db_choice">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	133 <param name="metaphlan2_db_selector" type="select" label="Database with clade-specific marker genes">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	134 <option value="cached" selected="true">Default MetaPhlAn2 database</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	135 <option value="history">From history</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	136 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	137 <when value="cached">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	138 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	139 <options from_data_table="metaphlan2_database" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	140 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	141 </when>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	142 <when value="history">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	143 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	144 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	145 </when>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	146 </conditional>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	147 </when>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	148 </conditional>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	149 <conditional name="nucleotide_db">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	150 <param name="nucleotide_db_selector" type="select" label="Nucleotide database" help="For locally cached databases, you need first to execute the tool to download HUMAnN2 databases">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	151 <option value="cached" selected="true">Locally cached</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	152 <option value="history">From history (as collection)</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	153 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	154 <when value="cached">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	155 <param name="nucleotide_database" type="select" label="Nucleotide database">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	156 <options from_data_table="humann2_nucleotide_database"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	157 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	158 </when>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	159 <when value="history">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	160 <param format="fasta" name="nucleotide_database" argument="--nucleotide-database" type="data_collection" collection_type="list" label="Nucleotide database from history" help="Each file must be named: ^[g__].[s__]"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	161 </when>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	162 </conditional>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	163 <param name="translated_alignment" argument="--translated-alignment" type="select" label="Software to use for translated alignment">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	164 <option value="rapsearch">Rapsearch</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	165 <option value="diamond" selected="true">Diamond</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	166 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	167 <conditional name="protein_db">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	168 <param name="protein_db_selector" type="select" label="Protein database" help="For locally cached databases, you need first to execute the tool to download HUMAnN2 databases">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	169 <option value="cached" selected="true">Locally cached</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	170 <option value="history">From history</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	171 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	172 <when value="cached">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	173 <param name="protein_database" type="select" label="Protein database">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	174 <options from_data_table="humann2_protein_database"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	175 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	176 </when>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	177 <when value="history">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	178 <param name="protein_database" argument="--protein-database" type="data" format="fasta" label="Protein database from history"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	179 </when>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	180 </conditional>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	181 <param name="search_mode" argument="--search-mode" type="select" label="Search for uniref50 or uniref90 gene families?">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	182 <option value="uniref50" selected="true">uniref50</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	183 <option value="uniref90">uniref90</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	184 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	185 <param name="pathways" type="select" label="Database to use for pathway computations" help="(--pathways)">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	186 <option value="metacyc" selected="true">MetaCyc</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	187 <option value="unipathway">UniPathway</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	188 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	189
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	190 <section name="adv" title="Advanced Options" expanded="False">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	191 <param name="annotation_gene_index" argument="--annotation-gene-index" type="integer" value="8" label="Index of the gene in the sequence annotation"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	192 <param argument="--evalue" type="float" value="1" label="E-value threshold to use with the translated search"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	193 <param name="prescreen_threshold" argument="--prescreen-threshold" type="float" value="0.01" label="Minimum percentage of reads matching a species"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	194 <param name="identity_threshold" argument="--identity-threshold" type="float" value="50" label="Identity threshold for alignments"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	195 <param name="translated_subject_coverage_threshold" argument="--translated-subject-coverage-threshold" type="float" value="50" label="Subject coverage threshold for translated alignments"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	196 <param name="translated_query_coverage_threshold" argument="--translated-query-coverage-threshold" type="float" value="50" label="Subject coverage threshold for translated alignments"/>
1 1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	197 <param name="id_mapping" argument="--id-mapping" type="data" format="tsv" optional="true" label="id mapping file for alignments"/>
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	198 <param argument="--xipe" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Use xipe computation?"/>
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	199 <param argument="--minpath" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use minpath computation?"/>
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	200 <param name="pick_frames" argument="--pick-frames" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use pick frames computation?"/>
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	201 <param name="gap_fill" argument="--gap-fill" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use gap fill computation?"/>
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	202 <param name="output_format" argument="--output-format" type="select" label="Format of the output files">
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	203 <option value="tsv" selected="true">TSV</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	204 <option value="biom">BIOM</option>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	205 </param>
1 1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	206 <param name="output_max_dec" argument="--output-max-decimals" type="integer" value="10" label="Number of decimals to output"/>
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	207 <param name="remove_statified_output" argument="--remove-stratified-output" type="boolean" truevalue="--remove-stratified-output" falsevalue="" checked="false" label="Remove stratification from output?"/>
1d6d855c10d8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee iuc parents: 0 diff changeset	208 <param name="remove_column_description_output" argument="--remove-column-description-output" type="boolean" truevalue="--remove-column-description-output" falsevalue="" checked="false" label="Remove stratification from output?"/>
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	209
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	210 </section>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	211 </inputs>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	212 <outputs>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	213 <data format="tsv" name="gene_families_tsv" from_work_dir="output/humann2_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	214 <filter>adv['output_format'] == "tsv"</filter>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	215 </data>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	216 <data format="biom1" name="gene_families_biom" from_work_dir="output/humann2_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" >
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	217 <filter>adv['output_format'] == "biom"</filter>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	218 </data>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	219 <data format="tsv" name="pathcoverage_tsv" from_work_dir="output/humann2_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" >
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	220 <filter>adv['output_format'] == "tsv"</filter>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	221 </data>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	222 <data format="biom1" name="pathcoverage_biom" from_work_dir="output/humann2_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage" >
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	223 <filter>adv['output_format'] == "biom"</filter>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	224 </data>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	225 <data format="tsv" name="pathabundance_tsv" from_work_dir="output/humann2_pathabundance.tsv" label="${tool.name} on ${on_string}: Pathways and their abundance" >
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	226 <filter>adv['output_format'] == "tsv"</filter>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	227 </data>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	228 <data format="biom1" name="pathabundance_biom" from_work_dir="output/humann2_pathabundance.biom" label="${tool.name} on ${on_string}: Pathways and their abundance" >
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	229 <filter>adv['output_format'] == "biom"</filter>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	230 </data>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	231 </outputs>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	232 <tests>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	233 <test>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	234 <param name="input" value="input_sequences.fasta"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	235 <param name="bypass_prescreen" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	236 <param name="bypass_nucleotide_index" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	237 <param name="bypass_translated_search" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	238 <param name="bypass_nucleotide_search" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	239 <param name="nucleotide_db_selector" value="history"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	240 <param name="nucleotide_database">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	241 <collection type="list">
3 b168c0ef3c14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 18fea370966f4b87c8180df4afa0f3b138b75908" iuc parents: 1 diff changeset	242 <element name="g__Bacteroides.s__Bacteroides_stercoris.centroids.v0.1.1" ftype="fasta.gz" value="g__Bacteroides.s__Bacteroides_stercoris.centroids.v0.1.1.ffn.gz" />
b168c0ef3c14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 18fea370966f4b87c8180df4afa0f3b138b75908" iuc parents: 1 diff changeset	243 <element name="g__Bacteroides.s__Bacteroides_thetaiotaomicron.centroids.v0.1.1" ftype="fasta.gz" value="g__Bacteroides.s__Bacteroides_thetaiotaomicron.centroids.v0.1.1.ffn.gz" />
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	244 </collection>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	245 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	246 <param name="annotation_gene_index" value="8" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	247 <param name="protein_db_selector" value="history"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	248 <param name="protein_database" value="reduced_uniref50.fasta"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	249 <param name="evalue" value="1"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	250 <param name="search_mode" value="uniref50"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	251 <param name="prescreen_threshold" value="0.01"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	252 <param name="identity_threshold" value="50"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	253 <param name="translated_subject_coverage_threshold" value="50"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	254 <param name="translated_query_coverage_threshold" value="50"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	255 <param name="taxonomic_profile_test" value="true"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	256 <param name="taxonomic_profile" value="taxonomic_profile.tabular"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	257 <param name="translated_alignment" value="diamond"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	258 <param name="xipe" value="off"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	259 <param name="minpath" value="on"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	260 <param name="pick_frames" value="on"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	261 <param name="gap_fill" value="off"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	262 <param name="output_format" value="tsv"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	263 <param name="output_max_dec" value="10"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	264 <param name="remove_statified_output" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	265 <param name="remove_column_description_output" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	266 <param name="pathways" value="metacyc"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	267 <output name="gene_families_tsv">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	268 <assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	269 <has_text text="UniRef50_R5C4D7\|g__Bacteroides.s__Bacteroides_thetaiotaomicron" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	270 <has_text text="UniRef50_R5NYX5: Sodium ion-translocating decarboxylase beta subunit\|g__Bacteroides.s__Bacteroides_thetaiotaomicron" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	271 <has_text text="UniRef50_A0A016FAQ7: N-6 DNA Methylase family protein (Fragment)\|g__Bacteroides.s__Bacteroides_stercoris"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	272 </assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	273 </output>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	274 <output name="pathcoverage_tsv">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	275 <assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	276 <has_text text="UNMAPPED" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	277 <has_text text="UNINTEGRATED" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	278 </assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	279 </output>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	280 <output name="pathabundance_tsv">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	281 <assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	282 <has_text text="UNMAPPED" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	283 <has_text text="UNINTEGRATED" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	284 </assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	285 </output>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	286 </test>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	287 <test>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	288 <param name="input" value="input_sequences.fasta"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	289 <param name="bypass_prescreen" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	290 <param name="bypass_nucleotide_index" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	291 <param name="bypass_translated_search" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	292 <param name="bypass_nucleotide_search" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	293 <param name="nucleotide_db_selector" value="history"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	294 <param name="nucleotide_database">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	295 <collection type="list">
3 b168c0ef3c14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 18fea370966f4b87c8180df4afa0f3b138b75908" iuc parents: 1 diff changeset	296 <element name="g__Bacteroides.s__Bacteroides_stercoris.centroids.v0.1.1" ftype="fasta.gz" value="g__Bacteroides.s__Bacteroides_stercoris.centroids.v0.1.1.ffn.gz" />
b168c0ef3c14 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 18fea370966f4b87c8180df4afa0f3b138b75908" iuc parents: 1 diff changeset	297 <element name="g__Bacteroides.s__Bacteroides_thetaiotaomicron.centroids.v0.1.1" ftype="fasta.gz" value="g__Bacteroides.s__Bacteroides_thetaiotaomicron.centroids.v0.1.1.ffn.gz" />
0 1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	298 </collection>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	299 </param>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	300 <param name="annotation_gene_index" value="8" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	301 <param name="protein_db_selector" value="history"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	302 <param name="protein_database" value="reduced_uniref50.fasta"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	303 <param name="evalue" value="1"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	304 <param name="search_mode" value="uniref90"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	305 <param name="prescreen_threshold" value="0.01"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	306 <param name="identity_threshold" value="50"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	307 <param name="translated_subject_coverage_threshold" value="50"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	308 <param name="translated_query_coverage_threshold" value="50"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	309 <param name="taxonomic_profile_test" value="false"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	310 <param name="metaphlan2_db_selector" value="history"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	311 <param name="bowtie2db" value="marker_sequences.fasta"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	312 <param name="mpa_pkl" value="marker_metadata.json"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	313 <param name="translated_alignment" value="rapsearch"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	314 <param name="xipe" value="off"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	315 <param name="minpath" value="on"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	316 <param name="pick_frames" value="on"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	317 <param name="gap_fill" value="off"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	318 <param name="output_format" value="tsv"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	319 <param name="output_max_dec" value="10"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	320 <param name="remove_statified_output" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	321 <param name="remove_column_description_output" value=""/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	322 <param name="pathways" value="unipathway"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	323 <output name="gene_families_tsv">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	324 <assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	325 <has_text text="UNMAPPED" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	326 <has_text text="# Gene Family" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	327 </assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	328 </output>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	329 <output name="pathcoverage_tsv">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	330 <assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	331 <has_text text="UNMAPPED" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	332 <has_text text="UNINTEGRATED" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	333 </assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	334 </output>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	335 <output name="pathabundance_tsv">
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	336 <assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	337 <has_text text="UNMAPPED" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	338 <has_text text="UNINTEGRATED" />
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	339 </assert_contents>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	340 </output>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	341 </test>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	342 </tests>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	343 <help><![CDATA[
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	344 @HELP_HEADER@
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	345
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	346 This tool corresponds to the main tool in HUMAnN2 pipeline.
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	347
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	348 Inputs
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	349
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	350 The input is a single file corresponding either to filtered shotgun sequencing metagenome file (fastq, fastq.gz, fasta, or fasta.gz format), alignment file (sam, bam or blastm8 format) or gene table file (tsv or biom format).
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	351
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	352 A file with a taxonomic profile (obtained with MetaPhlan2) can also be provided to avoid first step of taxonomic profiling needed to select pangenomes in protein database. Otherwise, default MetaPhlAn2 or custom databases can be used for taxonomic profiling. For custom databases, a fasta file with marker gene sequences is required and also a json file containing metadata:
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	353
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	354 ::
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	355
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	356 {
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	357 "taxonomy": {
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	358 "taxonomy of genome1": genome1_length,
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	359 "taxonomy of genome2": genome2_length,
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	360 ...
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	361 }
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	362 "markers": {
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	363 "marker1_name": {
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	364 "clade": the clade that the marker belongs to,
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	365 "ext": [list of external genomes where the marker appears],
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	366 "len": length of the marker,
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	367 "score": score of the marker,
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	368 "taxon": the taxon of the marker
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	369 }
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	370 ...
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	371 }
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	372 }
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	373
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	374 For functional profiling, HUMAnN2 uses multiple databases. Locally cached nucleotide or protein databases have to be downloaded database before using them (using the dedicated tool). Custom databases can also be used after upload. Nucleotide database have to be provided as a dataset.
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	375
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	376 Outputs
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	377
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	378 HUMAnN creates three output files:
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	379
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	380 - A file with gene families and their abundance
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	381 - A file with pathways and their abundance
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	382 - A file with pathways and their coverage
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	383
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	384 ]]></help>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	385 <expand macro="citations"/>
1ab06263e083 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty iuc parents: diff changeset	386 </tool>

Mercurial > repos > iuc > humann2

annotate humann2.xml @ 4:019864881779 draft