humann3: humann.xml annotate

annotate humann.xml @ 1:469b5fe416ad draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f

author	thanhlv
date	Tue, 14 Feb 2023 11:15:40 +0000
parents	ab86614989fd
children

rev	line source
0 ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1 <tool id="humann3" name="HUMAnN3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	2 <description>to profile presence/absence and abundance of microbial pathways and gene families</description>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	3 <macros>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	4 <import>macros.xml</import>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	5 <xml name="prescreen">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	6 <section name="prescreen" title="Prescreen / Identifying community species" expanded="true">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	7 <conditional name="metaphlan_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	8 <param name="selector" type="select" label="Database with clade-specific marker genes">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	9 <option value="cached" selected="true">Locally cached</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	10 <option value="history">From history</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	11 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	12 <when value="cached">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	13 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	14 <options from_data_table="metaphlan_database">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	15 <validator message="No MetaPhlAn database is available" type="no_options" />
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	16 </options>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	17 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	18 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	19 <when value="history">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	20 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	21 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	22 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	23 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	24 <param argument="--prescreen-threshold" type="float" value="0.01" min="0" max="100" label="Minimum percentage of reads matching a species"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	25 <!-- add metaphlan options -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	26 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	27 </xml>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	28 <token name="@PRESCREEN_PREPARE@"><![CDATA[
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	29 #if $wf.prescreen.metaphlan_db.selector == "history"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	30 mkdir metaphlan_db
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	31 &&
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	32 bowtie2-build --large-index '$wf.prescreen.metaphlan_db.bowtie2db' 'metaphlan_db/custom_db-v30'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	33 &&
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	34 python '$__tool_directory__/customizemetadata.py'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	35 transform_json_to_pkl
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	36 --json '$wf.prescreen.metaphlan_db.mpa_pkl'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	37 --pkl 'metaphlan_db/custom_db-v30.pkl'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	38 &&
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	39 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	40 ]]></token>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	41 <token name="@PRESCREEN_RUN@"><![CDATA[
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	42 #set $metaphlan_option = "-t rel_ab"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	43 #if $wf.prescreen.metaphlan_db.selector == "history"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	44 #set $metaphlan_option += " --bowtie2db metaphlan_db/"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	45 #set $metaphlan_option += " --index custom_db-v30"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	46 #else
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	47 #set $metaphlan_option += " --bowtie2db %s" % $wf.prescreen.metaphlan_db.cached_db.fields.path
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	48 #set $metaphlan_option += " --index %s" % $wf.prescreen.metaphlan_db.cached_db.fields.dbkey
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	49 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	50 --metaphlan-options="$metaphlan_option"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	51 --prescreen-threshold $wf.prescreen.prescreen_threshold
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	52 ]]></token>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	53 <xml name="nucleotide_database">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	54 <param argument="--nucleotide-database" type="data_collection" collection_type="list" format="fasta" label="Nucleotide database from history" help="Each file must be named: ^[g__].[s__]"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	55 </xml>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	56 <xml name="nucleotide_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	57 <section name="nucleotide_search" title="Nucleotide search / Mapping reads to community pangenomes" expanded="true">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	58 <conditional name="nucleotide_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	59 <param name="selector" type="select" label="Nucleotide database" help="For locally cached databases, you need first to execute the tool to download HUMAnN2 databases">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	60 <option value="cached" selected="true">Locally cached</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	61 <option value="history">From history</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	62 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	63 <when value="cached">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	64 <param name="nucleotide_database" type="select" label="Nucleotide database">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	65 <options from_data_table="humann_nucleotide_database">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	66 <validator message="No nucleotide database is available" type="no_options" />
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	67 </options>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	68 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	69 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	70 <when value="history">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	71 <expand macro="nucleotide_database"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	72 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	73 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	74 <!-- add bowtie2 options -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	75 <param argument="--nucleotide-identity-threshold" type="float" value="0" min="0" max="100"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	76 label="Identity threshold for nucleotide alignments"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	77 <param argument="--nucleotide-subject-coverage-threshold" type="float" value="50" min="0" max="100"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	78 label="Subject coverage threshold for nucleotide alignments"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	79 <param argument="--nucleotide-query-coverage-threshold" type="float" value="90" min="0" max="100"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	80 label="Query coverage threshold for nucleotide alignments"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	81 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	82 </xml>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	83 <token name="@NUCLEOTIDE_SEARCH_PREPARE@"><![CDATA[
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	84 #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	85 mkdir nucleotide_db
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	86 &&
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	87 #for $f in $wf.nucleotide_search.nucleotide_db.nucleotide_database:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	88 ln -s '$f' 'nucleotide_db/${re.sub('[^\w\-_.]', '_', f.element_identifier)}.v201901_v31' &&
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	89 #end for
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	90 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	91 ]]></token>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	92 <token name="@NUCLEOTIDE_SEARCH_RUN@"><![CDATA[
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	93 #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	94 --nucleotide-database nucleotide_db
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	95 #else
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	96 --nucleotide-database '$wf.nucleotide_search.nucleotide_db.nucleotide_database.fields.path'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	97 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	98 --nucleotide-identity-threshold $wf.nucleotide_search.nucleotide_identity_threshold
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	99 --nucleotide-subject-coverage-threshold $wf.nucleotide_search.nucleotide_subject_coverage_threshold
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	100 --nucleotide-query-coverage-threshold $wf.nucleotide_search.nucleotide_query_coverage_threshold
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	101 ]]></token>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	102 <xml name="translated_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	103 <section name="translated_search" title="Translated search / Aligning unmapped reads to a protein database" expanded="true">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	104 <conditional name="protein_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	105 <param name="selector" type="select" label="Protein database" help="For locally cached databases, you need first to execute the tool to download HUMAnN2 databases">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	106 <option value="cached" selected="true">Locally cached</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	107 <option value="history">From history</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	108 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	109 <when value="cached">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	110 <param name="protein_database" type="select" label="Protein database">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	111 <options from_data_table="humann_protein_database">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	112 <validator message="No protein database is available" type="no_options" />
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	113 </options>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	114 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	115 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	116 <when value="history">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	117 <param argument="--protein-database" type="data" format="fasta" label="Protein database from history"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	118 <param argument="--search-mode" type="select" label="Search mode">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	119 <option value="uniref50">UniRef50</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	120 <option value="uniref90" selected="true">UniRef90</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	121 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	122 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	123 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	124 <param argument="--evalue" type="float" value="1" label="E-value threshold to use with the translated search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	125 <!-- add diamond options -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	126 <param argument="--translated-identity-threshold" type="float" min="0" max="100" optional="true"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	127 label="Identity threshold for translated alignments"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	128 help="It is tuned automatically (based on uniref mode) unless a custom value is specified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	129 <param argument="--translated-subject-coverage-threshold" type="float" value="50" min="0" max="100"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	130 label="Subject coverage threshold for translated alignments"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	131 <param argument="--translated-query-coverage-threshold" type="float" value="90" min="0" max="100"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	132 label="Query coverage threshold for translated alignments"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	133 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	134 </xml>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	135 <token name="@TRANSLATED_SEARCH_PREPARE@"><![CDATA[
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	136 #if $wf.translated_search.protein_db.selector == 'history'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	137 mkdir protein_db
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	138 &&
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	139 diamond makedb
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	140 --in '$wf.translated_search.protein_db.protein_database'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	141 --db 'protein_db/protein-db-201901b'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	142 --threads "\${GALAXY_SLOTS:-4}"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	143 &&
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	144 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	145 ]]></token>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	146 <token name="@TRANSLATED_SEARCH_RUN@"><![CDATA[
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	147 --translated-alignment 'diamond'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	148 #if $wf.translated_search.protein_db.selector == 'history'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	149 --protein-database protein_db
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	150 --search-mode '$wf.translated_search.protein_db.search_mode'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	151 #else
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	152 --protein-database '$wf.translated_search.protein_db.protein_database.fields.path'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	153 #if 'uniref50' in $wf.translated_search.protein_db.protein_database.fields.value
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	154 --search-mode 'uniref50'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	155 #else
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	156 --search-mode 'uniref90'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	157 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	158 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	159 --evalue $wf.translated_search.evalue
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	160 #if str($wf.translated_search.translated_identity_threshold) != ''
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	161 --identity-threshold $wf.translated_search.translated_identity_threshold
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	162 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	163 --translated-subject-coverage-threshold $wf.translated_search.translated_subject_coverage_threshold
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	164 --translated-query-coverage-threshold $wf.translated_search.translated_query_coverage_threshold
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	165 ]]></token>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	166 </macros>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	167 <expand macro="edam_ontology"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	168 <expand macro="requirements"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	169 <expand macro="version"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	170 <command detect_errors="exit_code"><![CDATA[
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	171 #import re
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	172 #if $in.input.ext.startswith("fasta")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	173 #set ext="fasta"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	174 #else if $in.input.ext.startswith("fastq")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	175 #set ext="fastq"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	176 #else if $in.input.ext.endswith("bam")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	177 #set ext="bam"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	178 #else if $in.input.ext == 'sam'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	179 #set ext="sam"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	180 #else if $in.input.ext == 'biom1'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	181 #set ext="biom"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	182 #else
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	183 >&2 "unknown extension $in.input.ext"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	184 exit 1;
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	185 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	186 #if $in.input.ext.endswith(".gz")
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	187 #set ext+=".gz"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	188 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	189
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	190 #if $wf.selector == 'bypass_prescreen'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	191 @NUCLEOTIDE_SEARCH_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	192 @TRANSLATED_SEARCH_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	193 #else if $wf.selector == 'bypass_taxonomic_profiling'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	194 @NUCLEOTIDE_SEARCH_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	195 @TRANSLATED_SEARCH_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	196 #else if $wf.selector == 'bypass_nucleotide_index'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	197 @NUCLEOTIDE_SEARCH_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	198 @TRANSLATED_SEARCH_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	199 #else if $wf.selector == 'bypass_nucleotide_search'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	200 @TRANSLATED_SEARCH_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	201 #else if $wf.selector == 'bypass_translated_search'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	202 @PRESCREEN_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	203 @NUCLEOTIDE_SEARCH_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	204 #else if $wf.selector == 'none'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	205 @PRESCREEN_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	206 @NUCLEOTIDE_SEARCH_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	207 @TRANSLATED_SEARCH_PREPARE@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	208 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	209
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	210 humann
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	211 --input '$input'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	212 --input-format $ext
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	213 -o 'output'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	214 #if $wf.selector == 'bypass_prescreen'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	215 --bypass-prescreen
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	216 @NUCLEOTIDE_SEARCH_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	217 @TRANSLATED_SEARCH_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	218 #else if $wf.selector == 'bypass_taxonomic_profiling'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	219 --taxonomic-profile '$wf.taxonomic_profile'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	220 @NUCLEOTIDE_SEARCH_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	221 @TRANSLATED_SEARCH_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	222 #else if $wf.selector == 'bypass_nucleotide_index'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	223 --bypass-nucleotide-index
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	224 @NUCLEOTIDE_SEARCH_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	225 @TRANSLATED_SEARCH_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	226 #else if $wf.selector == 'bypass_nucleotide_search'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	227 --bypass-nucleotide-search
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	228 @TRANSLATED_SEARCH_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	229 #else if $wf.selector == 'bypass_translated_search'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	230 --bypass-translated-search
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	231 @PRESCREEN_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	232 @NUCLEOTIDE_SEARCH_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	233 #else if $wf.selector == 'none'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	234 @PRESCREEN_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	235 @NUCLEOTIDE_SEARCH_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	236 @TRANSLATED_SEARCH_RUN@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	237 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	238 --gap-fill '$g_p_quant.gap_fill'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	239 --minpath '$g_p_quant.minpath'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	240 --pathways '$g_p_quant.pathways'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	241 --xipe '$g_p_quant.xipe'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	242 --annotation-gene-index $g_p_quant.annotation_gene_index
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	243 #if $g_p_quant.id_mapping
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	244 --id-mapping '$g_p_quant.id_mapping'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	245 #end if
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	246 --log-level 'DEBUG'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	247 --o-log '$log'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	248 --output-basename '$out.output_basename'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	249 --output-format '$out.output_format'
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	250 --output-max-decimals $out.output_max_decimals
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	251 $out.remove_column_description_output
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	252 $out.remove_stratified_output
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	253 --threads "\${GALAXY_SLOTS:-4}"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	254 --memory-use minimum
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	255 ]]></command>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	256 <inputs>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	257 <conditional name="in">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	258 <param name="selector" type="select" label="Input(s)">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	259 <option value="raw" selected="true">Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	260 <option value="mapping">Pre-computed mappings of reads to database sequences</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	261 <option value="abundance">Pre-computed (typically gene) abundance tables</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	262 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	263 <when value="raw">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	264 <param name="input" type="data" format="fastq,fastq.gz,fasta,fasta.gz"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	265 label="Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	266 help="Paired-end Fasta/FastQ files should be merged first"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	267 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	268 <when value="mapping">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	269 <param name="input" type="data" format="sam,bam" label="Pre-computed mappings of reads to database sequences"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	270 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	271 <when value="abundance">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	272 <param name="input" type="data" format="tabular,tsv,biom1" label="Pre-computed (typically gene) abundance tables"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	273 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	274 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	275 <conditional name="wf">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	276 <param name="selector" type="select" label="Steps">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	277 <option value="bypass_prescreen">Bypass the prescreen step and run on the full ChocoPhlAn database (--bypass-prescreen)</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	278 <option value="bypass_taxonomic_profiling">Bypass the taxonomic profiling step and creates a custom ChocoPhlAn database of the species provided afterwards</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	279 <option value="bypass_nucleotide_index">Starts the workflow with the nucleotide alignment step using the provided indexed database (--bypass-nucleotide-index)</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	280 <option value="bypass_nucleotide_search">Bypass all of the alignment steps before the translated search (--bypass_nucleotide-search)</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	281 <option value="bypass_translated_search">Run all of the alignment steps except the translated search (--bypass_translated-search)</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	282 <option value="none" selected="true">Run the full workflow steps</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	283 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	284 <when value="bypass_prescreen">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	285 <expand macro="nucleotide_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	286 <expand macro="translated_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	287 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	288 <when value="bypass_taxonomic_profiling">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	289 <param argument="--taxonomic-profile" type="data" format="tabular,txt,tsv" label="Taxonomic profile file"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	290 <expand macro="nucleotide_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	291 <expand macro="translated_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	292 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	293 <when value="bypass_nucleotide_index">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	294 <expand macro="nucleotide_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	295 <expand macro="translated_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	296 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	297 <when value="bypass_nucleotide_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	298 <expand macro="translated_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	299 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	300 <when value="bypass_translated_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	301 <expand macro="prescreen"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	302 <expand macro="nucleotide_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	303 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	304 <when value="none">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	305 <expand macro="prescreen"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	306 <expand macro="nucleotide_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	307 <expand macro="translated_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	308 </when>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	309 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	310 <section name="g_p_quant" title="Gene and pathway quantification" expanded="true">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	311 <param argument="--gap-fill" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use gap fill computation?"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	312 <param argument="--minpath" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use minpath computation?"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	313 <param argument="--pathways" type="select" label="Database to use for pathway computations">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	314 <option value="metacyc" selected="true">MetaCyc</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	315 <option value="unipathway">UniPathway</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	316 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	317 <param argument="--xipe" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Use xipe computation?"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	318 <param argument="--annotation-gene-index" type="integer" value="3" label="Index of the gene in the sequence annotation"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	319 <param argument="--id-mapping" type="data" format="tsv" optional="true" label="id mapping file for alignments"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	320 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	321 <section name="out" title="Outputs" expanded="true">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	322 <param argument="--output-basename" type="text" value="humann" label="basename">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	323 <sanitizer invalid_char="">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	324 <valid initial="string.ascii_letters,string.digits">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	325 <add value="_" />
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	326 <add value="-" />
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	327 </valid>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	328 </sanitizer>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	329 <validator type="empty_field" />
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	330 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	331 <param argument="--output-format" type="select" label="Format of the output files">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	332 <option value="tsv" selected="true">Tabular</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	333 <option value="biom">BIOM</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	334 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	335 <param argument="--output-max-decimals" type="integer" value="10" label="Number of decimals to output"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	336 <param argument="--remove-column-description-output" type="boolean" truevalue="--remove-column-description-output" falsevalue="" checked="false" label="Remove description in the output column?"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	337 <param argument="--remove-stratified-output" type="boolean" truevalue="--remove-stratified-output" falsevalue="" checked="false" label="Remove stratification from output?"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	338 <param name="intermediate_temp" type="select" multiple="true" label="Intermediate output files">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	339 <option value="metaphlan_bowtie2">MetaPhlAn Bowtie2 output</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	340 <option value="metaphlan_bugs_list">MetaPhlAn bugs list</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	341 <option value="bowtie2_alignment">Bowtie2 alignment results</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	342 <option value="bowtie2_reduced_alignment">Bowtie2 reduced alignment results</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	343 <option value="bowtie2_unaligned">Unaligned reads after Bowtie2</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	344 <option value="custom_chocophlan_database">Custom ChocoPhlAn database</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	345 <option value="diamond_aligned">Translated alignment results</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	346 <option value="diamond_unaligned">Translated alignment unaligned reads</option>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	347 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	348 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	349 </inputs>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	350 <outputs>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	351 <data name="gene_families_tsv" format="tabular" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	352 <filter>out['output_format'] == "tsv"</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	353 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	354 <data name="gene_families_biom" format="biom1" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	355 <filter>out['output_format'] == "biom"</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	356 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	357 <data name="pathcoverage_tsv" format="tabular" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	358 <filter>out['output_format'] == "tsv"</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	359 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	360 <data name="pathcoverage_biom" format="biom1" from_work_dir="output/*_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	361 <filter>out['output_format'] == "biom"</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	362 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	363 <data name="pathabundance_tsv" format="tabular" from_work_dir="output/*_pathabundance.tsv" label="${tool.name} on ${on_string}: Pathways and their abundance" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	364 <filter>out['output_format'] == "tsv"</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	365 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	366 <data name="pathabundance_biom" format="biom1" from_work_dir="output/*_pathabundance.biom" label="${tool.name} on ${on_string}: Pathways and their abundance" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	367 <filter>out['output_format'] == "biom"</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	368 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	369 <data format="txt" name="log" label="${tool.name} on ${on_string}: Log"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	370 <data format="tabular" name="metaphlan_bowtie2" from_work_dir="output/_temp/_metaphlan_bowtie2.txt" label="${tool.name} on ${on_string}: MetaPhlAn Bowtie2 output" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	371 <filter>out['intermediate_temp'] and "metaphlan_bowtie2" in out['intermediate_temp']</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	372 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	373 <data format="tabular" name="metaphlan_bugs_list" from_work_dir="output/_temp/_metaphlan_bugs_list.tsv" label="${tool.name} on ${on_string}: MetaPhlAn bugs list" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	374 <filter>out['intermediate_temp'] and "metaphlan_bugs_list" in out['intermediate_temp']</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	375 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	376 <data format="sam" name="bowtie2_alignment" from_work_dir="output/_temp/_bowtie2_aligned.sam" label="${tool.name} on ${on_string}: Bowtie2 alignment results" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	377 <filter>out['intermediate_temp'] and "bowtie2_alignment" in out['intermediate_temp']</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	378 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	379 <data format="tabular" name="bowtie2_reduced_alignment" from_work_dir="output/_temp/_bowtie2_aligned.tsv" label="${tool.name} on ${on_string}: Bowtie2 reduced alignment results" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	380 <filter>out['intermediate_temp'] and "bowtie2_reduced_alignment" in out['intermediate_temp']</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	381 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	382 <data format="fasta" name="bowtie2_unaligned" from_work_dir="output/_temp/_bowtie2_unaligned.fa" label="${tool.name} on ${on_string}: Unaligned reads after Bowtie2" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	383 <filter>out['intermediate_temp'] and "bowtie2_unaligned" in out['intermediate_temp']</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	384 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	385 <data format="fasta" name="custom_chocophlan_database" from_work_dir="output/_temp/_custom_chocophlan_database.ffn" label="${tool.name} on ${on_string}: Custom ChocoPhlAn database" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	386 <filter>out['intermediate_temp'] and "custom_chocophlan_database" in out['intermediate_temp']</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	387 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	388 <data format="tabular" name="diamond_aligned" from_work_dir="output/_temp/_diamond_aligned.tsv" label="${tool.name} on ${on_string}: Translated alignment results" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	389 <filter>out['intermediate_temp'] and "diamond_aligned" in out['intermediate_temp']</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	390 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	391 <data format="fasta" name="diamond_unaligned" from_work_dir="output/_temp/_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" >
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	392 <filter>out['intermediate_temp'] and "diamond_unaligned" in out['intermediate_temp']</filter>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	393 </data>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	394 </outputs>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	395 <tests>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	396 <!-- This test refers to the Metaphlan v3 DB format, and hence should fail, which is to be caught gracefully. -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	397 <test expect_exit_code="42" expect_failure="true">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	398 <conditional name="in">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	399 <!-- raw fasta file -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	400 <param name="selector" value="raw"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	401 <param name="input" value="demo.fastq.gz"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	402 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	403 <conditional name="wf">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	404 <!-- full workflow -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	405 <param name="selector" value="none"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	406 <section name="prescreen">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	407 <conditional name="metaphlan_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	408 <param name="selector" value="history"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	409 <param name="bowtie2db" value="test-db/metaphlan-db/demo-db-v30.fasta"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	410 <param name="mpa_pkl" value="test-db/metaphlan-db/old-structure/demo-db-v30.json"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	411 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	412 <param name="prescreen_threshold" value="0.01"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	413 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	414 <section name="nucleotide_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	415 <conditional name="nucleotide_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	416 <param name="selector" value="history"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	417 <param name="nucleotide_database">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	418 <collection type="list">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	419 <element name="g__Bacteroides.s__Bacteroides_stercoris.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v201901_v31.ffn.gz" />
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	420 <element name="g__Bacteroides.s__Bacteroides_vulgatus.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v201901_v31.ffn.gz" />
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	421 </collection>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	422 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	423 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	424 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	425 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	426 </test>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	427 <!-- This test refers to the Metaphlan v4 DB format, and hence should be a straight pass. -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	428 <test expect_num_outputs="12">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	429 <conditional name="in">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	430 <!-- raw fasta file -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	431 <param name="selector" value="raw"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	432 <param name="input" value="demo.fastq.gz"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	433 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	434 <conditional name="wf">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	435 <!-- full workflow -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	436 <param name="selector" value="none"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	437 <section name="prescreen">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	438 <conditional name="metaphlan_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	439 <param name="selector" value="history"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	440 <param name="bowtie2db" value="test-db/metaphlan-db/demo-db-v30.fasta"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	441 <param name="mpa_pkl" value="test-db/metaphlan-db/demo-db-v30.json"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	442 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	443 <param name="prescreen_threshold" value="0.01"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	444 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	445 <section name="nucleotide_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	446 <conditional name="nucleotide_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	447 <param name="selector" value="history"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	448 <param name="nucleotide_database">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	449 <collection type="list">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	450 <element name="g__Bacteroides.s__Bacteroides_stercoris.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v201901_v31.ffn.gz"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	451 <element name="g__Bacteroides.s__Bacteroides_vulgatus.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v201901_v31.ffn.gz"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	452 </collection>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	453 </param>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	454 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	455 <param name="nucleotide_identity_threshold" value="0"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	456 <param name="nucleotide_subject_coverage_threshold" value="50"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	457 <param name="nucleotide_query_coverage_threshold" value="90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	458 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	459 <section name="translated_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	460 <conditional name="protein_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	461 <param name="selector" value="history"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	462 <param name="protein_database" value="test-db/protein-db/uniref90_demo_prots_v201901b.fasta"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	463 <param name="search_mode" value="uniref90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	464 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	465 <param name="evalue" value="1"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	466 <param name="translated_subject_coverage_threshold" value="50"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	467 <param name="translated_query_coverage_threshold" value="90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	468 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	469 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	470 <section name="g_p_quant">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	471 <param name="gap_fill" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	472 <param name="minpath" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	473 <param name="pathways" value="metacyc"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	474 <param name="xipe" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	475 <param name="annotation_gene_index" value="3"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	476 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	477 <section name="out">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	478 <!-- intermediate files -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	479 <param name="output_basename" value="humann"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	480 <param name="log_level" value="DEBUG"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	481 <param name="output_format" value="tsv"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	482 <param name="output_max_decimals" value="10"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	483 <param name="remove_column_description_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	484 <param name="remove_statified_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	485 <param name="intermediate_temp"
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	486 value="metaphlan_bowtie2,metaphlan_bugs_list,bowtie2_alignment,bowtie2_reduced_alignment,bowtie2_unaligned,custom_chocophlan_database,diamond_aligned,diamond_unaligned"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	487 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	488 <output name="gene_families_tsv" ftype="tabular" value="demo_genefamilies.tsv" compare="sim_size">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	489 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	490 <has_text text="humann_Abundance-RPKs"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	491 <has_text text="UniRef90_A0A078RDY6\|g__Bacteroides.s__Bacteroides_vulgatus"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	492 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	493 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	494 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	495 <output name="pathcoverage_tsv" ftype="tabular" value="demo_pathcoverage.tsv" compare="sim_size">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	496 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	497 <has_text text="humann_Coverage"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	498 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	499 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	500 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	501 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	502 <output name="pathabundance_tsv" ftype="tabular" value="demo_pathabundance.tsv" compare="sim_size">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	503 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	504 <has_text text="humann_Abundance"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	505 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	506 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	507 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	508 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	509 <output name="log" ftype="txt">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	510 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	511 <has_text text="DATABASE SETTINGS"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	512 <has_text text="humann.utilities"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	513 <has_text text="humann_genefamilies"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	514 <has_text text="humann_pathabundance"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	515 <has_text text="humann_pathcoverage"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	516 <has_text text="g__Bacteroides.s__Bacteroides_dorei"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	517 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	518 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	519 <output name="metaphlan_bowtie2" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	520 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	521 <has_text text="s__Bacteroides_dorei_read000116"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	522 <has_text text="357276__I9R1V6__DXD47_04125"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	523 <has_text text="s__Bacteroides_dorei_read000129"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	524 <has_text text="357276__B6W1Y5__IY41_11405"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	525 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	526 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	527 <output name="metaphlan_bugs_list" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	528 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	529 <has_text text="relative_abundance"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	530 <has_text text="k__Bacteria\|p__Bacteroidetes\|c__Bacteroidia\|o__Bacteroidales\|f__Bacteroidaceae\|g__Bacteroides\|s__Bacteroides_vulgatus"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	531 <has_text text="k__Bacteria\|p__Bacteroidetes\|c__Bacteroidia\|o__Bacteroidales\|f__Bacteroidaceae\|g__Bacteroides\|s__Bacteroides_dorei"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	532 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	533 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	534 <output name="bowtie2_alignment" ftype="sam">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	535 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	536 <has_text text="SN:821__F3PQ30__HMPREF9446_00822\|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_vulgatus\|UniRef90_F3PQ30\|UniRef50_F3PQ30\|510"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	537 <has_text text="s__Bacteroides_dorei_read009840"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	538 <has_text text="PN:bowtie2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	539 <has_text text="LN:1281"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	540 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	541 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	542 <output name="bowtie2_reduced_alignment" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	543 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	544 <has_text text="s__Bacteroides_dorei_read000001"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	545 <has_text text="821__A6L5K0__BVU_3338\|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_vulgatus\|UniRef90_A6L5K0\|UniRef50_A6L5K0\|468"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	546 <has_text text="s__Bacteroides_vulgatus_read003845"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	547 <has_text text="821__A0A396BBC3__DXC03_14350\|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_vulgatus\|UniRef90_A0A396BBC3\|UniRef50_A0A174FNA3\|2934"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	548 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	549 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	550 <output name="bowtie2_unaligned" ftype="fasta">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	551 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	552 <has_text text=">s__Bacteroides_dorei_read000001\|100"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	553 <has_text text=">s__Bacteroides_dorei_read000002\|100"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	554 <has_text text=">unclassified_read000971\|100"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	555 <has_text text=">s__Bacteroides_vulgatus_read004473\|100"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	556 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	557 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	558 <output name="custom_chocophlan_database" ftype="fasta">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	559 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	560 <has_text text=">821__F3PQ30__HMPREF9446_00822\|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_vulgatus\|UniRef90_F3PQ30\|UniRef50_F3PQ30\|510"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	561 <has_text text=">821__F3PUY1__HMPREF9446_02555\|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_vulgatus\|UniRef90_F3PUY1\|UniRef50_A0A3E5DX68\|411"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	562 <has_text text=">821__A0A3E4KCH0__DXD33_19495\|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_vulgatus\|UniRef90_A0A3E4KCH0\|UniRef50_F3PP72\|3582"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	563 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	564 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	565 <output name="diamond_aligned" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	566 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	567 <has_text text="UniRef90_Z5XVM9\|969"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	568 <has_text text="s__Bacteroides_vulgatus_read"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	569 <has_text text="s__Bacteroides_vulgatus_read"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	570 <has_text text="UniRef90_Y0KEF3\|618"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	571 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	572 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	573 <output name="diamond_unaligned" ftype="fasta">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	574 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	575 <has_text text=">s__Bacteroides_dorei_read000001\|100"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	576 <has_text text=">s__Bacteroides_vulgatus_read006412\|100"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	577 <has_text text=">unclassified_read000867\|100"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	578 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	579 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	580 </test>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	581 <test expect_num_outputs="4">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	582 <conditional name="in">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	583 <!-- fastq file -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	584 <param name="selector" value="raw"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	585 <param name="input" value="demo.fasta.gz"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	586 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	587 <conditional name="wf">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	588 <!-- bypass_prescreen -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	589 <param name="selector" value="bypass_prescreen"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	590 <section name="nucleotide_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	591 <conditional name="nucleotide_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	592 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	593 <param name="nucleotide_database" value="chocophlan-DEMO-20210421"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	594 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	595 <param name="nucleotide_identity_threshold" value="0"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	596 <param name="nucleotide_subject_coverage_threshold" value="50"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	597 <param name="nucleotide_query_coverage_threshold" value="90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	598 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	599 <section name="translated_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	600 <conditional name="protein_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	601 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	602 <param name="protein_database" value="uniref-DEMO_diamond-20210421"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	603 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	604 <param name="evalue" value="1"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	605 <param name="translated_subject_coverage_threshold" value="50"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	606 <param name="translated_query_coverage_threshold" value="90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	607 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	608 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	609 <section name="g_p_quant">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	610 <param name="gap_fill" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	611 <param name="minpath" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	612 <param name="pathways" value="metacyc"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	613 <param name="xipe" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	614 <param name="annotation_gene_index" value="3"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	615 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	616 <section name="out">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	617 <!-- Biom -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	618 <param name="output_basename" value="humann"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	619 <param name="log_level" value="DEBUG"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	620 <param name="output_format" value="biom"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	621 <param name="output_max_decimals" value="10"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	622 <param name="remove_column_description_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	623 <param name="remove_statified_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	624 <param name="intermediate_temp" value=""/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	625 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	626 <output name="gene_families_biom" ftype="biom1">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	627 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	628 <has_text text="biom-format"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	629 <has_text text="UniRef90_A0A396BPQ7\|g__Bacteroides.s__Bacteroides_vulgatus"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	630 <has_text text="UniRef90_W8YTG4\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	631 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	632 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	633 <output name="pathcoverage_biom" ftype="biom1">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	634 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	635 <has_text text="TREE"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	636 <has_text text="format-url"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	637 <has_text text="biom-format"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	638 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	639 <has_text text="humann_Coverage"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	640 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	641 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	642 <output name="pathabundance_biom" ftype="biom1">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	643 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	644 <has_text text="TREE"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	645 <has_text text="format-url"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	646 <has_text text="biom-format"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	647 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	648 <has_text text="humann_Abundance"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	649 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	650 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	651 <output name="log" ftype="txt">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	652 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	653 <has_text text="Running bowtie2-build ........"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	654 <has_text text="Total bugs from nucleotide alignment: 2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	655 <has_text text="Total gene families from nucleotide alignment: "/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	656 <has_text text="Aligning to reference database: "/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	657 <has_text text="Total gene families after translated alignment: "/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	658 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	659 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	660 </test>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	661 <test expect_num_outputs="4">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	662 <conditional name="in">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	663 <param name="selector" value="raw"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	664 <param name="input" value="demo.fasta.gz"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	665 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	666 <conditional name="wf">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	667 <!-- bypass_taxonomic_profiling -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	668 <param name="selector" value="bypass_taxonomic_profiling"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	669 <param name="taxonomic_profile" value="demo-taxonomic-profile.tabular"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	670 <section name="nucleotide_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	671 <conditional name="nucleotide_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	672 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	673 <param name="nucleotide_database" value="chocophlan-DEMO-20210421"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	674 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	675 <param name="nucleotide_identity_threshold" value="0"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	676 <param name="nucleotide_subject_coverage_threshold" value="50"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	677 <param name="nucleotide_query_coverage_threshold" value="90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	678 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	679 <section name="translated_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	680 <conditional name="protein_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	681 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	682 <param name="protein_database" value="uniref-DEMO_diamond-20210421"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	683 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	684 <param name="evalue" value="1"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	685 <param name="translated_subject_coverage_threshold" value="50"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	686 <param name="translated_query_coverage_threshold" value="90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	687 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	688 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	689 <section name="g_p_quant">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	690 <param name="gap_fill" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	691 <param name="minpath" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	692 <param name="pathways" value="metacyc"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	693 <param name="xipe" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	694 <param name="annotation_gene_index" value="3"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	695 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	696 <section name="out">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	697 <param name="output_basename" value="humann"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	698 <param name="log_level" value="DEBUG"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	699 <param name="output_format" value="tsv"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	700 <param name="output_max_decimals" value="10"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	701 <param name="remove_column_description_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	702 <param name="remove_statified_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	703 <param name="intermediate_temp" value=""/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	704 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	705 <output name="gene_families_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	706 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	707 <has_text text="humann_Abundance-RPKs"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	708 <has_text text="UniRef90_G1UL42\|g__Bacteroides.s__Bacteroides_dorei"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	709 <has_text text="UniRef90_A0A078RDY6\|g__Bacteroides.s__Bacteroides_vulgatus"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	710 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	711 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	712 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	713 <output name="pathcoverage_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	714 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	715 <has_text text="humann_Coverage"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	716 <has_text text="UNINTEGRATED\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	717 <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	718 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	719 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	720 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	721 <output name="pathabundance_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	722 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	723 <has_text text="humann_Abundance"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	724 <has_text text="UNINTEGRATED\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	725 <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	726
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	727 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	728 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	729 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	730 <output name="log" ftype="txt">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	731 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	732 <has_text text="Found g__Bacteroides.s__Bacteroides_vulgatus : "/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	733 <has_text text="Total species selected from prescreen: 2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	734 <has_text text="Total bugs from nucleotide alignment: 2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	735 <has_text text="g__Bacteroides.s__Bacteroides_vulgatus: "/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	736 <has_text text="g__Bacteroides.s__Bacteroides_dorei: "/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	737 <has_text text="Total gene families from nucleotide alignment: "/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	738 <has_text text="Total bugs after translated alignment: 3"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	739 <has_text text="Total gene families after translated alignment"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	740 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	741 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	742 </test>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	743 <test expect_num_outputs="4">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	744 <conditional name="in">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	745 <!-- mapping SAM file -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	746 <param name="selector" value="mapping"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	747 <param name="input" value="demo.sam"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	748 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	749 <conditional name="wf">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	750 <!-- bypass_nucleotide_index -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	751 <param name="selector" value="bypass_nucleotide_index"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	752 <section name="nucleotide_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	753 <conditional name="nucleotide_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	754 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	755 <param name="nucleotide_database" value="chocophlan-DEMO-20210421"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	756 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	757 <param name="nucleotide_identity_threshold" value="0"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	758 <param name="nucleotide_subject_coverage_threshold" value="50"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	759 <param name="nucleotide_query_coverage_threshold" value="90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	760 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	761 <section name="translated_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	762 <conditional name="protein_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	763 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	764 <param name="protein_database" value="uniref-DEMO_diamond-20210421"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	765 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	766 <param name="evalue" value="1"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	767 <param name="translated_subject_coverage_threshold" value="50"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	768 <param name="translated_query_coverage_threshold" value="90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	769 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	770 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	771 <section name="g_p_quant">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	772 <param name="gap_fill" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	773 <param name="minpath" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	774 <param name="pathways" value="metacyc"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	775 <param name="xipe" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	776 <param name="annotation_gene_index" value="3"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	777 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	778 <section name="out">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	779 <param name="output_basename" value="humann"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	780 <param name="log_level" value="DEBUG"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	781 <param name="output_format" value="tsv"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	782 <param name="output_max_decimals" value="10"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	783 <param name="remove_column_description_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	784 <param name="remove_statified_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	785 <param name="intermediate_temp" value=""/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	786 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	787 <output name="gene_families_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	788 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	789 <has_text text="UniRef90_R6HHA8\|g__Bacteroides.s__Bacteroides_dorei"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	790 <has_text text="UniRef90_unknown\|g__Bacteroides.s__Bacteroides_vulgatus"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	791 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	792 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	793 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	794 <output name="pathcoverage_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	795 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	796 <has_text text="UNMAPPED"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	797 <has_text text="UNINTEGRATED"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	798 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	799 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	800 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	801 <output name="pathabundance_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	802 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	803 <has_text text="UNMAPPED"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	804 <has_text text="UNINTEGRATED"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	805 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	806 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	807 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	808 <output name="log" ftype="txt">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	809 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	810 <has_text text="Process the sam mapping results"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	811 <has_text text="Computing gene families"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	812 <has_text text="Computing pathways abundance and coverage"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	813 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	814 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	815 </test>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	816 <test expect_num_outputs="4">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	817 <conditional name="in">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	818 <!-- raw fasta file -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	819 <param name="selector" value="raw"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	820 <param name="input" value="demo.fastq.gz"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	821 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	822 <conditional name="wf">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	823 <!-- bypass_nucleotide_search -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	824 <param name="selector" value="bypass_nucleotide_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	825 <section name="translated_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	826 <conditional name="protein_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	827 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	828 <param name="protein_database" value="uniref-DEMO_diamond-20210421"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	829 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	830 <param name="evalue" value="1"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	831 <param name="translated_subject_coverage_threshold" value="50"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	832 <param name="translated_query_coverage_threshold" value="90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	833 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	834 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	835 <section name="g_p_quant">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	836 <param name="gap_fill" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	837 <param name="minpath" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	838 <param name="pathways" value="metacyc"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	839 <param name="xipe" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	840 <param name="annotation_gene_index" value="3"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	841 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	842 <section name="out">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	843 <param name="output_basename" value="humann"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	844 <param name="log_level" value="DEBUG"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	845 <param name="output_format" value="tsv"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	846 <param name="output_max_decimals" value="10"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	847 <param name="remove_column_description_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	848 <param name="remove_statified_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	849 <param name="intermediate_temp" value=""/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	850 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	851 <output name="gene_families_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	852 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	853 <has_text text="humann_Abundance-RPKs"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	854 <has_text text="UniRef90_Q9ZUH4\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	855 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	856 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	857 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	858 <output name="pathcoverage_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	859 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	860 <has_text text="humann_Coverage"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	861 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	862 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	863 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	864 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	865 <output name="pathabundance_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	866 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	867 <has_text text="humann_Abundance"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	868 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis\|unclassified"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	869 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	870 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	871 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	872 <output name="log" ftype="txt">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	873 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	874 <has_text text="Total bugs after translated alignment: 1"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	875 <has_text text="unclassified: "/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	876 <has_text text="Unaligned reads after translated alignment: "/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	877 <has_text text="Total gene families"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	878 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	879 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	880 </test>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	881 <test expect_num_outputs="4">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	882 <conditional name="in">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	883 <!-- raw fasta file -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	884 <param name="selector" value="raw"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	885 <param name="input" value="demo.fastq.gz"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	886 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	887 <conditional name="wf">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	888 <!-- bypass_translated_search -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	889 <param name="selector" value="bypass_translated_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	890 <section name="prescreen">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	891 <conditional name="metaphlan_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	892 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	893 <param name="cached_db" value="metaphlan-demo-db-20210421"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	894 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	895 <param name="prescreen_threshold" value="0.01"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	896 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	897 <section name="nucleotide_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	898 <conditional name="nucleotide_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	899 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	900 <param name="nucleotide_database" value="chocophlan-DEMO-20210421"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	901 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	902 <param name="nucleotide_identity_threshold" value="0"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	903 <param name="nucleotide_subject_coverage_threshold" value="50"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	904 <param name="nucleotide_query_coverage_threshold" value="90"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	905 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	906 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	907 <section name="g_p_quant">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	908 <param name="gap_fill" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	909 <param name="minpath" value="true"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	910 <param name="pathways" value="metacyc"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	911 <param name="xipe" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	912 <param name="annotation_gene_index" value="3"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	913 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	914 <section name="out">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	915 <param name="output_basename" value="newname"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	916 <param name="log_level" value="DEBUG"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	917 <param name="output_format" value="tsv"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	918 <param name="output_max_decimals" value="10"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	919 <param name="remove_column_description_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	920 <param name="remove_statified_output" value="false"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	921 <param name="intermediate_temp" value=""/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	922 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	923 <output name="gene_families_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	924 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	925 <has_text text="newname_Abundance-RPKs"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	926 <has_text text="UniRef90_G1UL42\|g__Bacteroides.s__Bacteroides_dorei"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	927 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	928 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	929 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	930 <output name="pathcoverage_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	931 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	932 <has_text text="newname_Coverage"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	933 <has_text text="UNMAPPED"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	934 <has_text text="UNINTEGRATED"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	935 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	936 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	937 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	938 <output name="pathabundance_tsv" ftype="tabular">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	939 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	940 <has_text text="newname_Abundance"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	941 <has_text text="UNMAPPED"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	942 <has_text text="UNINTEGRATED"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	943 <has_n_columns n="2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	944 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	945 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	946 <output name="log" ftype="txt">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	947 <assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	948 <has_text text="Total bugs from nucleotide alignment: 2"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	949 <has_text text="g__Bacteroides.s__Bacteroides_vulgatus: 1195 hits"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	950 <has_text text="g__Bacteroides.s__Bacteroides_dorei: 1260 hits"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	951 <has_text text="Total gene families from nucleotide alignment: 545"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	952 <has_text text="Bypass translated search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	953 </assert_contents>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	954 </output>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	955 </test>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	956 <!-- This test should fail for as metaphlan v4 is invoked on outdated input DB. -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	957 <test expect_exit_code="1" expect_failure="true">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	958 <conditional name="in">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	959 <!-- raw fasta file -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	960 <param name="selector" value="raw"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	961 <param name="input" value="demo.fastq.gz"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	962 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	963 <conditional name="wf">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	964 <!-- bypass_translated_search -->
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	965 <param name="selector" value="bypass_translated_search"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	966 <section name="prescreen">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	967 <conditional name="metaphlan_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	968 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	969 <param name="cached_db" value="metaphlan-db-old-structure"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	970 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	971 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	972 <section name="nucleotide_search">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	973 <conditional name="nucleotide_db">
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	974 <param name="selector" value="cached"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	975 <param name="nucleotide_database" value="chocophlan-DEMO-20210421"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	976 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	977 </section>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	978 </conditional>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	979 </test>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	980 </tests>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	981 <help><![CDATA[
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	982 @HELP_HEADER@
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	983
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	984 This tool corresponds to the main tool in HUMAnN pipeline:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	985
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	986
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	987 1. Taxomonic prescreen
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	988
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	989 Reads are mapped (with MetaPhlAn) to clade-specific marker genes to rapidly identify community species
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	990
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	991 2. Pangenome search (nucleotide search)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	992
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	993 Reads are mapped (with Bowtie2) to pangenomes of identified species
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	994
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	995 3. Translated search
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	996
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	997 Unclassified reads are aligned to a comprehensive and non-redundant protein database
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	998
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	999 4. Gene family and pathway quantification
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1000
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1001 - Gene abundance estimation
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1002
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1003 Mapping results are processed to estimate per-species and community total gene family abundance, weighting by
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1004
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1005 - alignment Quality
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1006 - gene length
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1007 - gene coverage
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1008
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1009 - Per-species and community-level metabolic network reconstruction
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1010
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1011 Genes are mapped to metabolic reactions to identify a parsiomonious set of pathways that explains each species' observed reactions
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1012
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1013 Pathway abundance and coverage are quantified by:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1014
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1015 1. optimizing over alternative subpathways
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1016 2. imputing abundance for conspicuously depleted reactions
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1017
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1018
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1019 Inputs
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1020 ======
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1021
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1022 HUMAnN can start from a few different types of input data each in a few different types of formats:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1023
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1024 - Quality-controlled shotgun sequencing reads
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1025
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1026 This is the most common starting point : A metagenome (DNA reads) or metatranscriptome (RNA reads)
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1027
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1028 - Pre-computed mappings of reads to database sequences
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1029
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1030 - Pre-computed (typically gene) abundance tables
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1031
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1032
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1033 HUMAnN uses 3 reference databases
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1034 Locally cached databases have to be downloaded before using them (using the dedicated tool). Custom databases can also be used after upload.
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1035
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1036 Outputs
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1037 =======
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1038
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1039 HUMAnN creates three output files:
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1040
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1041 - Gene families and their abundance
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1042 - Pathways and their abundance
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1043 - Pathways and their coverage
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1044
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1045 Ten intermediate temp output files can also be retrieved.
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1046
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1047 ]]></help>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1048 <expand macro="citations"/>
ab86614989fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f thanhlv parents: diff changeset	1049 </tool>

Mercurial > repos > thanhlv > humann3

annotate humann.xml @ 1:469b5fe416ad draft default tip