metaphlan4: metaphlan.xml annotate

author	thanhlv
date	Mon, 13 Feb 2023 11:36:42 +0000
parents
children

rev	line source
0 12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	1 <tool id="metaphlan4" name="MetaPhlAn4" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	2 <description>to profile the composition of microbial communities</description>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	3 <macros>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	4 <import>macros.xml</import>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	5 <xml name="tax_lev">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	6 <conditional name="tax_lev">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	7 <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	8 <option value="a" selected="true">All taxonomic levels</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	9 <option value="k">Kingdoms only</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	10 <option value="p">Phyla only</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	11 <option value="c">Classes only</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	12 <option value="o">Orders only</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	13 <option value="f">Families only</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	14 <option value="g">Genera only</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	15 <option value="s">Species only</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	16 </param>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	17 <when value="a">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	18 <param name="split_levels" type='boolean' checked="false" truevalue='true' falsevalue='false'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	19 label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	20 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	21 <when value="k"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	22 <when value="p"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	23 <when value="c"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	24 <when value="o"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	25 <when value="f"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	26 <when value="g"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	27 <when value="s"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	28 </conditional>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	29 </xml>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	30 <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2</token>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	31 </macros>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	32 <expand macro="edam_ontology"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	33 <expand macro="requirements"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	34 <version_command>metaphlan -v</version_command>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	35 <command detect_errors="aggressive"><![CDATA[
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	36 #if $inputs.in.selector == "raw"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	37 #if $inputs.in.raw_in.selector == "single"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	38 #set full_ext=$inputs.in.raw_in.in.datatype.file_ext
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	39 #if $full_ext.endswith("gz")
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	40 #set $file_path="in"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	41 zcat '$inputs.in.raw_in.in' > '$file_path'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	42 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	43 #else if $full_ext.endswith("bz2")
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	44 #set $file_path="in"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	45 bzcat '$inputs.in.raw_in.in' > '$file_path'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	46 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	47 #else
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	48 #set $file_path=$inputs.in.raw_in.in
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	49 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	50 #else if $inputs.in.raw_in.selector == "multiple"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	51 #set full_ext=$inputs.in.raw_in.in[0].datatype.file_ext
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	52 #set file_path=""
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	53 #set sep=""
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	54 #for $i, $f in enumerate($inputs.in.raw_in.in)
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	55 #if $f.datatype.file_ext != $full_ext
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	56 echo "Different datatypes for input files"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	57 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	58 exit 1
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	59 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	60 #if $full_ext.endswith("gz")
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	61 #set fp="input_%s" % ($i)
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	62 zcat '$f' > '$fp'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	63 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	64 #else if $full_ext.endswith("bz2")
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	65 #set fp="input_%s" % ($i)
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	66 bzcat '$f' > '$fp'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	67 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	68 #else
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	69 #set fp=$f
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	70 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	71 #set $file_path+="%s%s" % ($sep, $fp)
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	72 #set $sep=","
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	73 #end for
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	74 #else if $inputs.in.raw_in.selector == "paired"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	75 #set full_ext=$inputs.in.raw_in.in_f.datatype.file_ext
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	76 #if $full_ext != $inputs.in.raw_in.in_r.datatype.file_ext
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	77 echo "Different datatypes for input paired-end files"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	78 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	79 exit 1
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	80 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	81 #if $full_ext.endswith("gz")
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	82 zcat '$inputs.in.raw_in.in_f' > 'in_f'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	83 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	84 zcat '$inputs.in.raw_in.in_r' > 'in_r'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	85 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	86 #set file_path="in_f,in_r"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	87 #else if $full_ext.endswith("bz2")
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	88 bzcat '$inputs.in.raw_in.in_f' > 'in_f'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	89 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	90 bzcat '$inputs.in.raw_in.in_r' > 'in_r'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	91 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	92 #set file_path="in_f,in_r"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	93 #else
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	94 #set file_path="%s,%s" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r)
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	95 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	96 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	97
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	98 #if $full_ext.startswith("fastq")
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	99 #set ext='fastq'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	100 #else if $full_ext.startswith("fasta") and $full_ext.endswith(("gz","bz2"))
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	101 #set ext='fasta'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	102 #else
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	103 #set ext=$full_ext
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	104 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	105 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	106
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	107 #if $inputs.db.db_selector == "history"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	108 mkdir 'ref_db'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	109 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	110 bowtie2-build --large-index '$inputs.db.bowtie2db' 'ref_db/custom_db'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	111 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	112 python '$__tool_directory__/customizemetadata.py'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	113 transform_json_to_pkl
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	114 --json '$inputs.db.mpa_pkl'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	115 --pkl 'ref_db/custom_db.pkl'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	116 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	117 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	118
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	119 metaphlan
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	120 #if $inputs.in.selector == "raw"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	121 '$file_path'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	122 --input_type '$ext'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	123 --read_min_len $inputs.in.read_min_len
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	124 --bt2_ps '$inputs.in.mapping.bt2_ps'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	125 --min_mapq_val $inputs.in.mapping.min_mapq_val
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	126 #if $ext == "sam"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	127 --nreads \$(cat '$file_path' \| grep -c -v '^@')
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	128 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	129 #else
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	130 '$inputs.in.in'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	131 --input_type '$inputs.in.selector'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	132 #if $inputs.in.selector == "sam"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	133 --nreads \$(cat '$inputs.in.in' \| grep -c -v '^@')
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	134 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	135 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	136 #if $inputs.db.db_selector == "cached"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	137 --bowtie2db '$inputs.db.cached_db.fields.path'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	138 --index '$inputs.db.cached_db.fields.dbkey'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	139 #else
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	140 --bowtie2db 'ref_db/'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	141 --index 'custom_db'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	142 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	143 -t '$analysis.analysis_type.t'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	144 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	145 --tax_lev '$analysis.analysis_type.tax_lev.tax_lev'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	146 #else if $analysis.analysis_type.t == "clade_specific_strain_tracker"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	147 --clade '$analysis.analysis_type.clade'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	148 #if str($analysis.analysis_type.min_ab) != ''
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	149 --min_ab $analysis.analysis_type.min_ab
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	150 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	151 #else if $analysis.analysis_type.t == "marker_ab_table" and str($analysis.analysis_type.nreads) != ''
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	152 --nreads $$analysis.analysis_type.nreads
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	153 #else if $analysis.analysis_type.t == "marker_pres_table" and str($analysis.analysis_type.pres_th) != ''
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	154 --pres_th $analysis.analysis_type.pres_th
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	155 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	156 --min_cu_len $analysis.min_cu_len
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	157 #if str($analysis.min_alignment_len) != ''
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	158 --min_alignment_len $analysis.min_alignment_len
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	159 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	160 #if 'add_viruses' in $analysis.organism_profiling
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	161 --add_viruses
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	162 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	163 #if 'ignore_eukaryotes' in $analysis.organism_profiling
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	164 --ignore_eukaryotes
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	165 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	166 #if 'ignore_bacteria' in $analysis.organism_profiling
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	167 --ignore_bacteria
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	168 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	169 #if 'ignore_archaea' in $analysis.organism_profiling
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	170 --ignore_archaea
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	171 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	172 --stat_q $analysis.stat_q
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	173 --perc_nonzero $analysis.perc_nonzero
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	174 #if $analysis.ignore_markers
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	175 --ignore_markers '$analysis.ignore_markers'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	176 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	177 $analysis.avoid_disqm
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	178 --sample_id_key '$out.sample_id_key'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	179 --sample_id '$out.sample_id'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	180 $out.use_group_representative
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	181 $out.legacy_output
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	182 $out.CAMI_format_output
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	183 $out.unknown_estimation
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	184 -o '$output_file'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	185 --bowtie2out 'bowtie2out'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	186 -s '$sam_output_file'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	187 --biom '$biom_output_file'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	188 --nproc \${GALAXY_SLOTS:-4}
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	189
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	190 #if $inputs.in.selector == "raw"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	191 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	192 mv 'bowtie2out' '$bowtie2out'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	193 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	194
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	195 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	196 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	197 mkdir 'split_levels'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	198 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	199 python '$__tool_directory__/formatoutput.py'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	200 split_levels
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	201 --metaphlan_output '$output_file'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	202 --outdir 'split_levels'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	203 $out.legacy_output
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	204
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	205 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	206
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	207 #if $out.krona_output
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	208 &&
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	209 python '$__tool_directory__/formatoutput.py'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	210 format_for_krona
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	211 --metaphlan_output '$output_file'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	212 --krona_output '$krona_output_file'
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	213 #end if
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	214 ]]></command>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	215 <inputs>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	216 <section name="inputs" title="Inputs" expanded="true">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	217 <conditional name="in">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	218 <param name="selector" type="select" label="Input(s)">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	219 <option value="raw" selected="true">Fasta/FastQ file(s) with microbiota reads</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	220 <option value="sam">Externally BowTie2-mapped SAM file</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	221 <option value="bowtie2out">Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	222 </param>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	223 <when value="raw">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	224 <conditional name="raw_in">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	225 <param name="selector" type="select" label="Fasta/FastQ file(s) with microbiota reads">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	226 <option value="single" selected="true">One single-end file</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	227 <option value="multiple">Multiple single-end files</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	228 <option value="paired">Paired-end files</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	229 </param>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	230 <when value="single">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	231 <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ file with microbiota reads"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	232 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	233 <when value="multiple">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	234 <param name="in" type="data" format="@FILE_FORMATS@" multiple="true" label="Single-end Fasta/FastQ files with microbiota reads"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	235 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	236 <when value="paired">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	237 <param name="in_f" type="data" format="@FILE_FORMATS@" label="Forward paired-end Fasta/FastQ file with microbiota reads"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	238 <param name="in_r" type="data" format="@FILE_FORMATS@" label="Reverse paired-end Fasta/FastQ file with microbiota reads"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	239 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	240 </conditional>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	241 <param argument="--read_min_len" type="integer" value="70" label="Minimum length of the reads to be considered when parsing the input file"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	242 <section name="mapping" title="Mapping" expanded="true">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	243 <param argument="--bt2_ps" type="select" label="Presets options for BowTie2" help="Applied only with FASTA files">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	244 <option value="sensitive">Sensitive</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	245 <option value="very-sensitive" selected="true">Very sensitive</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	246 <option value="sensitive-local">Sensitive local</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	247 <option value="very-sensitive-local">Very sensitive local</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	248 </param>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	249 <param argument="--min_mapq_val" type="integer" value="5" label="Minimum mapping quality value (MAPQ)"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	250 </section>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	251 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	252 <when value="sam">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	253 <param name="in" type="data" format="sam" label="Externally BowTie2-mapped SAM file" help="BowTie2 needs to be used first to map microbiota reads"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	254 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	255 <when value="bowtie2out">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	256 <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	257 help="File needs to be generated with MetaPhlAn versions >3.0"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	258 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	259 </conditional>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	260 <conditional name="db">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	261 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	262 <option value="cached" selected="true">Locally cached</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	263 <option value="history">From history</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	264 </param>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	265 <when value="cached">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	266 <param name="cached_db" type="select" label="Cached database with clade-specific marker genes">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	267 <options from_data_table="@IDX_DATA_TABLE@">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	268 <filter type="static_value" column="4" value="@IDX_VERSION@"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	269 <validator message="No compatible MetaPhlAn database is available" type="no_options"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	270 </options>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	271 </param>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	272 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	273 <when value="history">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	274 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	275 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	276 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	277 </conditional>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	278 </section>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	279 <section name="analysis" title="Analysis" expanded="true">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	280 <conditional name="analysis_type">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	281 <param argument="-t" type="select" label="Type of analysis to perform">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	282 <option value="rel_ab" selected="true">rel_ab: Profiling a microbiota in terms of relative abundances</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	283 <option value="rel_ab_w_read_stats">rel_ab_w_read_stats: Profiling a microbiota in terms of relative abundances and estimate the number of reads comming from each clade</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	284 <option value="reads_map">reads_map: Mapping from reads to clades (only reads hitting a marker)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	285 <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	286 <option value="clade_specific_strain_tracker">clade_specific_strain_tracker: List of markers present for a specific clade and all its subclades</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	287 <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when > 0.0 and normalized by microbiota size if number of reads is specified)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	288 <option value="marker_counts">marker_counts: Non-normalized marker counts (use with extreme caution)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	289 <option value="marker_pres_table">marker_pres_table: List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	290 </param>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	291 <when value="rel_ab">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	292 <expand macro="tax_lev"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	293 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	294 <when value="rel_ab_w_read_stats">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	295 <expand macro="tax_lev"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	296 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	297 <when value="reads_map"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	298 <when value="clade_profiles"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	299 <when value="clade_specific_strain_tracker">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	300 <param argument="--clade" type="text" value="" label="Clade for which to extract list of markers present"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	301 help="Markers are also extracted for subclades" />
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	302 <param argument="--min_ab" type="float" optional="true" label="The minimum percentage abundance for the clade"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	303 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	304 <when value="marker_ab_table">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	305 <param argument="--nreads" type="integer" optional="true" label="Total number of reads in the original microbiota"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	306 help="It is used for normalizing the length-normalized counts with the microbiota size as well. No normalization applied if the value is not specified"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	307 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	308 <when value="marker_counts"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	309 <when value="marker_pres_table">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	310 <param argument="--pres_th" type="integer" optional="true" label="Threshold for calling a marker present"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	311 </when>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	312 </conditional>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	313 <param argument="--min_cu_len" type="integer" value="2000"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	314 label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	315 <param argument="--min_alignment_len" type="integer" optional="true"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	316 label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	317 <param name="organism_profiling" type="select" multiple="true" optional="true" label="Organisms to profile">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	318 <option value="add_viruses" selected="true">Profile viral organisms (add_viruses)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	319 <option value="ignore_eukaryotes">Ignore eukaryotic organisms (ignore_eukaryotes)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	320 <option value="ignore_bacteria">Ignore bacteria organisms (ignore_bacteria)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	321 <option value="ignore_archaea">Ignore archea organisms (ignore_archaea)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	322 </param>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	323 <param argument="--stat" type="select" label="Statistical approach for converting marker abundances into clade abundances">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	324 <option value="avg_g">avg_g: Clade global (i.e. normalizing all markers together) average (avg_g)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	325 <option value="avg_l">avg_l: Average of length-normalized marker counts</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	326 <option value="tavg_g" selected="true">tavg_g: Truncated clade global average at --stat_q quantile</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	327 <option value="tavg_l">tavg_l: Truncated average of length-normalized marker counts (at --stat_q)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	328 <option value="wavg_g">wavg_g: Winsorized clade global average (at --stat_q)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	329 <option value="wavg_l">wavg_l: Winsorized average of length-normalized marker counts (at --stat_q)</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	330 <option value="med">med: Median of length-normalized marker counts</option>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	331 </param>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	332 <param argument="--stat_q" type="float" value="0.2" label="Quantile value for the robust average"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	333 <param argument="--perc_nonzero" type="float" value="0.33" label="Percentage of markers with a non zero relative abundance for misidentify a species"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	334 <param argument="--ignore_markers" type="data" format="txt,tabular" optional="true" label="File containing a list of markers to ignore" help="One marker per line"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	335 <param argument="--avoid_disqm" type='boolean' checked="true" truevalue='--avoid_disqm' falsevalue=''
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	336 label="Deactivate the procedure of disambiguating the quasi-markers based on the marker abundance pattern found in the sample?"
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	337 help="It is generally recommended to keep the disambiguation procedure in order to minimize false positives"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	338 </section>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	339 <section name="out" title="Outputs" expanded="true">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	340 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	341 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	342 <param argument="--use_group_representative" type='boolean' checked="false" truevalue='--use_group_representative' falsevalue=''
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	343 label="Use a species as representative for species groups?"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	344 <param argument="--legacy-output" type='boolean' checked="false" truevalue='--legacy-output' falsevalue=''
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	345 label="Old MetaPhlAn2 two columns output?"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	346 <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue=''
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	347 label="Report the profiling using the CAMI output format?"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	348 <param argument="--unknown_estimation" type='boolean' checked="false" truevalue='--unknown_estimation' falsevalue=''
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	349 label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	350 <param name="krona_output" type='boolean' checked="false" truevalue='true' falsevalue='false' label="Output for Krona?"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	351 </section>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	352 </inputs>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	353 <outputs>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	354 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances" />
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	355 <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	356 <filter>inputs['in']['selector'] == "raw"</filter>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	357 </data>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	358 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	359 <filter>inputs['in']['selector'] == "raw"</filter>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	360 </data>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	361 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	362 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" >
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	363 <discover_datasets pattern="(?P<designation>.+)" directory="split_levels/" format="tabular"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	364 <filter>analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	365 </collection>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	366 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	367 <filter>out['krona_output']</filter>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	368 </data>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	369 </outputs>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	370 <tests>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	371 <test expect_num_outputs="6">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	372 <section name="inputs">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	373 <conditional name="in">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	374 <param name="selector" value="raw"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	375 <conditional name="raw_in">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	376 <!-- Single GZ file -->
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	377 <param name="selector" value="single"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	378 <param name="in" value="no_taxon_input.fasta"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	379 </conditional>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	380 <param name="read_min_len" value="70"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	381 <section name="mapping">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	382 <param name="bt2_ps" value="sensitive"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	383 <param name="min_mapq_val" value="5"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	384 </section>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	385 </conditional>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	386 <conditional name="db">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	387 <!-- Cached db -->
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	388 <param name="db_selector" value="cached"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	389 <param name="cached_db" value="test-db-20210409"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	390 </conditional>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	391 </section>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	392 <section name="analysis">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	393 <conditional name="analysis_type">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	394 <param name="t" value="rel_ab"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	395 <conditional name="tax_lev">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	396 <param name="tax_lev" value="a"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	397 <param name="split_levels" value="true"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	398 </conditional>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	399 </conditional>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	400 <param name="min_cu_len" value="2000"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	401 <param name="organism_profiling" value="add_viruses"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	402 <param name="stat" value="avg_g"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	403 <param name="stat_q" value="0.2"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	404 <param name="perc_nonzero" value="0.33"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	405 <param name="avoid_disqm" value="true"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	406 </section>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	407 <section name="out">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	408 <param name="sample_id_key" value="SampleID"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	409 <param name="sample_id" value="Metaphlan_Analysis"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	410 <param name="use_group_representative" value="false"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	411 <param name="legacy_output" value="false"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	412 <param name="CAMI_format_output" value="false"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	413 <param name="unknown_estimation" value="false"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	414 <param name="krona_output" value="true"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	415 </section>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	416 <output name="output_file" ftype="tabular">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	417 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	418 <has_text text="UNCLASSIFIED"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	419 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	420 </output>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	421 <output name="bowtie2out" ftype="tabular">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	422 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	423 <not_has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	424 <has_n_lines n="2"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	425 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	426 </output>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	427 <output name="sam_output_file" ftype="sam">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	428 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	429 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	430 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	431 </output>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	432 <output name="biom_output_file" ftype="biom1">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	433 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	434 <not_has_text text="k__Bacteria"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	435 <not_has_text text="p__Actinobacteria"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	436 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	437 </output>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	438 <output_collection name="levels" type="list" >
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	439
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	440 <element name="all" ftype="tabular">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	441 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	442 <has_text text="class"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	443 <has_n_columns n="17"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	444 <has_n_lines n="1"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	445 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	446 </element>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	447 <element name="class" ftype="tabular">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	448 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	449 <has_text text="class_id"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	450 <not_has_text text="phylum_id"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	451 <has_n_columns n="3"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	452 <has_n_lines n="1"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	453 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	454 </element>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	455 <element name="family" ftype="tabular">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	456 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	457 <has_text text="family_id"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	458 <not_has_text text="order"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	459 <has_n_columns n="3"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	460 <has_n_lines n="1"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	461 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	462 </element>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	463 <element name="genus" ftype="tabular">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	464 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	465 <has_text text="genus_id"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	466 <not_has_text text="family"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	467 <has_n_columns n="3"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	468 <has_n_lines n="1"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	469 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	470 </element>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	471 <element name="kingdom" ftype="tabular">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	472 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	473 <has_text text="kingdom_id"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	474 <has_n_columns n="3"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	475 <has_n_lines n="1"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	476 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	477 </element>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	478 <element name="order" ftype="tabular">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	479 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	480 <has_text text="order_id"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	481 <not_has_text text="class_id"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	482 <has_n_columns n="3"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	483 <has_n_lines n="1"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	484 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	485 </element>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	486 <element name="phylum" ftype="tabular">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	487 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	488 <has_text text="phylum_id"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	489 <not_has_text text="kingdom_id"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	490 <has_n_columns n="3"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	491 <has_n_lines n="1"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	492 </assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	493 </element>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	494 <element name="species" ftype="tabular">
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	495 <assert_contents>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	496 <has_text text="species_id"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	497 <not_has_text text="genus"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	498 <has_n_columns n="3"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	499 <has_n_lines n="1"/>
12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/ thanhlv parents: diff changeset	500 </assert_contents>

0

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1 <tool id="metaphlan4" name="MetaPhlAn4" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

2 <description>to profile the composition of microbial communities</description>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

3 <macros>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

4 <import>macros.xml</import>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

5 <xml name="tax_lev">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

6 <conditional name="tax_lev">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

7 <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

8 <option value="a" selected="true">All taxonomic levels</option>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

9 <option value="k">Kingdoms only</option>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

10 <option value="p">Phyla only</option>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

11 <option value="c">Classes only</option>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12 <option value="o">Orders only</option>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

13 <option value="f">Families only</option>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

14 <option value="g">Genera only</option>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

15 <option value="s">Species only</option>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

16 </param>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

17 <when value="a">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

18 <param name="split_levels" type='boolean' checked="false" truevalue='true' falsevalue='false'

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

19 label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

20 </when>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

21 <when value="k"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

22 <when value="p"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

23 <when value="c"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

24 <when value="o"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

25 <when value="f"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

26 <when value="g"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

27 <when value="s"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

28 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

29 </xml>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

30 <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2</token>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

31 </macros>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

32 <expand macro="edam_ontology"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

33 <expand macro="requirements"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

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parents:

diff changeset

34 <version_command>metaphlan -v</version_command>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

35 <command detect_errors="aggressive"><![CDATA[

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

36 #if $inputs.in.selector == "raw"

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

37 #if $inputs.in.raw_in.selector == "single"

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

38 #set full_ext=$inputs.in.raw_in.in.datatype.file_ext

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

39 #if $full_ext.endswith("gz")

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

40 #set $file_path="in"

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

41 zcat '$inputs.in.raw_in.in' > '$file_path'

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

42 &&

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

43 #else if $full_ext.endswith("bz2")

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

44 #set $file_path="in"

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

45 bzcat '$inputs.in.raw_in.in' > '$file_path'

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

46 &&

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

47 #else

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

48 #set $file_path=$inputs.in.raw_in.in

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

49 #end if

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

50 #else if $inputs.in.raw_in.selector == "multiple"

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

51 #set full_ext=$inputs.in.raw_in.in[0].datatype.file_ext

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

52 #set file_path=""

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

53 #set sep=""

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

54 #for $i, $f in enumerate($inputs.in.raw_in.in)

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

55 #if $f.datatype.file_ext != $full_ext

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

56 echo "Different datatypes for input files"

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

57 &&

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

58 exit 1

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

59 #end if

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

60 #if $full_ext.endswith("gz")

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

61 #set fp="input_%s" % ($i)

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

62 zcat '$f' > '$fp'

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

63 &&

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

64 #else if $full_ext.endswith("bz2")

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

65 #set fp="input_%s" % ($i)

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

66 bzcat '$f' > '$fp'

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

67 &&

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

68 #else

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

69 #set fp=$f

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

70 #end if

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

71 #set $file_path+="%s%s" % ($sep, $fp)

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

72 #set $sep=","

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

73 #end for

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

74 #else if $inputs.in.raw_in.selector == "paired"

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

75 #set full_ext=$inputs.in.raw_in.in_f.datatype.file_ext

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

76 #if $full_ext != $inputs.in.raw_in.in_r.datatype.file_ext

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

77 echo "Different datatypes for input paired-end files"

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

78 &&

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

79 exit 1

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

80 #end if

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

81 #if $full_ext.endswith("gz")

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82 zcat '$inputs.in.raw_in.in_f' > 'in_f'

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83 &&

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84 zcat '$inputs.in.raw_in.in_r' > 'in_r'

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diff changeset

85 &&

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diff changeset

86 #set file_path="in_f,in_r"

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diff changeset

87 #else if $full_ext.endswith("bz2")

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88 bzcat '$inputs.in.raw_in.in_f' > 'in_f'

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89 &&

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diff changeset

90 bzcat '$inputs.in.raw_in.in_r' > 'in_r'

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diff changeset

91 &&

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diff changeset

92 #set file_path="in_f,in_r"

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93 #else

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94 #set file_path="%s,%s" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r)

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

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diff changeset

95 #end if

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96 #end if

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97

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diff changeset

98 #if $full_ext.startswith("fastq")

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99 #set ext='fastq'

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100 #else if $full_ext.startswith("fasta") and $full_ext.endswith(("gz","bz2"))

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101 #set ext='fasta'

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102 #else

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103 #set ext=$full_ext

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104 #end if

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105 #end if

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106

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107 #if $inputs.db.db_selector == "history"

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108 mkdir 'ref_db'

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109 &&

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110 bowtie2-build --large-index '$inputs.db.bowtie2db' 'ref_db/custom_db'

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111 &&

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112 python '$__tool_directory__/customizemetadata.py'

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113 transform_json_to_pkl

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114 --json '$inputs.db.mpa_pkl'

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115 --pkl 'ref_db/custom_db.pkl'

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116 &&

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117 #end if

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118

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119 metaphlan

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120 #if $inputs.in.selector == "raw"

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121 '$file_path'

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122 --input_type '$ext'

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123 --read_min_len $inputs.in.read_min_len

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124 --bt2_ps '$inputs.in.mapping.bt2_ps'

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125 --min_mapq_val $inputs.in.mapping.min_mapq_val

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126 #if $ext == "sam"

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127 --nreads \$(cat '$file_path' | grep -c -v '^@')

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128 #end if

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129 #else

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130 '$inputs.in.in'

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131 --input_type '$inputs.in.selector'

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132 #if $inputs.in.selector == "sam"

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133 --nreads \$(cat '$inputs.in.in' | grep -c -v '^@')

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134 #end if

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135 #end if

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136 #if $inputs.db.db_selector == "cached"

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137 --bowtie2db '$inputs.db.cached_db.fields.path'

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138 --index '$inputs.db.cached_db.fields.dbkey'

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139 #else

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140 --bowtie2db 'ref_db/'

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141 --index 'custom_db'

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142 #end if

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143 -t '$analysis.analysis_type.t'

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144 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats"

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145 --tax_lev '$analysis.analysis_type.tax_lev.tax_lev'

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146 #else if $analysis.analysis_type.t == "clade_specific_strain_tracker"

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147 --clade '$analysis.analysis_type.clade'

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148 #if str($analysis.analysis_type.min_ab) != ''

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149 --min_ab $analysis.analysis_type.min_ab

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150 #end if

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151 #else if $analysis.analysis_type.t == "marker_ab_table" and str($analysis.analysis_type.nreads) != ''

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152 --nreads $$analysis.analysis_type.nreads

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153 #else if $analysis.analysis_type.t == "marker_pres_table" and str($analysis.analysis_type.pres_th) != ''

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154 --pres_th $analysis.analysis_type.pres_th

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155 #end if

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156 --min_cu_len $analysis.min_cu_len

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157 #if str($analysis.min_alignment_len) != ''

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158 --min_alignment_len $analysis.min_alignment_len

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159 #end if

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160 #if 'add_viruses' in $analysis.organism_profiling

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161 --add_viruses

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162 #end if

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163 #if 'ignore_eukaryotes' in $analysis.organism_profiling

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164 --ignore_eukaryotes

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165 #end if

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166 #if 'ignore_bacteria' in $analysis.organism_profiling

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167 --ignore_bacteria

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168 #end if

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169 #if 'ignore_archaea' in $analysis.organism_profiling

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170 --ignore_archaea

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171 #end if

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172 --stat_q $analysis.stat_q

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173 --perc_nonzero $analysis.perc_nonzero

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174 #if $analysis.ignore_markers

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175 --ignore_markers '$analysis.ignore_markers'

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176 #end if

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177 $analysis.avoid_disqm

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178 --sample_id_key '$out.sample_id_key'

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179 --sample_id '$out.sample_id'

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180 $out.use_group_representative

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181 $out.legacy_output

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182 $out.CAMI_format_output

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183 $out.unknown_estimation

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184 -o '$output_file'

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185 --bowtie2out 'bowtie2out'

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186 -s '$sam_output_file'

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187 --biom '$biom_output_file'

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188 --nproc \${GALAXY_SLOTS:-4}

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189

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190 #if $inputs.in.selector == "raw"

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191 &&

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192 mv 'bowtie2out' '$bowtie2out'

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193 #end if

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194

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195 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels

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196 &&

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197 mkdir 'split_levels'

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198 &&

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199 python '$__tool_directory__/formatoutput.py'

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200 split_levels

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201 --metaphlan_output '$output_file'

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202 --outdir 'split_levels'

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203 $out.legacy_output

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204

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205 #end if

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206

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207 #if $out.krona_output

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208 &&

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209 python '$__tool_directory__/formatoutput.py'

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210 format_for_krona

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211 --metaphlan_output '$output_file'

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212 --krona_output '$krona_output_file'

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213 #end if

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214 ]]></command>

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215 <inputs>

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216 <section name="inputs" title="Inputs" expanded="true">

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217 <conditional name="in">

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218 <param name="selector" type="select" label="Input(s)">

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219 <option value="raw" selected="true">Fasta/FastQ file(s) with microbiota reads</option>

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220 <option value="sam">Externally BowTie2-mapped SAM file</option>

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221 <option value="bowtie2out">Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run</option>

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222 </param>

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223 <when value="raw">

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224 <conditional name="raw_in">

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225 <param name="selector" type="select" label="Fasta/FastQ file(s) with microbiota reads">

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226 <option value="single" selected="true">One single-end file</option>

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227 <option value="multiple">Multiple single-end files</option>

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228 <option value="paired">Paired-end files</option>

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229 </param>

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230 <when value="single">

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231 <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ file with microbiota reads"/>

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232 </when>

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233 <when value="multiple">

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234 <param name="in" type="data" format="@FILE_FORMATS@" multiple="true" label="Single-end Fasta/FastQ files with microbiota reads"/>

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235 </when>

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236 <when value="paired">

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237 <param name="in_f" type="data" format="@FILE_FORMATS@" label="Forward paired-end Fasta/FastQ file with microbiota reads"/>

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238 <param name="in_r" type="data" format="@FILE_FORMATS@" label="Reverse paired-end Fasta/FastQ file with microbiota reads"/>

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239 </when>

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240 </conditional>

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241 <param argument="--read_min_len" type="integer" value="70" label="Minimum length of the reads to be considered when parsing the input file"/>

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242 <section name="mapping" title="Mapping" expanded="true">

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243 <param argument="--bt2_ps" type="select" label="Presets options for BowTie2" help="Applied only with FASTA files">

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244 <option value="sensitive">Sensitive</option>

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245 <option value="very-sensitive" selected="true">Very sensitive</option>

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246 <option value="sensitive-local">Sensitive local</option>

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247 <option value="very-sensitive-local">Very sensitive local</option>

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248 </param>

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249 <param argument="--min_mapq_val" type="integer" value="5" label="Minimum mapping quality value (MAPQ)"/>

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250 </section>

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251 </when>

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252 <when value="sam">

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253 <param name="in" type="data" format="sam" label="Externally BowTie2-mapped SAM file" help="BowTie2 needs to be used first to map microbiota reads"/>

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254 </when>

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255 <when value="bowtie2out">

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256 <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run"

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257 help="File needs to be generated with MetaPhlAn versions >3.0"/>

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258 </when>

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259 </conditional>

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260 <conditional name="db">

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261 <param name="db_selector" type="select" label="Database with clade-specific marker genes">

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262 <option value="cached" selected="true">Locally cached</option>

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263 <option value="history">From history</option>

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264 </param>

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265 <when value="cached">

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266 <param name="cached_db" type="select" label="Cached database with clade-specific marker genes">

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267 <options from_data_table="@IDX_DATA_TABLE@">

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268 <filter type="static_value" column="4" value="@IDX_VERSION@"/>

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269 <validator message="No compatible MetaPhlAn database is available" type="no_options"/>

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270 </options>

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271 </param>

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272 </when>

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273 <when value="history">

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274 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>

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275 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>

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276 </when>

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277 </conditional>

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278 </section>

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279 <section name="analysis" title="Analysis" expanded="true">

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280 <conditional name="analysis_type">

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281 <param argument="-t" type="select" label="Type of analysis to perform">

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282 <option value="rel_ab" selected="true">rel_ab: Profiling a microbiota in terms of relative abundances</option>

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283 <option value="rel_ab_w_read_stats">rel_ab_w_read_stats: Profiling a microbiota in terms of relative abundances and estimate the number of reads comming from each clade</option>

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284 <option value="reads_map">reads_map: Mapping from reads to clades (only reads hitting a marker)</option>

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285 <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option>

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286 <option value="clade_specific_strain_tracker">clade_specific_strain_tracker: List of markers present for a specific clade and all its subclades</option>

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287 <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when > 0.0 and normalized by microbiota size if number of reads is specified)</option>

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288 <option value="marker_counts">marker_counts: Non-normalized marker counts (use with extreme caution)</option>

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289 <option value="marker_pres_table">marker_pres_table: List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>

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290 </param>

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291 <when value="rel_ab">

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292 <expand macro="tax_lev"/>

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293 </when>

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294 <when value="rel_ab_w_read_stats">

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295 <expand macro="tax_lev"/>

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296 </when>

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297 <when value="reads_map"/>

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298 <when value="clade_profiles"/>

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299 <when value="clade_specific_strain_tracker">

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300 <param argument="--clade" type="text" value="" label="Clade for which to extract list of markers present"

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301 help="Markers are also extracted for subclades" />

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302 <param argument="--min_ab" type="float" optional="true" label="The minimum percentage abundance for the clade"/>

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303 </when>

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304 <when value="marker_ab_table">

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305 <param argument="--nreads" type="integer" optional="true" label="Total number of reads in the original microbiota"

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306 help="It is used for normalizing the length-normalized counts with the microbiota size as well. No normalization applied if the value is not specified"/>

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307 </when>

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308 <when value="marker_counts"/>

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309 <when value="marker_pres_table">

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310 <param argument="--pres_th" type="integer" optional="true" label="Threshold for calling a marker present"/>

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311 </when>

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312 </conditional>

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313 <param argument="--min_cu_len" type="integer" value="2000"

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314 label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/>

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315 <param argument="--min_alignment_len" type="integer" optional="true"

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316 label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/>

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317 <param name="organism_profiling" type="select" multiple="true" optional="true" label="Organisms to profile">

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318 <option value="add_viruses" selected="true">Profile viral organisms (add_viruses)</option>

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319 <option value="ignore_eukaryotes">Ignore eukaryotic organisms (ignore_eukaryotes)</option>

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320 <option value="ignore_bacteria">Ignore bacteria organisms (ignore_bacteria)</option>

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321 <option value="ignore_archaea">Ignore archea organisms (ignore_archaea)</option>

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322 </param>

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323 <param argument="--stat" type="select" label="Statistical approach for converting marker abundances into clade abundances">

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324 <option value="avg_g">avg_g: Clade global (i.e. normalizing all markers together) average (avg_g)</option>

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325 <option value="avg_l">avg_l: Average of length-normalized marker counts</option>

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326 <option value="tavg_g" selected="true">tavg_g: Truncated clade global average at --stat_q quantile</option>

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327 <option value="tavg_l">tavg_l: Truncated average of length-normalized marker counts (at --stat_q)</option>

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328 <option value="wavg_g">wavg_g: Winsorized clade global average (at --stat_q)</option>

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329 <option value="wavg_l">wavg_l: Winsorized average of length-normalized marker counts (at --stat_q)</option>

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330 <option value="med">med: Median of length-normalized marker counts</option>

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331 </param>

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332 <param argument="--stat_q" type="float" value="0.2" label="Quantile value for the robust average"/>

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333 <param argument="--perc_nonzero" type="float" value="0.33" label="Percentage of markers with a non zero relative abundance for misidentify a species"/>

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334 <param argument="--ignore_markers" type="data" format="txt,tabular" optional="true" label="File containing a list of markers to ignore" help="One marker per line"/>

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335 <param argument="--avoid_disqm" type='boolean' checked="true" truevalue='--avoid_disqm' falsevalue=''

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336 label="Deactivate the procedure of disambiguating the quasi-markers based on the marker abundance pattern found in the sample?"

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337 help="It is generally recommended to keep the disambiguation procedure in order to minimize false positives"/>

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338 </section>

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339 <section name="out" title="Outputs" expanded="true">

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340 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/>

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341 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/>

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342 <param argument="--use_group_representative" type='boolean' checked="false" truevalue='--use_group_representative' falsevalue=''

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343 label="Use a species as representative for species groups?"/>

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344 <param argument="--legacy-output" type='boolean' checked="false" truevalue='--legacy-output' falsevalue=''

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345 label="Old MetaPhlAn2 two columns output?"/>

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346 <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue=''

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347 label="Report the profiling using the CAMI output format?"/>

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348 <param argument="--unknown_estimation" type='boolean' checked="false" truevalue='--unknown_estimation' falsevalue=''

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349 label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>

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350 <param name="krona_output" type='boolean' checked="false" truevalue='true' falsevalue='false' label="Output for Krona?"/>

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351 </section>

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352 </inputs>

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353 <outputs>

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354 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances" />

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355 <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output">

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356 <filter>inputs['in']['selector'] == "raw"</filter>

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357 </data>

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358 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file">

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359 <filter>inputs['in']['selector'] == "raw"</filter>

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360 </data>

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361 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />

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362 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" >

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363 <discover_datasets pattern="(?P<designation>.+)" directory="split_levels/" format="tabular"/>

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364 <filter>analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>

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365 </collection>

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366 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona">

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367 <filter>out['krona_output']</filter>

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368 </data>

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369 </outputs>

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370 <tests>

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371 <test expect_num_outputs="6">

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372 <section name="inputs">

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373 <conditional name="in">

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374 <param name="selector" value="raw"/>

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375 <conditional name="raw_in">

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376

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377 <param name="selector" value="single"/>

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378 <param name="in" value="no_taxon_input.fasta"/>

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379 </conditional>

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380 <param name="read_min_len" value="70"/>

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381 <section name="mapping">

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382 <param name="bt2_ps" value="sensitive"/>

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383 <param name="min_mapq_val" value="5"/>

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384 </section>

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385 </conditional>

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386 <conditional name="db">

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387

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388 <param name="db_selector" value="cached"/>

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389 <param name="cached_db" value="test-db-20210409"/>

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390 </conditional>

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391 </section>

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392 <section name="analysis">

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393 <conditional name="analysis_type">

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394 <param name="t" value="rel_ab"/>

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395 <conditional name="tax_lev">

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396 <param name="tax_lev" value="a"/>

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397 <param name="split_levels" value="true"/>

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398 </conditional>

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399 </conditional>

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diff changeset

400 <param name="min_cu_len" value="2000"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

401 <param name="organism_profiling" value="add_viruses"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

402 <param name="stat" value="avg_g"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

403 <param name="stat_q" value="0.2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

404 <param name="perc_nonzero" value="0.33"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

405 <param name="avoid_disqm" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

406 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

407 <section name="out">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

408 <param name="sample_id_key" value="SampleID"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

409 <param name="sample_id" value="Metaphlan_Analysis"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

410 <param name="use_group_representative" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

411 <param name="legacy_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

412 <param name="CAMI_format_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

413 <param name="unknown_estimation" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

414 <param name="krona_output" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

415 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

416 <output name="output_file" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

417 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

418 <has_text text="UNCLASSIFIED"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

419 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

420 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

421 <output name="bowtie2out" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

422 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

423 <not_has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

424 <has_n_lines n="2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

425 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

426 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

427 <output name="sam_output_file" ftype="sam">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

428 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

429 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

430 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

431 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

432 <output name="biom_output_file" ftype="biom1">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

433 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

434 <not_has_text text="k__Bacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

435 <not_has_text text="p__Actinobacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

436 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

437 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

438 <output_collection name="levels" type="list" >

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

439

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

440 <element name="all" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

441 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

442 <has_text text="class"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

443 <has_n_columns n="17"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

444 <has_n_lines n="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

445 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

446 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

447 <element name="class" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

448 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

449 <has_text text="class_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

450 <not_has_text text="phylum_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

451 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

452 <has_n_lines n="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

453 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

454 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

455 <element name="family" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

456 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

457 <has_text text="family_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

458 <not_has_text text="order"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

459 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

460 <has_n_lines n="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

461 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

462 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

463 <element name="genus" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

464 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

465 <has_text text="genus_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

466 <not_has_text text="family"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

467 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

468 <has_n_lines n="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

469 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

470 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

471 <element name="kingdom" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

472 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

473 <has_text text="kingdom_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

474 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

475 <has_n_lines n="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

476 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

477 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

478 <element name="order" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

479 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

480 <has_text text="order_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

481 <not_has_text text="class_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

482 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

483 <has_n_lines n="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

484 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

485 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

486 <element name="phylum" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

487 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

488 <has_text text="phylum_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

489 <not_has_text text="kingdom_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

490 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

491 <has_n_lines n="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

492 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

493 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

494 <element name="species" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

495 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

496 <has_text text="species_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

497 <not_has_text text="genus"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

498 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

499 <has_n_lines n="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

500 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

501 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

502 <element name="strains" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

503 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

504 <has_text text="strains_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

505 <not_has_text text="species_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

506 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

507 <has_n_lines n="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

508 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

509 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

510 </output_collection>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

511 <output name="krona_output_file" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

512 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

513 <not_has_text text="k__Bacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

514 <has_n_lines n="1" delta="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

515 <has_size value="1" delta="1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

516 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

517 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

518 </test>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

519 <test expect_num_outputs="6">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

520 <section name="inputs">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

521 <conditional name="in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

522 <param name="selector" value="raw"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

523 <conditional name="raw_in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

524

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

525 <param name="selector" value="single"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

526 <param name="in" value="SRS014464-Anterior_nares.fasta.gz"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

527 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

528 <param name="read_min_len" value="70"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

529 <section name="mapping">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

530 <param name="bt2_ps" value="sensitive"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

531 <param name="min_mapq_val" value="5"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

532 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

533 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

534 <conditional name="db">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

535

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

536 <param name="db_selector" value="cached"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

537 <param name="cached_db" value="test-db-20210409"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

538 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

539 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

540 <section name="analysis">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

541 <conditional name="analysis_type">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

542 <param name="t" value="rel_ab"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

543 <conditional name="tax_lev">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

544 <param name="tax_lev" value="a"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

545 <param name="split_levels" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

546 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

547 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

548 <param name="min_cu_len" value="2000"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

549 <param name="organism_profiling" value="add_viruses"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

550 <param name="stat" value="avg_g"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

551 <param name="stat_q" value="0.2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

552 <param name="perc_nonzero" value="0.33"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

553 <param name="avoid_disqm" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

554 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

555 <section name="out">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

556 <param name="sample_id_key" value="SampleID"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

557 <param name="sample_id" value="Metaphlan_Analysis"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

558 <param name="use_group_representative" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

559 <param name="legacy_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

560 <param name="CAMI_format_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

561 <param name="unknown_estimation" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

562 <param name="krona_output" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

563 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

564 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

565 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

567 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

568 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

569 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-bowtie2out.tabular" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

570 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

571 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

572 <has_text text="37637__U2I1U8__N579_01580"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

573 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

574 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

575 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares.sam" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

576 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

577 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

578 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

579 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

580 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

581 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

583 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

584 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

585 <output_collection name="levels" type="list" >

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

586 <element name="all" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

587 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

588 <has_text text="Gammaproteobacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

589 <has_text text="Corynebacterium accolens"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

590 <has_n_columns n="17"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

591 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

592 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

593 <element name="class" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

594 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

595 <has_text text="class_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

596 <not_has_text text="phylum_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

597 <has_text text="Actinobacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

598 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

599 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

600 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

601 <element name="family" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

602 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

603 <has_text text="family_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

604 <not_has_text text="order"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

605 <has_text text="Propionibacteriaceae"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

606 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

607 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

608 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

609 <element name="genus" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

610 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

611 <has_text text="genus_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

612 <not_has_text text="family"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

613 <has_text text="Cutibacterium"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

614 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

615 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

616 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

617 <element name="kingdom" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

618 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

619 <has_text text="kingdom_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

620 <has_text text="Bacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

621 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

622 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

623 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

624 <element name="order" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

625 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

626 <has_text text="order_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

627 <not_has_text text="class_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

628 <has_text text="Propionibacteriales"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

629 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

630 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

631 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

632 <element name="phylum" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

633 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

634 <has_text text="phylum_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

635 <not_has_text text="kingdom_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

636 <has_text text="Firmicutes"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

637 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

638 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

639 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

640 <element name="species" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

641 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

642 <has_text text="species_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

643 <not_has_text text="genus"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

644 <has_text text="Corynebacterium accolens"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

645 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

646 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

647 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

648 <element name="strains" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

649 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

650 <has_text text="strains_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

651 <not_has_text text="species_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

652 <has_n_columns n="3"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

653 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

654 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

655 </output_collection>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

656 <output name="krona_output_file" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

657 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

658 <not_has_text text="k__Bacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

659 <has_text text="Corynebacterium accolens"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

660 <has_n_columns n="9"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

661 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

662 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

663 </test>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

664 <test expect_num_outputs="4">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

665 <section name="inputs">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

666 <conditional name="in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

667 <param name="selector" value="raw"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

668 <conditional name="raw_in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

669

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

670 <param name="selector" value="multiple"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

671 <param name="in" value="SRS014464-Anterior_nares.fasta.gz,SRS014464-Anterior_nares.fasta.gz"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

672 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

673 <param name="read_min_len" value="70"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

674 <section name="mapping">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

675 <param name="bt2_ps" value="sensitive"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

676 <param name="min_mapq_val" value="5"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

677 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

678 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

679 <conditional name="db">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

680

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

681 <param name="db_selector" value="history"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

682 <param name="bowtie2db" value="test-db.fasta"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

683 <param name="mpa_pkl" value="test-db.json"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

684 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

685 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

686 <section name="analysis">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

687 <conditional name="analysis_type">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

688 <param name="t" value="rel_ab"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

689 <conditional name="tax_lev">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

690 <param name="tax_lev" value="a"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

691 <param name="split_levels" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

692 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

693 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

694 <param name="min_cu_len" value="2000"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

695 <param name="organism_profiling" value="add_viruses"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

696 <param name="stat" value="avg_g"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

697 <param name="stat_q" value="0.2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

698 <param name="perc_nonzero" value="0.33"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

699 <param name="avoid_disqm" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

700 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

701 <section name="out">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

702 <param name="sample_id_key" value="SampleID"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

703 <param name="sample_id" value="Metaphlan_Analysis"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

704 <param name="use_group_representative" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

705 <param name="legacy_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

706 <param name="CAMI_format_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

707 <param name="unknown_estimation" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

708 <param name="krona_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

709 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

710 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

711 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

713 <has_text text="relative_abundance"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

714 <has_text text="NCBI_tax_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

715 <has_text text="clade_name"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

716 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

717 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

718 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

719 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

720 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

721 <has_text text="37637__U2I1U8__N579_01580"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

722 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

723 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

724 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares-two-inputs.sam" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

725 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

726 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

727 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

728 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

729 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

730 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

732 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

733 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

734 </test>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

735 <test expect_num_outputs="4">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

736 <section name="inputs">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

737 <conditional name="in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

738 <param name="selector" value="raw"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

739 <conditional name="raw_in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

740

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

741 <param name="selector" value="paired"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

742 <param name="in_f" value="SRS014464-Anterior_nares.fasta.gz"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

743 <param name="in_r" value="SRS014464-Anterior_nares.fasta.gz"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

744 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

745 <param name="read_min_len" value="70"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

746 <section name="mapping">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

747 <param name="bt2_ps" value="sensitive"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

748 <param name="min_mapq_val" value="5"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

749 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

750 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

751 <conditional name="db">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

752

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

753 <param name="db_selector" value="cached"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

754 <param name="cached_db" value="test-db-20210409"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

755 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

756 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

757 <section name="analysis">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

758 <conditional name="analysis_type">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

759 <param name="t" value="rel_ab"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

760 <conditional name="tax_lev">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

761 <param name="tax_lev" value="a"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

762 <param name="split_levels" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

763 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

764 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

765 <param name="min_cu_len" value="2000"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

766 <param name="organism_profiling" value="add_viruses"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

767 <param name="stat" value="avg_g"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

768 <param name="stat_q" value="0.2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

769 <param name="perc_nonzero" value="0.33"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

770 <param name="avoid_disqm" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

771 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

772 <section name="out">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

773 <param name="sample_id_key" value="SampleID"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

774 <param name="sample_id" value="Metaphlan_Analysis"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

775 <param name="use_group_representative" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

776 <param name="legacy_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

777 <param name="CAMI_format_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

778 <param name="unknown_estimation" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

779 <param name="krona_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

780 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

781 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

782 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

784 <has_text text="relative_abundance"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

785 <has_text text="NCBI_tax_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

786 <has_text text="clade_name"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

787 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

788 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

789 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

790 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

791 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

792 <has_text text="37637__U2I1U8__N579_01580"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

793 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

794 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

795 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares-two-inputs.sam" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

796 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

797 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

798 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

799 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

800 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

801 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

803 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

804 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

805 </test>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

806 <test expect_num_outputs="2">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

807 <section name="inputs">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

808 <conditional name="in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

809

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

810 <param name="selector" value="sam"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

811 <param name="in" value="SRS014464-Anterior_nares.sam"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

812 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

813 <conditional name="db">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

814

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

815 <param name="db_selector" value="cached"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

816 <param name="cached_db" value="test-db-20210409"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

817 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

818 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

819 <section name="analysis">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

820 <conditional name="analysis_type">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

821 <param name="t" value="rel_ab"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

822 <conditional name="tax_lev">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

823 <param name="tax_lev" value="a"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

824 <param name="split_levels" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

825 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

826 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

827 <param name="min_cu_len" value="2000"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

828 <param name="organism_profiling" value="add_viruses"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

829 <param name="stat" value="avg_g"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

830 <param name="stat_q" value="0.2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

831 <param name="perc_nonzero" value="0.33"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

832 <param name="avoid_disqm" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

833 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

834 <section name="out">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

835 <param name="sample_id_key" value="SampleID"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

836 <param name="sample_id" value="Metaphlan_Analysis"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

837 <param name="use_group_representative" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

838 <param name="legacy_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

839 <param name="CAMI_format_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

840 <param name="unknown_estimation" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

841 <param name="krona_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

842 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

843 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

844 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

846 <has_text text="relative_abundance"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

847 <has_text text="NCBI_tax_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

848 <has_text text="clade_name"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

849 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

850 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

851 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

852 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

854 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

855 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

856 </test>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

857 <test expect_num_outputs="2">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

858 <section name="inputs">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

859 <conditional name="in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

860

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

861 <param name="selector" value="bowtie2out"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

862 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

863 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

864 <conditional name="db">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

865

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

866 <param name="db_selector" value="cached"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

867 <param name="cached_db" value="test-db-20210409"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

868 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

869 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

870 <conditional name="in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

871 <param name="selector" value="bowtie2out"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

872 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

873 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

874 <section name="mapping">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

875 <param name="bt2_ps" value="sensite"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

876 <param name="min_mapq_val" value="5"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

877 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

878 <section name="analysis">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

879 <conditional name="analysis_type">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

880 <param name="t" value="rel_ab"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

881 <conditional name="tax_lev">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

882 <param name="tax_lev" value="a"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

883 <param name="split_levels" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

884 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

885 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

886 <param name="min_cu_len" value="2000"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

887 <param name="organism_profiling" value="add_viruses"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

888 <param name="stat" value="avg_g"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

889 <param name="stat_q" value="0.2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

890 <param name="perc_nonzero" value="0.33"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

891 <param name="avoid_disqm" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

892 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

893 <section name="out">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

894 <param name="sample_id_key" value="SampleID"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

895 <param name="sample_id" value="Metaphlan_Analysis"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

896 <param name="use_group_representative" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

897 <param name="legacy_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

898 <param name="CAMI_format_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

899 <param name="unknown_estimation" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

900 <param name="krona_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

901 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

902 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

903 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

905 <has_text text="relative_abundance"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

906 <has_text text="NCBI_tax_id"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

907 <has_text text="clade_name"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

908 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

909 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

910 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

911 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

913 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

914 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

915 </test>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

916 <test expect_num_outputs="6">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

917 <section name="inputs">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

918 <conditional name="in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

919 <param name="selector" value="raw"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

920 <conditional name="raw_in">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

921

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

922 <param name="selector" value="single"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

923 <param name="in" value="SRS014464-Anterior_nares.fasta"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

924 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

925 <param name="read_min_len" value="70"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

926 <section name="mapping">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

927 <param name="bt2_ps" value="sensitive"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

928 <param name="min_mapq_val" value="5"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

929 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

930 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

931 <conditional name="db">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

932

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

933 <param name="db_selector" value="cached"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

934 <param name="cached_db" value="test-db-20210409"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

935 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

936 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

937 <section name="analysis">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

938 <conditional name="analysis_type">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

939 <param name="t" value="rel_ab"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

940 <conditional name="tax_lev">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

941 <param name="tax_lev" value="a"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

942 <param name="split_levels" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

943 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

944 </conditional>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

945 <param name="min_cu_len" value="2000"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

946 <param name="organism_profiling" value="add_viruses"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

947 <param name="stat" value="avg_g"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

948 <param name="stat_q" value="0.2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

949 <param name="perc_nonzero" value="0.33"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

950 <param name="ignore_markers" value="marker.txt"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

951 <param name="avoid_disqm" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

952 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

953 <section name="out">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

954 <param name="sample_id_key" value="SampleID"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

955 <param name="sample_id" value="Metaphlan_Analysis"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

956 <param name="use_group_representative" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

957 <param name="legacy_output" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

958 <param name="CAMI_format_output" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

959 <param name="unknown_estimation" value="false"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

960 <param name="krona_output" value="true"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

961 </section>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

962 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

963 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

965 <has_text text="SampleID"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

966 <has_text text="Metaphlan_Analysis"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

967 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

968 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

969 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-bowtie2out.tabular" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

970 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

971 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

972 <has_text text="37637__U2I1U8__N579_01580"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

973 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

974 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

975 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares.sam" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

976 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

977 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

978 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

979 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

980 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

981 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

983 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

984 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

985 <output_collection name="levels" type="list" >

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

986 <element name="all" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

987 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

988 <has_text text="Gammaproteobacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

989 <has_text text="Corynebacterium accolens"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

990 <has_n_columns n="9"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

991 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

992 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

993 <element name="class" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

994 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

995 <has_text text="class"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

996 <has_text text="Actinobacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

997 <has_n_columns n="2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

998 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

999 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1000 <element name="family" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1001 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1002 <has_text text="family"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1003 <has_text text="Propionibacteriaceae"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1004 <has_n_columns n="2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1005 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1006 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1007 <element name="genus" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1008 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1009 <has_text text="genus"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1010 <has_text text="Cutibacterium"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1011 <has_n_columns n="2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1012 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1013 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1014 <element name="kingdom" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1015 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1016 <has_text text="kingdom"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1017 <has_text text="Bacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1018 <has_n_columns n="2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1019 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1020 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1021 <element name="order" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1022 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1023 <has_text text="order"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1024 <has_text text="Propionibacteriales"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1025 <has_n_columns n="2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1026 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1027 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1028 <element name="phylum" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1029 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1030 <has_text text="phylum"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1031 <has_text text="Firmicutes"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1032 <has_n_columns n="2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1033 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1034 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1035 <element name="species" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1036 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1037 <has_text text="species"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1038 <has_text text="Corynebacterium accolens"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1039 <has_n_columns n="2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1040 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1041 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1042 <element name="strains" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1043 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1044 <has_text text="strains"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1045 <has_n_columns n="2"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1046 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1047 </element>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1048 </output_collection>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1049 <output name="krona_output_file" ftype="tabular">

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1050 <assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1051 <not_has_text text="k__Bacteria"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1052 <has_text text="Corynebacterium accolens"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1053 <has_n_columns n="9"/>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1054 </assert_contents>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1055 </output>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1056 </test>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1057 </tests>

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1058 <help><![CDATA[

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1059 What it does

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1060 ============

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1061

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1062 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria,

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1063 Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) at species-level.

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1064

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1065 MetaPhlAn relies on ~1.1M unique clade-specific marker genes identified from ~100,000 reference genomes

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1066 (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing:

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1067

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1068 - unambiguous taxonomic assignments;

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1069 - accurate estimation of organismal relative abundance;

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1070 - species-level resolution for bacteria, archaea, eukaryotes and viruses;

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thanhlv

parents:

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1071 - strain identification and tracking

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thanhlv

parents:

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1072 - orders of magnitude speedups compared to existing methods.

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thanhlv

parents:

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1073 - microbiota strain-level population genomics

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thanhlv

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1074

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thanhlv

parents:

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1075 MetaPhlAn clade-abundance estimation

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thanhlv

parents:

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1076 ------------------------------------

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1077

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thanhlv

parents:

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1078 The basic usage of MetaPhlAn consists in the identification of the clades (from phyla to species and

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1079 strains in particular cases) present in the microbiota obtained from a microbiome sample and their

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1080 relative abundance.

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thanhlv

parents:

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1081

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thanhlv

parents:

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1082 Marker level analysis

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1083 ---------------------

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thanhlv

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1084

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thanhlv

parents:

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1085 MetaPhlAn introduces the capability of characterizing organisms at the strain level using non

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1086 aggregated marker information. Such capability comes with several slightly different flavours and

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1087 are a way to perform strain tracking and comparison across multiple samples.

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thanhlv

parents:

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1088

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thanhlv

parents:

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1089 Usually, MetaPhlAn is first ran with default parameters for the type of analysis to profile the

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1090 species present in the community, and then a strain-level profiling can be performed to zoom-in on

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1091 specific species of interest. This operation can be performed quickly as it exploits the bowtie2out

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1092 intermediate file saved during the execution of the default analysis type.

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parents:

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1093

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thanhlv

parents:

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1094 Inputs

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thanhlv

parents:

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1095 ======

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thanhlv

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1096

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thanhlv

parents:

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1097 Metaphlan takes as input either:

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1098

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thanhlv

parents:

diff changeset

1099 - one or several sequence files in Fasta, FastQ (whether compressed or not)

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1100 - a BowTie2 produced SAM file

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1101 - an intermediary mapping file of the microbiota generated by a previous MetaPhlAn run

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thanhlv

parents:

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1102

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parents:

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1103 It also needs the reference database, which can be locally installed or customized using the dedicated tools.

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1104

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thanhlv

parents:

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1105 Outputs

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1106 =======

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thanhlv

parents:

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1107

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

diff changeset

1108 The main output is a tab-separated file with the predicted taxon relative abundances.

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

thanhlv

parents:

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1109

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thanhlv

parents:

diff changeset

1110 It also generates a BIOM file and some intermediate files (SAM and BowTie2out) if sequence files are given as inputs.

12e29dbb7041 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/

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1111

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1112

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thanhlv

parents:

diff changeset

1113 More help and use cases

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parents:

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1114 =======================

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1115

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1116 To get more information about MetaPhlAn usage and use cases, please refer to the `Metaphlan documentation`_.

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1117

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thanhlv

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1118 .. _Metaphlan documentation: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#Basic-Usage

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1119

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1120 ]]></help>

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thanhlv

parents:

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1121 <expand macro="citations"/>

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1122 </tool>

Mercurial > repos > thanhlv > metaphlan4

annotate metaphlan.xml @ 0:12e29dbb7041 draft default tip