metaphlan: metaphlan.xml annotate

annotate metaphlan.xml @ 8:1a6cdf55390f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c

author	iuc
date	Thu, 20 Apr 2023 11:26:53 +0000
parents	2131d7dca455
children	289b3807e80c

rev	line source
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	2 <description>to profile the composition of microbial communities</description>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	3 <macros>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	4 <import>macros.xml</import>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	5 <xml name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	6 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	7 <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	8 <option value="a" selected="true">All taxonomic levels</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	9 <option value="k">Kingdoms only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	10 <option value="p">Phyla only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	11 <option value="c">Classes only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	12 <option value="o">Orders only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	13 <option value="f">Families only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	14 <option value="g">Genera only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	15 <option value="s">Species only</option>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	16 </param>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	17 <when value="a">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	18 <param name="split_levels" type='boolean' checked="false" truevalue='true' falsevalue='false'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	19 label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	20 </when>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	21 <when value="k"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	22 <when value="p"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	23 <when value="c"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	24 <when value="o"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	25 <when value="f"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	26 <when value="g"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	27 <when value="s"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	28 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	29 </xml>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	30 <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2</token>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	31 </macros>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	32 <expand macro="edam_ontology"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	33 <expand macro="requirements"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	34 <version_command>metaphlan -v</version_command>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	35 <command detect_errors="aggressive"><![CDATA[
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	36 #if $inputs.in.selector == "raw"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	37 #if $inputs.in.raw_in.selector == "single"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	38 #set full_ext=$inputs.in.raw_in.in.datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	39 #if $full_ext.endswith("gz")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	40 #set $file_path="in"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	41 zcat '$inputs.in.raw_in.in' > '$file_path'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	42 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	43 #else if $full_ext.endswith("bz2")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	44 #set $file_path="in"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	45 bzcat '$inputs.in.raw_in.in' > '$file_path'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	46 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	47 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	48 #set $file_path=$inputs.in.raw_in.in
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	49 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	50 #else if $inputs.in.raw_in.selector == "multiple"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	51 #set full_ext=$inputs.in.raw_in.in[0].datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	52 #set file_path=""
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	53 #set sep=""
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	54 #for $i, $f in enumerate($inputs.in.raw_in.in)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	55 #if $f.datatype.file_ext != $full_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	56 echo "Different datatypes for input files"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	57 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	58 exit 1
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	59 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	60 #if $full_ext.endswith("gz")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	61 #set fp="input_%s" % ($i)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	62 zcat '$f' > '$fp'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	63 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	64 #else if $full_ext.endswith("bz2")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	65 #set fp="input_%s" % ($i)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	66 bzcat '$f' > '$fp'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	67 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	68 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	69 #set fp=$f
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	70 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	71 #set $file_path+="%s%s" % ($sep, $fp)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	72 #set $sep=","
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	73 #end for
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	74 #else if $inputs.in.raw_in.selector == "paired"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	75 #set full_ext=$inputs.in.raw_in.in_f.datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	76 #if $full_ext != $inputs.in.raw_in.in_r.datatype.file_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	77 echo "Different datatypes for input paired-end files"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	78 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	79 exit 1
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	80 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	81 #if $full_ext.endswith("gz")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	82 zcat '$inputs.in.raw_in.in_f' > 'in_f'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	83 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	84 zcat '$inputs.in.raw_in.in_r' > 'in_r'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	85 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	86 #set file_path="in_f,in_r"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	87 #else if $full_ext.endswith("bz2")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	88 bzcat '$inputs.in.raw_in.in_f' > 'in_f'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	89 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	90 bzcat '$inputs.in.raw_in.in_r' > 'in_r'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	91 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	92 #set file_path="in_f,in_r"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	93 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	94 #set file_path="%s,%s" % ($inputs.in.raw_in.in_f,$inputs.in.raw_in.in_r)
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	95 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	96 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	97
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	98 #if $full_ext.startswith("fastq")
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	99 #set ext='fastq'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	100 #else if $full_ext.startswith("fasta") and $full_ext.endswith(("gz","bz2"))
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	101 #set ext='fasta'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	102 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	103 #set ext=$full_ext
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	104 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	105 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	106
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	107 #if $inputs.db.db_selector == "history"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	108 mkdir 'ref_db'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	109 &&
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	110 bowtie2-build --large-index '$inputs.db.bowtie2db' 'ref_db/custom_db'
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	111 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	112 python '$__tool_directory__/customizemetadata.py'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	113 transform_json_to_pkl
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	114 --json '$inputs.db.mpa_pkl'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	115 --pkl 'ref_db/custom_db.pkl'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	116 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	117 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	118
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	119 metaphlan
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	120 #if $inputs.in.selector == "raw"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	121 '$file_path'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	122 --input_type '$ext'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	123 --read_min_len $inputs.in.read_min_len
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	124 --bt2_ps '$inputs.in.mapping.bt2_ps'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	125 --min_mapq_val $inputs.in.mapping.min_mapq_val
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	126 #if $ext == "sam"
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	127 --nreads \$(cat '$file_path' \| grep -c -v '^@')
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	128 #end if
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	129 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	130 '$inputs.in.in'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	131 --input_type '$inputs.in.selector'
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	132 #if $inputs.in.selector == "sam"
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	133 --nreads \$(cat '$inputs.in.in' \| grep -c -v '^@')
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	134 #end if
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	135 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	136 #if $inputs.db.db_selector == "cached"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	137 --bowtie2db '$inputs.db.cached_db.fields.path'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	138 --index '$inputs.db.cached_db.fields.dbkey'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	139 #else
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	140 --bowtie2db 'ref_db/'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	141 --index 'custom_db'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	142 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	143 -t '$analysis.analysis_type.t'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	144 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats"
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	145 --tax_lev '$analysis.analysis_type.tax_lev.tax_lev'
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	146 #else if $analysis.analysis_type.t == "clade_specific_strain_tracker"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	147 --clade '$analysis.analysis_type.clade'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	148 #if str($analysis.analysis_type.min_ab) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	149 --min_ab $analysis.analysis_type.min_ab
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	150 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	151 #else if $analysis.analysis_type.t == "marker_ab_table" and str($analysis.analysis_type.nreads) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	152 --nreads $$analysis.analysis_type.nreads
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	153 #else if $analysis.analysis_type.t == "marker_pres_table" and str($analysis.analysis_type.pres_th) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	154 --pres_th $analysis.analysis_type.pres_th
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	155 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	156 --min_cu_len $analysis.min_cu_len
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	157 #if str($analysis.min_alignment_len) != ''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	158 --min_alignment_len $analysis.min_alignment_len
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	159 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	160 #if 'add_viruses' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	161 --add_viruses
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	162 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	163 #if 'ignore_eukaryotes' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	164 --ignore_eukaryotes
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	165 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	166 #if 'ignore_bacteria' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	167 --ignore_bacteria
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	168 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	169 #if 'ignore_archaea' in $analysis.organism_profiling
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	170 --ignore_archaea
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	171 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	172 --stat_q $analysis.stat_q
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	173 --perc_nonzero $analysis.perc_nonzero
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	174 #if $analysis.ignore_markers
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	175 --ignore_markers '$analysis.ignore_markers'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	176 #end if
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	177 $analysis.avoid_disqm
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	178 --sample_id_key '$out.sample_id_key'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	179 --sample_id '$out.sample_id'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	180 $out.use_group_representative
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	181 $out.legacy_output
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	182 $out.CAMI_format_output
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	183 $out.unknown_estimation
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	184 -o '$output_file'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	185 --bowtie2out 'bowtie2out'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	186 -s '$sam_output_file'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	187 --biom '$biom_output_file'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	188 --nproc \${GALAXY_SLOTS:-4}
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	189
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	190 #if $inputs.in.selector == "raw"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	191 &&
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	192 mv 'bowtie2out' '$bowtie2out'
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	193 #end if
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	194
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	195
8 1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	196 #if $analysis.analysis_type.t in ['rel_ab', 'rel_ab_w_read_stats']
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	197 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	198 &&
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	199 mkdir 'split_levels'
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	200 &&
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	201 python '$__tool_directory__/formatoutput.py'
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	202 split_levels
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	203 --metaphlan_output '$output_file'
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	204 --outdir 'split_levels'
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	205 $out.legacy_output
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	206 #end if
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	207 #end if
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	208
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	209 #if $out.krona_output
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	210 &&
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	211 python '$__tool_directory__/formatoutput.py'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	212 format_for_krona
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	213 --metaphlan_output '$output_file'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	214 --krona_output '$krona_output_file'
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	215 #end if
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	216 ]]></command>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	217 <inputs>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	218 <section name="inputs" title="Inputs" expanded="true">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	219 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	220 <param name="selector" type="select" label="Input(s)">
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	221 <option value="raw" selected="true">Fasta/FastQ file(s) with microbiota reads</option>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	222 <option value="sam">Externally BowTie2-mapped SAM file</option>
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	223 <option value="bowtie2out">Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run</option>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	224 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	225 <when value="raw">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	226 <conditional name="raw_in">
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	227 <param name="selector" type="select" label="Fasta/FastQ file(s) with microbiota reads">
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	228 <option value="single" selected="true">One single-end file</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	229 <option value="multiple">Multiple single-end files</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	230 <option value="paired">Paired-end files</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	231 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	232 <when value="single">
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	233 <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ file with microbiota reads"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	234 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	235 <when value="multiple">
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	236 <param name="in" type="data" format="@FILE_FORMATS@" multiple="true" label="Single-end Fasta/FastQ files with microbiota reads"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	237 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	238 <when value="paired">
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	239 <param name="in_f" type="data" format="@FILE_FORMATS@" label="Forward paired-end Fasta/FastQ file with microbiota reads"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	240 <param name="in_r" type="data" format="@FILE_FORMATS@" label="Reverse paired-end Fasta/FastQ file with microbiota reads"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	241 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	242 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	243 <param argument="--read_min_len" type="integer" value="70" label="Minimum length of the reads to be considered when parsing the input file"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	244 <section name="mapping" title="Mapping" expanded="true">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	245 <param argument="--bt2_ps" type="select" label="Presets options for BowTie2" help="Applied only with FASTA files">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	246 <option value="sensitive">Sensitive</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	247 <option value="very-sensitive" selected="true">Very sensitive</option>
3 ff8f55893e7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit edceb1050e9e312ef8b1201cee35992720667b6a" iuc parents: 2 diff changeset	248 <option value="sensitive-local">Sensitive local</option>
ff8f55893e7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit edceb1050e9e312ef8b1201cee35992720667b6a" iuc parents: 2 diff changeset	249 <option value="very-sensitive-local">Very sensitive local</option>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	250 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	251 <param argument="--min_mapq_val" type="integer" value="5" label="Minimum mapping quality value (MAPQ)"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	252 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	253 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	254 <when value="sam">
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	255 <param name="in" type="data" format="sam" label="Externally BowTie2-mapped SAM file" help="BowTie2 needs to be used first to map microbiota reads"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	256 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	257 <when value="bowtie2out">
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	258 <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run"
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	259 help="File needs to be generated with MetaPhlAn versions >3.0"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	260 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	261 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	262 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	263 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	264 <option value="cached" selected="true">Locally cached</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	265 <option value="history">From history</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	266 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	267 <when value="cached">
6 2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	268 <param name="cached_db" type="select" label="Cached database with clade-specific marker genes">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	269 <options from_data_table="@IDX_DATA_TABLE@">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	270 <filter type="static_value" column="4" value="@IDX_VERSION@"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	271 <validator message="No compatible MetaPhlAn database is available" type="no_options"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	272 </options>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	273 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	274 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	275 <when value="history">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	276 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
6 2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	277 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	278 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	279 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	280 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	281 <section name="analysis" title="Analysis" expanded="true">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	282 <conditional name="analysis_type">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	283 <param argument="-t" type="select" label="Type of analysis to perform">
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	284 <option value="rel_ab" selected="true">rel_ab: Profiling a microbiota in terms of relative abundances</option>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	285 <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>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	286 <option value="reads_map">reads_map: Mapping from reads to clades (only reads hitting a marker)</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	287 <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	288 <option value="clade_specific_strain_tracker">clade_specific_strain_tracker: List of markers present for a specific clade and all its subclades</option>
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	289 <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>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	290 <option value="marker_counts">marker_counts: Non-normalized marker counts (use with extreme caution)</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	291 <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>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	292 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	293 <when value="rel_ab">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	294 <expand macro="tax_lev"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	295 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	296 <when value="rel_ab_w_read_stats">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	297 <expand macro="tax_lev"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	298 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	299 <when value="reads_map"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	300 <when value="clade_profiles"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	301 <when value="clade_specific_strain_tracker">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	302 <param argument="--clade" type="text" value="" label="Clade for which to extract list of markers present"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	303 help="Markers are also extracted for subclades" />
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	304 <param argument="--min_ab" type="float" optional="true" label="The minimum percentage abundance for the clade"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	305 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	306 <when value="marker_ab_table">
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	307 <param argument="--nreads" type="integer" optional="true" label="Total number of reads in the original microbiota"
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	308 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"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	309 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	310 <when value="marker_counts"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	311 <when value="marker_pres_table">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	312 <param argument="--pres_th" type="integer" optional="true" label="Threshold for calling a marker present"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	313 </when>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	314 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	315 <param argument="--min_cu_len" type="integer" value="2000"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	316 label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	317 <param argument="--min_alignment_len" type="integer" optional="true"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	318 label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	319 <param name="organism_profiling" type="select" multiple="true" optional="true" label="Organisms to profile">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	320 <option value="add_viruses" selected="true">Profile viral organisms (add_viruses)</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	321 <option value="ignore_eukaryotes">Ignore eukaryotic organisms (ignore_eukaryotes)</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	322 <option value="ignore_bacteria">Ignore bacteria organisms (ignore_bacteria)</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	323 <option value="ignore_archaea">Ignore archea organisms (ignore_archaea)</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	324 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	325 <param argument="--stat" type="select" label="Statistical approach for converting marker abundances into clade abundances">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	326 <option value="avg_g">avg_g: Clade global (i.e. normalizing all markers together) average (avg_g)</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	327 <option value="avg_l">avg_l: Average of length-normalized marker counts</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	328 <option value="tavg_g" selected="true">tavg_g: Truncated clade global average at --stat_q quantile</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	329 <option value="tavg_l">tavg_l: Truncated average of length-normalized marker counts (at --stat_q)</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	330 <option value="wavg_g">wavg_g: Winsorized clade global average (at --stat_q)</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	331 <option value="wavg_l">wavg_l: Winsorized average of length-normalized marker counts (at --stat_q)</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	332 <option value="med">med: Median of length-normalized marker counts</option>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	333 </param>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	334 <param argument="--stat_q" type="float" value="0.2" label="Quantile value for the robust average"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	335 <param argument="--perc_nonzero" type="float" value="0.33" label="Percentage of markers with a non zero relative abundance for misidentify a species"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	336 <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"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	337 <param argument="--avoid_disqm" type='boolean' checked="true" truevalue='--avoid_disqm' falsevalue=''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	338 label="Deactivate the procedure of disambiguating the quasi-markers based on the marker abundance pattern found in the sample?"
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	339 help="It is generally recommended to keep the disambiguation procedure in order to minimize false positives"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	340 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	341 <section name="out" title="Outputs" expanded="true">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	342 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	343 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	344 <param argument="--use_group_representative" type='boolean' checked="false" truevalue='--use_group_representative' falsevalue=''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	345 label="Use a species as representative for species groups?"/>
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	346 <param argument="--legacy-output" type='boolean' checked="false" truevalue='--legacy-output' falsevalue=''
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	347 label="Old MetaPhlAn2 two columns output?"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	348 <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue=''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	349 label="Report the profiling using the CAMI output format?"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	350 <param argument="--unknown_estimation" type='boolean' checked="false" truevalue='--unknown_estimation' falsevalue=''
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	351 label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	352 <param name="krona_output" type='boolean' checked="false" truevalue='true' falsevalue='false' label="Output for Krona?"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	353 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	354 </inputs>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	355 <outputs>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	356 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances" />
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	357 <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	358 <filter>inputs['in']['selector'] == "raw"</filter>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	359 </data>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	360 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	361 <filter>inputs['in']['selector'] == "raw"</filter>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	362 </data>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	363 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	364 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" >
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	365 <discover_datasets pattern="(?P<designation>.+)" directory="split_levels/" format="tabular"/>
8 1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	366 <filter>analysis['analysis_type']['t'] in ['rel_ab', 'rel_ab_w_read_stats'] and analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	367 </collection>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	368 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	369 <filter>out['krona_output']</filter>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	370 </data>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	371 </outputs>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	372 <tests>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	373 <test expect_num_outputs="6">
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	374 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	375 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	376 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	377 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	378 <!-- Single GZ file -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	379 <param name="selector" value="single"/>
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	380 <param name="in" value="no_taxon_input.fasta"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	381 </conditional>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	382 <param name="read_min_len" value="70"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	383 <section name="mapping">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	384 <param name="bt2_ps" value="sensitive"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	385 <param name="min_mapq_val" value="5"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	386 </section>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	387 </conditional>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	388 <conditional name="db">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	389 <!-- Cached db -->
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	390 <param name="db_selector" value="cached"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	391 <param name="cached_db" value="test-db-20210409"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	392 </conditional>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	393 </section>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	394 <section name="analysis">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	395 <conditional name="analysis_type">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	396 <param name="t" value="rel_ab"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	397 <conditional name="tax_lev">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	398 <param name="tax_lev" value="a"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	399 <param name="split_levels" value="true"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	400 </conditional>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	401 </conditional>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	402 <param name="min_cu_len" value="2000"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	403 <param name="organism_profiling" value="add_viruses"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	404 <param name="stat" value="avg_g"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	405 <param name="stat_q" value="0.2"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	406 <param name="perc_nonzero" value="0.33"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	407 <param name="avoid_disqm" value="true"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	408 </section>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	409 <section name="out">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	410 <param name="sample_id_key" value="SampleID"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	411 <param name="sample_id" value="Metaphlan_Analysis"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	412 <param name="use_group_representative" value="false"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	413 <param name="legacy_output" value="false"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	414 <param name="CAMI_format_output" value="false"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	415 <param name="unknown_estimation" value="false"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	416 <param name="krona_output" value="true"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	417 </section>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	418 <output name="output_file" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	419 <assert_contents>
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	420 <has_text text="UNCLASSIFIED"/>
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	421 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	422 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	423 <output name="bowtie2out" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	424 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	425 <not_has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	426 <has_n_lines n="2"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	427 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	428 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	429 <output name="sam_output_file" ftype="sam">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	430 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	431 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	432 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	433 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	434 <output name="biom_output_file" ftype="biom1">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	435 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	436 <not_has_text text="k__Bacteria"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	437 <not_has_text text="p__Actinobacteria"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	438 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	439 </output>
8 1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	440 <output_collection name="levels" type="list">
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	441 <element name="all" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	442 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	443 <has_text text="class"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	444 <has_n_columns n="17"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	445 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	446 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	447 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	448 <element name="class" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	449 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	450 <has_text text="class_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	451 <not_has_text text="phylum_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	452 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	453 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	454 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	455 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	456 <element name="family" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	457 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	458 <has_text text="family_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	459 <not_has_text text="order"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	460 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	461 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	462 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	463 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	464 <element name="genus" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	465 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	466 <has_text text="genus_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	467 <not_has_text text="family"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	468 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	469 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	470 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	471 </element>
6 2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	472 <element name="kingdom" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	473 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	474 <has_text text="kingdom_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	475 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	476 <has_n_lines n="1"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	477 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	478 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	479 <element name="order" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	480 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	481 <has_text text="order_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	482 <not_has_text text="class_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	483 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	484 <has_n_lines n="1"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	485 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	486 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	487 <element name="phylum" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	488 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	489 <has_text text="phylum_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	490 <not_has_text text="kingdom_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	491 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	492 <has_n_lines n="1"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	493 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	494 </element>
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	495 <element name="species" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	496 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	497 <has_text text="species_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	498 <not_has_text text="genus"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	499 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	500 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	501 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	502 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	503 <element name="strains" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	504 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	505 <has_text text="strains_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	506 <not_has_text text="species_id"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	507 <has_n_columns n="3"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	508 <has_n_lines n="1"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	509 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	510 </element>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	511 </output_collection>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	512 <output name="krona_output_file" ftype="tabular">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	513 <assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	514 <not_has_text text="k__Bacteria"/>
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	515 <has_n_lines n="1" delta="1"/>
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	516 <has_size value="1" delta="1"/>
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	517 </assert_contents>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	518 </output>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	519 </test>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	520 <test expect_num_outputs="6">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	521 <section name="inputs">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	522 <conditional name="in">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	523 <param name="selector" value="raw"/>
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	524 <conditional name="raw_in">
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	525 <!-- Single GZ file -->
a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	526 <param name="selector" value="single"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	527 <param name="in" value="SRS014464-Anterior_nares.fasta.gz"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	528 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	529 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	530 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	531 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	532 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	533 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	534 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	535 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	536 <!-- Cached db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	537 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	538 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	539 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	540 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	541 <section name="analysis">
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	542 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	543 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	544 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	545 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	546 <param name="split_levels" value="true"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	547 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	548 </conditional>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	549 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	550 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	551 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	552 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	553 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	554 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	555 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	556 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	557 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	558 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	559 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	560 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	561 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	562 <param name="unknown_estimation" value="false"/>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	563 <param name="krona_output" value="true"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	564 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	565 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	566 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	567 <has_text text="k__Bacteria\|p__Actinobacteria\|c__Actinobacteria\|o__Corynebacteriales\|f__Corynebacteriaceae\|g__Corynebacterium\|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	568 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	569 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	570 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	571 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	572 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	573 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	574 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	575 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	576 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	577 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	578 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	579 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	580 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	581 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	582 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	583 <has_text text="k__Bacteria\|p__Proteobacteria\|c__Gammaproteobacteria\|o__Pseudomonadales\|f__Moraxellaceae\|g__Moraxella\|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	584 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	585 </output>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	586 <output_collection name="levels" type="list" >
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	587 <element name="all" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	588 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	589 <has_text text="Gammaproteobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	590 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	591 <has_n_columns n="17"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	592 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	593 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	594 <element name="class" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	595 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	596 <has_text text="class_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	597 <not_has_text text="phylum_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	598 <has_text text="Actinobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	599 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	600 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	601 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	602 <element name="family" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	603 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	604 <has_text text="family_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	605 <not_has_text text="order"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	606 <has_text text="Propionibacteriaceae"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	607 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	608 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	609 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	610 <element name="genus" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	611 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	612 <has_text text="genus_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	613 <not_has_text text="family"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	614 <has_text text="Cutibacterium"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	615 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	616 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	617 </element>
6 2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	618 <element name="kingdom" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	619 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	620 <has_text text="kingdom_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	621 <has_text text="Bacteria"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	622 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	623 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	624 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	625 <element name="order" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	626 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	627 <has_text text="order_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	628 <not_has_text text="class_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	629 <has_text text="Propionibacteriales"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	630 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	631 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	632 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	633 <element name="phylum" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	634 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	635 <has_text text="phylum_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	636 <not_has_text text="kingdom_id"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	637 <has_text text="Firmicutes"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	638 <has_n_columns n="3"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	639 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	640 </element>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	641 <element name="species" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	642 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	643 <has_text text="species_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	644 <not_has_text text="genus"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	645 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	646 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	647 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	648 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	649 <element name="strains" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	650 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	651 <has_text text="strains_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	652 <not_has_text text="species_id"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	653 <has_n_columns n="3"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	654 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	655 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	656 </output_collection>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	657 <output name="krona_output_file" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	658 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	659 <not_has_text text="k__Bacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	660 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	661 <has_n_columns n="9"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	662 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	663 </output>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	664 </test>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	665 <test expect_num_outputs="4">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	666 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	667 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	668 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	669 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	670 <!-- Multiple GZ file -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	671 <param name="selector" value="multiple"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	672 <param name="in" value="SRS014464-Anterior_nares.fasta.gz,SRS014464-Anterior_nares.fasta.gz"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	673 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	674 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	675 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	676 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	677 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	678 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	679 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	680 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	681 <!-- Local db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	682 <param name="db_selector" value="history"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	683 <param name="bowtie2db" value="test-db.fasta"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	684 <param name="mpa_pkl" value="test-db.json"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	685 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	686 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	687 <section name="analysis">
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	688 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	689 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	690 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	691 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	692 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	693 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	694 </conditional>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	695 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	696 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	697 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	698 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	699 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	700 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	701 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	702 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	703 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	704 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	705 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	706 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	707 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	708 <param name="unknown_estimation" value="false"/>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	709 <param name="krona_output" value="false"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	710 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	711 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	712 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	713 <has_text text="k__Bacteria\|p__Actinobacteria\|c__Actinobacteria\|o__Corynebacteriales\|f__Corynebacteriaceae\|g__Corynebacterium\|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	714 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	715 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	716 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	717 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	718 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	719 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	720 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	721 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	722 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	723 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	724 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	725 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares-two-inputs.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	726 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	727 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	728 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	729 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	730 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	731 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	732 <has_text text="k__Bacteria\|p__Proteobacteria\|c__Gammaproteobacteria\|o__Pseudomonadales\|f__Moraxellaceae\|g__Moraxella\|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	733 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	734 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	735 </test>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	736 <test expect_num_outputs="4">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	737 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	738 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	739 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	740 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	741 <!-- Paired GZ file -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	742 <param name="selector" value="paired"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	743 <param name="in_f" value="SRS014464-Anterior_nares.fasta.gz"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	744 <param name="in_r" value="SRS014464-Anterior_nares.fasta.gz"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	745 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	746 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	747 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	748 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	749 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	750 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	751 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	752 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	753 <!-- Cached db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	754 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	755 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	756 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	757 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	758 <section name="analysis">
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	759 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	760 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	761 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	762 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	763 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	764 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	765 </conditional>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	766 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	767 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	768 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	769 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	770 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	771 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	772 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	773 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	774 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	775 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	776 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	777 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	778 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	779 <param name="unknown_estimation" value="false"/>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	780 <param name="krona_output" value="false"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	781 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	782 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	783 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	784 <has_text text="k__Bacteria\|p__Actinobacteria\|c__Actinobacteria\|o__Corynebacteriales\|f__Corynebacteriaceae\|g__Corynebacterium\|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	785 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	786 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	787 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	788 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	789 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	790 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	791 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	792 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	793 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	794 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	795 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	796 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares-two-inputs.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	797 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	798 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	799 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	800 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	801 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	802 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	803 <has_text text="k__Bacteria\|p__Proteobacteria\|c__Gammaproteobacteria\|o__Pseudomonadales\|f__Moraxellaceae\|g__Moraxella\|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	804 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	805 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	806 </test>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	807 <test expect_num_outputs="2">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	808 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	809 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	810 <!-- SAM -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	811 <param name="selector" value="sam"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	812 <param name="in" value="SRS014464-Anterior_nares.sam"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	813 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	814 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	815 <!-- Cached db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	816 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	817 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	818 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	819 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	820 <section name="analysis">
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	821 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	822 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	823 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	824 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	825 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	826 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	827 </conditional>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	828 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	829 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	830 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	831 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	832 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	833 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	834 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	835 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	836 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	837 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	838 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	839 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	840 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	841 <param name="unknown_estimation" value="false"/>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	842 <param name="krona_output" value="false"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	843 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	844 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	845 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	846 <has_text text="k__Bacteria\|p__Actinobacteria\|c__Actinobacteria\|o__Corynebacteriales\|f__Corynebacteriaceae\|g__Corynebacterium\|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	847 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	848 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	849 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	850 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	851 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	852 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	853 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	854 <has_text text="k__Bacteria\|p__Proteobacteria\|c__Gammaproteobacteria\|o__Pseudomonadales\|f__Moraxellaceae\|g__Moraxella\|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	855 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	856 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	857 </test>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	858 <test expect_num_outputs="2">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	859 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	860 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	861 <!-- bowtie2out -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	862 <param name="selector" value="bowtie2out"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	863 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	864 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	865 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	866 <!-- Cached db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	867 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	868 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	869 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	870 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	871 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	872 <param name="selector" value="bowtie2out"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	873 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	874 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	875 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	876 <param name="bt2_ps" value="sensite"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	877 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	878 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	879 <section name="analysis">
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	880 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	881 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	882 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	883 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	884 <param name="split_levels" value="false"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	885 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	886 </conditional>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	887 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	888 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	889 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	890 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	891 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	892 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	893 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	894 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	895 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	896 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	897 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	898 <param name="legacy_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	899 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	900 <param name="unknown_estimation" value="false"/>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	901 <param name="krona_output" value="false"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	902 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	903 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	904 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	905 <has_text text="k__Bacteria\|p__Actinobacteria\|c__Actinobacteria\|o__Corynebacteriales\|f__Corynebacteriaceae\|g__Corynebacterium\|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	906 <has_text text="relative_abundance"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	907 <has_text text="NCBI_tax_id"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	908 <has_text text="clade_name"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	909 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	910 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	911 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	912 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	913 <has_text text="k__Bacteria\|p__Proteobacteria\|c__Gammaproteobacteria\|o__Pseudomonadales\|f__Moraxellaceae\|g__Moraxella\|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	914 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	915 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	916 </test>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	917 <test expect_num_outputs="6">
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	918 <section name="inputs">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	919 <conditional name="in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	920 <param name="selector" value="raw"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	921 <conditional name="raw_in">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	922 <!-- Single FASTA file -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	923 <param name="selector" value="single"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	924 <param name="in" value="SRS014464-Anterior_nares.fasta"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	925 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	926 <param name="read_min_len" value="70"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	927 <section name="mapping">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	928 <param name="bt2_ps" value="sensitive"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	929 <param name="min_mapq_val" value="5"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	930 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	931 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	932 <conditional name="db">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	933 <!-- Cached db -->
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	934 <param name="db_selector" value="cached"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	935 <param name="cached_db" value="test-db-20210409"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	936 </conditional>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	937 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	938 <section name="analysis">
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	939 <conditional name="analysis_type">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	940 <param name="t" value="rel_ab"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	941 <conditional name="tax_lev">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	942 <param name="tax_lev" value="a"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	943 <param name="split_levels" value="true"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	944 </conditional>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	945 </conditional>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	946 <param name="min_cu_len" value="2000"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	947 <param name="organism_profiling" value="add_viruses"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	948 <param name="stat" value="avg_g"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	949 <param name="stat_q" value="0.2"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	950 <param name="perc_nonzero" value="0.33"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	951 <param name="ignore_markers" value="marker.txt"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	952 <param name="avoid_disqm" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	953 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	954 <section name="out">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	955 <param name="sample_id_key" value="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	956 <param name="sample_id" value="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	957 <param name="use_group_representative" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	958 <param name="legacy_output" value="true"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	959 <param name="CAMI_format_output" value="false"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	960 <param name="unknown_estimation" value="false"/>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	961 <param name="krona_output" value="true"/>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	962 </section>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	963 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	964 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	965 <has_text text="k__Bacteria\|p__Actinobacteria\|c__Actinobacteria\|o__Corynebacteriales\|f__Corynebacteriaceae\|g__Corynebacterium\|s__Corynebacterium_accolens"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	966 <has_text text="SampleID"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	967 <has_text text="Metaphlan_Analysis"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	968 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	969 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	970 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-bowtie2out.tabular" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	971 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	972 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	973 <has_text text="37637__U2I1U8__N579_01580"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	974 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	975 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	976 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares.sam" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	977 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	978 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	979 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	980 </output>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	981 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	982 <assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	983 <has_text text="k__Bacteria\|p__Proteobacteria\|c__Gammaproteobacteria\|o__Pseudomonadales\|f__Moraxellaceae\|g__Moraxella\|s__Moraxella_lacunata"/>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	984 </assert_contents>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	985 </output>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	986 <output_collection name="levels" type="list" >
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	987 <element name="all" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	988 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	989 <has_text text="Gammaproteobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	990 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	991 <has_n_columns n="9"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	992 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	993 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	994 <element name="class" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	995 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	996 <has_text text="class"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	997 <has_text text="Actinobacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	998 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	999 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1000 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1001 <element name="family" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1002 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1003 <has_text text="family"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1004 <has_text text="Propionibacteriaceae"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1005 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1006 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1007 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1008 <element name="genus" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1009 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1010 <has_text text="genus"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1011 <has_text text="Cutibacterium"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1012 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1013 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1014 </element>
6 2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1015 <element name="kingdom" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1016 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1017 <has_text text="kingdom"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1018 <has_text text="Bacteria"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1019 <has_n_columns n="2"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1020 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1021 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1022 <element name="order" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1023 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1024 <has_text text="order"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1025 <has_text text="Propionibacteriales"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1026 <has_n_columns n="2"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1027 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1028 </element>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1029 <element name="phylum" ftype="tabular">
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1030 <assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1031 <has_text text="phylum"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1032 <has_text text="Firmicutes"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1033 <has_n_columns n="2"/>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1034 </assert_contents>
2131d7dca455 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2 iuc parents: 5 diff changeset	1035 </element>
1 b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1036 <element name="species" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1037 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1038 <has_text text="species"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1039 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1040 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1041 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1042 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1043 <element name="strains" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1044 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1045 <has_text text="strains"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1046 <has_n_columns n="2"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1047 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1048 </element>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1049 </output_collection>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1050 <output name="krona_output_file" ftype="tabular">
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1051 <assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1052 <not_has_text text="k__Bacteria"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1053 <has_text text="Corynebacterium accolens"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1054 <has_n_columns n="9"/>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1055 </assert_contents>
b89b0765695d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f" iuc parents: 0 diff changeset	1056 </output>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1057 </test>
8 1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1058 <!-- Check a non-default analysis mode -->
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1059 <test expect_num_outputs="4">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1060 <section name="inputs">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1061 <conditional name="in">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1062 <param name="selector" value="raw"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1063 <conditional name="raw_in">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1064 <param name="selector" value="single"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1065 <param name="in" value="SRS014464-Anterior_nares.fasta"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1066 </conditional>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1067 </conditional>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1068 <conditional name="db">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1069 <param name="db_selector" value="cached"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1070 <param name="cached_db" value="test-db-20210409"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1071 </conditional>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1072 </section>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1073 <section name="analysis">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1074 <conditional name="analysis_type">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1075 <param name="t" value="marker_ab_table"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1076 </conditional>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1077 </section>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1078 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1079 <assert_contents>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1080 <has_text text="29394__H3NC06__B8A41_08715"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1081 <has_text text="SampleID"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1082 <has_text text="Metaphlan_Analysis"/>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1083 </assert_contents>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1084 </output>
1a6cdf55390f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c iuc parents: 6 diff changeset	1085 </test>
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1086 </tests>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1087 <help><![CDATA[
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1088 What it does
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1089 ============
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1090
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1091 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria,
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	1092 Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) at species-level.
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1093
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1094 MetaPhlAn relies on ~1.1M unique clade-specific marker genes identified from ~100,000 reference genomes
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1095 (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing:
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1096
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1097 - unambiguous taxonomic assignments;
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1098 - accurate estimation of organismal relative abundance;
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1099 - species-level resolution for bacteria, archaea, eukaryotes and viruses;
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1100 - strain identification and tracking
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1101 - orders of magnitude speedups compared to existing methods.
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	1102 - microbiota strain-level population genomics
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1103
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1104 MetaPhlAn clade-abundance estimation
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1105 ------------------------------------
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1106
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1107 The basic usage of MetaPhlAn consists in the identification of the clades (from phyla to species and
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	1108 strains in particular cases) present in the microbiota obtained from a microbiome sample and their
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1109 relative abundance.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1110
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1111 Marker level analysis
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1112 ---------------------
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1113
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1114 MetaPhlAn introduces the capability of characterizing organisms at the strain level using non
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1115 aggregated marker information. Such capability comes with several slightly different flavours and
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1116 are a way to perform strain tracking and comparison across multiple samples.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1117
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	1118 Usually, MetaPhlAn is first ran with default parameters for the type of analysis to profile the
6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	1119 species present in the community, and then a strain-level profiling can be performed to zoom-in on
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1120 specific species of interest. This operation can be performed quickly as it exploits the bowtie2out
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1121 intermediate file saved during the execution of the default analysis type.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1122
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1123 Inputs
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1124 ======
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1125
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1126 Metaphlan takes as input either:
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1127
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	1128 - one or several sequence files in Fasta, FastQ (whether compressed or not)
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1129 - a BowTie2 produced SAM file
2 a92a632c4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f1c6f4fe1e572ace84cf9106bc253603f55aac55" iuc parents: 1 diff changeset	1130 - an intermediary mapping file of the microbiota generated by a previous MetaPhlAn run
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1131
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	1132 It also needs the reference database, which can be locally installed or customized using the dedicated tools.
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1133
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1134 Outputs
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1135 =======
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1136
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	1137 The main output is a tab-separated file with the predicted taxon relative abundances.
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1138
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1139 It also generates a BIOM file and some intermediate files (SAM and BowTie2out) if sequence files are given as inputs.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1140
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1141
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1142 More help and use cases
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1143 =======================
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1144
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1145 To get more information about MetaPhlAn usage and use cases, please refer to the `Metaphlan documentation`_.
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1146
5 6dee4abadccb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6 iuc parents: 3 diff changeset	1147 .. _Metaphlan documentation: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#Basic-Usage
0 f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1148
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1149 ]]></help>
f5df500fcc3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c" iuc parents: diff changeset	1150 <expand macro="citations"/>
3 ff8f55893e7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit edceb1050e9e312ef8b1201cee35992720667b6a" iuc parents: 2 diff changeset	1151 </tool>

Mercurial > repos > iuc > metaphlan

annotate metaphlan.xml @ 8:1a6cdf55390f draft