recentrifuge: recentrifuge.xml annotate

annotate recentrifuge.xml @ 2:b135c5908e8c draft

"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"

author	pimarin
date	Wed, 06 Apr 2022 13:52:48 +0000
parents	e5474449c35d
children	2890083b1a84

rev	line source
0 e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	1 <?xml version="1.0" encoding="UTF-8"?>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	2
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	3 <tool id="recentrifuge" name="Recentrifuge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	4 <description>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	5 Robust comparative analysis and contamination removal for metagenomics
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	6 </description>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	7 <macros>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	8 <import>macro.xml</import>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	9 </macros>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	10 <expand macro='xrefs'/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	11 <expand macro="requirements" />
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	12 <expand macro="version_command" />
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	13 <command detect_errors="aggressive"><![CDATA[
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	14 ## database input ##
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	15 ## if database imported from history ##
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	16 #if $database.db_type.db_select == "cached"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	17 #set $rcf_db = $database.db_type.cached_db.fields.path
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	18 #else if $database.db_type.db_select == "history"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	19 mkdir rcf_db &&
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	20 #for i in $database.db_type.history_db
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	21 ln -s '$i' 'rcf_db/$i.element_identifier' &&
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	22 #end for
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	23 #set $rcf_db = "rcf_db"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	24 #end if
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	25 rcf
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	26 -n $rcf_db
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	27 ## input type ##
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	28 #if $input_option.file_type.filetype == "centrifuge"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	29 -f '$input_option.input_file'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	30 #else if $input_option.file_type.filetype == "lmat"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	31 -l '$input_option.input_file'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	32 #else if $input_option.file_type.filetype == "clark"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	33 -r '$input_option.input_file'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	34 #else if $input_option.file_type.filetype == "kraken"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	35 -k '$input_option.input_file'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	36 #else if $input_option.file_type.filetype == "generic"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	37 -g '$input_option.input_file'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	38 --format '$input_option.file_type.format'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	39 #end if
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	40 ## output option ##
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	41 -e $output_option.extra
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	42 -o output
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	43 $output_option.pickle
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	44 $output_option.nohtml
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	45 ## advanced options ##
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	46 #if $advanced_option.control_select.controls_type == "add_neg"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	47 --controls '$advanced_option.control_select.controls'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	48 #end if
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	49 #if $advanced_option.scoring != "DEFAULT"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	50 --scoring '$advanced_option.scoring'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	51 #end if
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	52 #if $advanced_option.minscore_select.minscore == "specify_minscore"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	53 --minscore '$advanced_option.minscore_select.minscore_value'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	54 #end if
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	55 #if $advanced_option.mintaxa_type.mintaxa_select == "specify_mintaxa"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	56 --mintaxa '$advanced_option.mintaxa_type.mintaxa'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	57 #end if
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	58 #if $advanced_option.exclude_taxa_type.exclude_taxa_select == "yes_exclude"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	59 --exclude '$advanced_option.exclude_taxa_type.exclude_taxa_name'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	60 #end if
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	61 #if $advanced_option.include_taxa_type.include_taxa_select == "yes_include"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	62 --include '$advanced_option.include_taxa_type.include_taxa_name'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	63 #end if
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	64 $advanced_option.avoidcross
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	65 ## MORE ADVANCED OPTION ##
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	66 #if $more_advanced_option.minscore_type.minscore_select == "specify_minscore"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	67 --ctrlminscore '$more_advanced_option.minscore_type.ctrlminscore'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	68 #end if
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	69 #if $more_advanced_option.ctrlmintaxa_type.ctrlmintaxa_select =="specify_ctrlmintaxa"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	70 --ctrlmintaxa '$more_advanced_option.ctrlmintaxa_type.ctrlmintaxa'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	71 #end if
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	72 --summary $more_advanced_option.summary
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	73 $more_advanced_option.takeoutroot
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	74 $more_advanced_option.nokollapse
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	75 $more_advanced_option.strain
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	76 $more_advanced_option.sequential
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	77 $more_advanced_option.debug
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	78 $more_advanced_option.version
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	79 ## LOG FILE OUTPUT ##
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	80 &> $logfile
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	81 ]]>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	82
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	83 </command>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	84 <inputs>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	85 <!-- INPUT FILES -->
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	86 <section name="input_option" title="Input options" expanded="true">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	87 <param name="input_file" type="data" format="tabular" label="Select taxonomy file tabular formated"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	88 <conditional name="file_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	89 <param name="filetype" type="select" label="Type of input file (centrifuge, CLARK, Generic, kraken, LMAT)" help="(-f, -r, -g, -k, -l)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	90 <option value="centrifuge">Centrifuge</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	91 <option value="clark">CLARK</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	92 <option value="generic">Generic</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	93 <option value="lmat" >LMAT</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	94 <option value="kraken" >Kraken</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	95 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	96 <when value="centrifuge"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	97 <when value="lmat"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	98 <when value="clark"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	99 <when value="kraken"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	100 <when value="generic">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	101 <param argument="--format" type="text" label="Format of the output files from a generic classifier"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	102 help="string like 'TYP:csv,TID:1,LEN:3,SCO:6,UNC:0'
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	103 where valid file TYPes are csv/tsv/ssv, and the rest of fields indicate the number of column used (starting in 1)
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	104 for the TaxIDs assigned,the LENgth of the read, the SCOre given to the assignment (--format)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	105 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	106 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	107 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	108 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	109 <!-- taxa databases -->
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	110 <section name="database" title="Database type" expanded="true">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	111 <conditional name="db_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	112 <param name="db_select" type="select" label="Cached database with clade-specific marker genes">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	113 <option value="cached" selected="true">Locally installed</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	114 <option value="history">From history</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	115 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	116 <when value="cached">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	117 <param name="cached_db" type="select" label="Cached database whith taxa ID">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	118 <options from_data_table="rcf_database">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	119 <validator message="No recentrifuge database is available" type="no_options"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	120 </options>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	121 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	122 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	123 <when value="history">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	124 <param name="history_db" type="data" multiple="true" format="txt" label="Database from history"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	125 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	126 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	127 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	128 <!-- output name -->
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	129 <section name="output_option" title="Output options">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	130 <param argument="--extra" type="select" label="Type of extra output to be generated (default on CSV)" help="(--extra)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	131 <option value="CSV" selected="true" >CSV</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	132 <option value="DYNOMICS">DYNOMICS</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	133 <option value="FULL">FULL</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	134 <option value="MULTICSV">MULTICSV</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	135 <option value="TSV" >TSV</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	136 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	137 <param argument="--pickle" type="boolean" truevalue="--pickle" falsevalue="" label="Serialize statistics and data results in pandas DataFrames" help="(--pickle)"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	138 <param argument="--nohtml" type="boolean" truevalue="--nohtml" falsevalue="" label="Suppress saving the HTML output file" help="(--nohtml)"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	139 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	140 <!-- ADVANCED OPTIONS -->
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	141 <section name="advanced_option" title="Coarse tuning of algorithm parameters">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	142 <conditional name="control_select">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	143 <param name="controls_type" type="select" label="Number of first samples will be treated as negative controls (default is 0)" help="(--controls)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	144 <option value="default">No control</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	145 <option value="add_neg">Add negative controls </option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	146 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	147 <when value="default">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	148 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	149 <when value="add_neg">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	150 <param name="controls" type="integer" min="0" value="0" label="Number of samples"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	151 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	152 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	153 <param name="scoring" type="select" label="Type of scoring to be applied" help="(--scoring)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	154 <option value="DEFAULT" selected="true">Default scoring</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	155 <option value="SHEL">SHEL</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	156 <option value="LENGTH">LENGTH</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	157 <option value="LOGLENGTH">LOGLENGTH</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	158 <option value="NORMA">NORMA</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	159 <option value="LMAT">LMAT</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	160 <option value="CLARK_C">CLARK_C</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	161 <option value="CLARK_G">CLARK_G</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	162 <option value="KRAKEN">KRAKEN</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	163 <option value="GENERIC">GENERIC</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	164 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	165 <conditional name="minscore_select">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	166 <param name="minscore" type="select" label="minimum score/confidence of the classification of a read to pass the quality filter; all pass by default" help="(--minscore)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	167 <option value="default" selected="true">Default all pass</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	168 <option value="specify_minscore">Specify value</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	169 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	170 <when value="default">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	171 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	172 <when value="specify_minscore">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	173 <param name="minscore_value" type="integer" min="0" value="0" label="minimum score/confidence value"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	174 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	175 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	176 <conditional name="mintaxa_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	177 <param name="mintaxa_select" type="select" label="Minimum taxa to avoid collapsing one level into the parent (if not specified a value will be automatically assigned)" help="(--mintaxa)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	178 <option value="default" selected="true">Automatically assigned</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	179 <option value="specify_mintaxa">Choose value</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	180 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	181 <when value="default">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	182 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	183 <when value="specify_mintaxa">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	184 <param name="mintaxa" type="integer" min="0" value="0" label="Minimum taxa number"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	185 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	186 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	187 <conditional name="exclude_taxa_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	188 <param name="exclude_taxa_select" type="select" label="NCBI taxid code to exclude a taxon and all underneath (default, no exclude)" help="(--exclude)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	189 <option value="no_exclude">No exclusion</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	190 <option value="yes_exclude">Specify excluded taxa</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	191 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	192 <when value="yes_exclude">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	193 <param name="exclude_taxa_name" type="text" label="NCBI taxid code to exclude" />
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	194 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	195 <when value="no_exclude"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	196 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	197 <conditional name="include_taxa_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	198 <param name="include_taxa_select" type="select" label="NCBI taxid code to include a taxon and all underneath" help="(--include)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	199 <option value="no_include">Default no taxa include</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	200 <option value="yes_include">Specify included taxa</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	201 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	202 <when value="yes_include">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	203 <param name="include_taxa_name" type="text" label="NCBI taxid code to include"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	204 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	205 <when value="no_include"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	206 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	207 <param argument="--avoidcross" type="boolean" truevalue="--avoidcross" falsevalue="" label="Avoid cross analysis" help="(--avoidcross)"> </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	208 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	209 <!-- Detailed more fine parameters -->
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	210 <section name="more_advanced_option" title=" Fine tuning of algorithm parameters">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	211 <conditional name="minscore_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	212 <param name="minscore_select" type="select" label="minimum score/confidence of the classification of a read in control samples to pass the quality filter; it defaults to minscore" help="(--ctrlminscore)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	213 <option value="default_minscore">Default minscore</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	214 <option value="specify_minscore">Specify minscore</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	215 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	216 <when value="default_minscore"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	217 <when value="specify_minscore">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	218 <param name="ctrlminscore" type="integer" value="0" label="minimum score/confidence"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	219 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	220 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	221 <conditional name="ctrlmintaxa_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	222 <param name="ctrlmintaxa_select" type="select" label="Minimum taxa to avoid collapsing one level into the parent" help="(--ctrlmintaxa)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	223 <option value="default_ctrlmintaxa">Default value</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	224 <option value="specify_ctrlmintaxa">Specify minimum taxa number</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	225 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	226 <when value="default_ctrlmintaxa"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	227 <when value="specify_ctrlmintaxa">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	228 <param name="ctrlmintaxa" type="integer" value="0" label="Minimum taxa number"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	229 </when>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	230 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	231 <param name="summary" type="select" label="select to 'add' summary samples to other samples, or to 'only' show summary samples or to 'avoid' summaries at all" help="(--summary)">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	232 <option value="ADD" selected="true">ADD</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	233 <option value="ONLY">ONLY</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	234 <option value="AVOID">AVOID</option>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	235 </param>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	236 <param argument="--takeoutroot" type="boolean" truevalue="--takeoutroot" falsevalue="" label="remove counts directly assigned to the root level" help="(--takeoutroot)"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	237 <param argument="--nokollapse" type="boolean" truevalue="--nokollapse" falsevalue="" label="show the cellular organisms taxon" help="(--nokollapse)"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	238 <param argument="--strain" type="boolean" truevalue="--strain" falsevalue="" label="Strain level instead of species as the resolution limit for the robust contamination removal algorithm; use with caution, this is an experimental feature" help="(--strain)" />
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	239 <param argument="--sequential" type="boolean" truevalue="--sequential" falsevalue="" label="deactivate parallel processing" help="(--sequential)" />
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	240 <param argument="--debug" type="boolean" truevalue="--debug" falsevalue="" label="increase output verbosity and perform additional checks" help="(--debug)" />
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	241 <param argument="--version" type="boolean" truevalue="--version" falsevalue="" label=" show program's version number and exit" help="(--version)" />
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	242 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	243 </inputs>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	244 <!-- OUTPUT FILE, TYPE DEPENDING ON extra PARAMETER -->
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	245 <outputs>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	246 <data name="html_report" format="html" from_work_dir="output.rcf.html" label="${tool.name} on ${on_string}: html report">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	247 <filter> output_option['nohtml'] == False</filter>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	248 </data>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	249 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	250
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	251 <data name="data_csv" format="csv" from_work_dir="output.rcf.data.csv" label="${tool.name} on ${on_string}: data.csv">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	252 <filter> output_option['extra'] == 'CSV' </filter>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	253 </data>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	254 <data name="stat_csv" format="csv" from_work_dir="output.rcf.stat.csv" label="${tool.name} on ${on_string}: stat csv">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	255 <filter> output_option['extra'] == 'CSV' or output_option['extra'] == 'MULTICSV' </filter>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	256 </data>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	257 <data name="data_tsv" format="tabular" from_work_dir="output.rcf.data.tsv" label="${tool.name} on ${on_string}: data tsv">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	258 <filter> output_option['extra'] == 'TSV' </filter>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	259 </data>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	260 <data name="stat_tsv" format="tabular" from_work_dir="output.rcf.stat.tsv" label="${tool.name} on ${on_string}: stat tsv">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	261 <filter> output_option['extra'] == 'TSV' </filter>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	262 </data>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	263 <data name="xls_report" format="xlsx" from_work_dir="output.rcf.xlsx" label="${tool.name} on ${on_string}: xlsx report">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	264 <filter> output_option['extra'] == 'FULL' or output_option['extra'] == 'DYNOMICS'</filter>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	265 </data>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	266 <data name="stat_bz" format="bz2" from_work_dir="output.rcf.stat.pkl.bz2" label="${tool.name} on ${on_string}: stat.pkl.bz2">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	267 <filter> output_option['pickle'] == True </filter>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	268 </data>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	269 <data name="data_bz" format="bz2" from_work_dir="output.rcf.data.pkl.bz2" label="${tool.name} on ${on_string}: data.pkl.bz2">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	270 <filter> output_option['pickle'] == True </filter>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	271 </data>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	272 </outputs>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	273 <tests>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	274 <test> <!-- kraken input and CSV output TEST_1-->
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	275 <section name="database">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	276 <conditional name="db">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	277 <param name="db_selector" value="cached"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	278 <param name="cached_db" value="test-db-2022"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	279 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	280 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	281 <section name="input_option">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	282 <param name="input_file" value="kraken_test/kraken.out"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	283 <conditional name="file_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	284 <param name="filetype" value="kraken"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	285 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	286 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	287 <section name="output_option">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	288 <param name="output_type" value="default_type"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	289 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	290 <section name="more_advanced_option">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	291 <param name="summary" value="AVOID"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	292 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	293 <output name="data_csv" file="kraken_test/test1_csv.rcf.data.csv" lines_diff="2"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	294 <output name="stat_csv" file="kraken_test/test1_csv.rcf.stat.csv" lines_diff="2"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	295 <output name="html_report" file="kraken_test/test1_csv.rcf.html" lines_diff="2"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	296 <output name="logfile" file="kraken_test/test1_csv.log" lines_diff="7"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	297 </test>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	298 <test> <!-- centrifuge input and full options with imported database TEST_2 -->
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	299 <section name="database">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	300 <conditional name="db">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	301 <param name="db_selector" value="history"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	302 <param name="history_db" value="test-db/delnodes.dmp,test-db/division.dmp,test-db/gc.prt,test-db/gencode.dmp,test-db/merged.dmp,test-db/names.dmp,test-db/nodes.dmp,test-db/readme.txt"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	303 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	304 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	305 <section name="input_option">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	306 <param name="input_file" value="centrifuge_test/centrifuge.out"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	307 <conditional name="file_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	308 <param name="filetype" value="centrifuge"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	309 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	310 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	311 <section name="output_option">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	312 <param name="extra" value="MULTICSV"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	313 <param name="pickle" value="false"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	314 <param name="nohtml" value="true"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	315 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	316 <section name="advanced_option">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	317 <conditional name="control_select">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	318 <param name="controls_type" value="add_neg"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	319 <param name="controls" value="0"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	320 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	321 <param name="scoring" value="NORMA"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	322 <conditional name="minscore_select">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	323 <param name="minscore" value="specify_minscore"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	324 <param name="minscore_value" value="0"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	325 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	326 <param name="avoidcross" value="true"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	327 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	328 <section name="more_advanced_option">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	329 <conditional name="minscore_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	330 <param name="minscore_select" value="specify_minscore"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	331 <param name="ctrlminscore" value="0"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	332 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	333 <param name="summary" value="AVOID"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	334 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	335 <output name="stat_csv" file="centrifuge_test/test2_multicsv.rcf.stat.csv" lines_diff="2"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	336 <output name="logfile" file="centrifuge_test/test2_multicsv.log" lines_diff="20"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	337 </test>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	338 <test> <!-- kraken input cached DB several option added and .bz2 files generated TEST_3 -->
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	339 <section name="database">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	340 <conditional name="db_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	341 <param name="db_select" value="cached"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	342 <param name="cached_db" value="test-db-2022"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	343 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	344 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	345 <section name="input_option">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	346 <param name="input_file" value="kraken_test/kraken.out"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	347 <conditional name="file_type">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	348 <param name="filetype" value="kraken"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	349 </conditional>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	350 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	351 <section name="output_option" >
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	352 <param name="extra" value="TSV"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	353 <param name="pickle" value="false"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	354 <param name="nohtml" value="true"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	355 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	356 <section name="advanced_option">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	357 <param name="scoring" value="LOGLENGTH"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	358 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	359 <section name="more_advanced_option">
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	360 <param name="summary" value="ONLY"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	361 <param name="strain" value="true"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	362 </section>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	363 <output name="data_tsv" file="kraken_test/test3_rcf.data.tsv" lines_diff="2"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	364 <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	365 <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="20"/>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	366 </test>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	367 </tests>
2 b135c5908e8c "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: 0 diff changeset	368 <help>
b135c5908e8c "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: 0 diff changeset	369 <![CDATA[
0 e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	370 =-= /home/pierre/anaconda3/envs/rcf/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-=
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	371 usage: rcf [-h] [-V] [-n PATH] [--format GENERIC_FORMAT]
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	372 (-f FILE \| -g FILE \| -l FILE \| -r FILE \| -k FILE) [-o FILE]
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	373 [-e OUTPUT_TYPE] [-p] [--nohtml] [-a \| -c CONTROLS_NUMBER]
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	374 [-s SCORING] [-y NUMBER] [-m INT] [-x TAXID] [-i TAXID] [-z NUMBER]
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	375 [-w INT] [-u SUMMARY_BEHAVIOR] [-t] [--nokollapse] [-d] [--strain]
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	376 [--sequential]
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	377 Robust comparative analysis and contamination removal for metagenomics
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	378 options:
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	379 -h, --help show this help message and exit
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	380 -V, --version show program's version number and exit
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	381 input:
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	382 Define Recentrifuge input files and formats
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	383 -n PATH, --nodespath PATH
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	384 path for the nodes information files (nodes.dmp and
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	385 names.dmp from NCBI)
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	386 --format GENERIC_FORMAT
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	387 format of the output files from a generic classifier
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	388 included with the option -g; It is a string like
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	389 "TYP:csv,TID:1,LEN:3,SCO:6,UNC:0" where valid file
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	390 TYPes are csv/tsv/ssv, and the rest of fields indicate
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	391 the number of column used (starting in 1) for the
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	392 TaxIDs assigned, the LENgth of the read, the SCOre
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	393 given to the assignment, and the taxid code used for
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	394 UNClassified reads
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	395 -f FILE, --file FILE Centrifuge output files; if a single directory is
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	396 entered, every .out file inside will be taken as a
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	397 different sample; multiple -f is available to include
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	398 several Centrifuge samples
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	399 -g FILE, --generic FILE
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	400 output file from a generic classifier; it requires the
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	401 flag --format (see such option for details); multiple
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	402 -g is available to include several generic samples
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	403 -l FILE, --lmat FILE LMAT output dir or file prefix; if just "." is
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	404 entered, every subdirectory under the current
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	405 directory will be taken as a sample and scanned
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	406 looking for LMAT output files; multiple -l is
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	407 available to include several samples
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	408 -r FILE, --clark FILE
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	409 CLARK full-mode output files; if a single directory is
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	410 entered, every .csv file inside will be taken as a
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	411 different sample; multiple -r is available to include
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	412 several CLARK, CLARK-l, and CLARK-S full-mode samples
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	413 -k FILE, --kraken FILE
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	414 Kraken output files; if a single directory is entered,
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	415 every .krk file inside will be taken as a different
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	416 sample; multiple -k is available to include several
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	417 Kraken (version 1 or 2) samples
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	418 output:
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	419 Related to the Recentrifuge output files
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	420 -o FILE, --outprefix FILE
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	421 output prefix; if not given, it will be inferred from
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	422 input files; an HTML filename is still accepted for
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	423 backwards compatibility with legacy --outhtml option
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	424 -e OUTPUT_TYPE, --extra OUTPUT_TYPE
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	425 type of extra output to be generated, and can be one
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	426 of ['FULL', 'CSV', 'MULTICSV', 'TSV', 'DYNOMICS']
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	427 -p, --pickle pickle (serialize) statistics and data results in
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	428 pandas DataFrames (format affected by selection of
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	429 --extra)
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	430 --nohtml suppress saving the HTML output file
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	431 tuning:
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	432 Coarse tuning of algorithm parameters
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	433 -a, --avoidcross avoid cross analysis
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	434 -c CONTROLS_NUMBER, --controls CONTROLS_NUMBER
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	435 this number of first samples will be treated as
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	436 negative controls; default is no controls
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	437 -s SCORING, --scoring SCORING
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	438 type of scoring to be applied, and can be one of
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	439 ['SHEL', 'LENGTH', 'LOGLENGTH', 'NORMA', 'LMAT',
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	440 'CLARK_C', 'CLARK_G', 'KRAKEN', 'GENERIC']
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	441 -y NUMBER, --minscore NUMBER
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	442 minimum score/confidence of the classification of a
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	443 read to pass the quality filter; all pass by default
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	444 -m INT, --mintaxa INT
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	445 minimum taxa to avoid collapsing one level into the
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	446 parent (if not specified a value will be automatically
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	447 assigned)
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	448 -x TAXID, --exclude TAXID
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	449 NCBI taxid code to exclude a taxon and all underneath
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	450 (multiple -x is available to exclude several taxid)
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	451 -i TAXID, --include TAXID
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	452 NCBI taxid code to include a taxon and all underneath
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	453 (multiple -i is available to include several taxid);
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	454 by default, all the taxa are considered for inclusion
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	455 fine tuning:
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	456 Fine tuning of algorithm parameters
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	457 -z NUMBER, --ctrlminscore NUMBER
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	458 minimum score/confidence of the classification of a
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	459 read in control samples to pass the quality filter; it
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	460 defaults to "minscore"
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	461 -w INT, --ctrlmintaxa INT
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	462 minimum taxa to avoid collapsing one level into the
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	463 parent (if not specified a value will be automatically
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	464 assigned)
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	465 -u SUMMARY_BEHAVIOR, --summary SUMMARY_BEHAVIOR
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	466 choice for summary behaviour, and can be one of
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	467 ['ADD', 'ONLY', 'AVOID']
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	468 -t, --takeoutroot remove counts directly assigned to the "root" level
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	469 --nokollapse show the "cellular organisms" taxon
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	470 advanced:
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	471 Advanced modes of running
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	472 -d, --debug increase output verbosity and perform additional
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	473 checks
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	474 --strain set strain level instead of species as the resolution
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	475 limit for the robust contamination removal algorithm;
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	476 use with caution, this is an experimental feature
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	477 --sequential deactivate parallel processing
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	478 rcf - Release 1.8.1 - Mar 2022
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	479 Copyright (C) 2017–2022, Jose Manuel Martí Martínez
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	480 This program is free software: you can redistribute it and/or modify
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	481 it under the terms of the GNU Affero General Public License as
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	482 published by the Free Software Foundation, either version 3 of the
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	483 License, or (at your option) any later version.
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	484 This program is distributed in the hope that it will be useful,
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	485 but WITHOUT ANY WARRANTY; without even the implied warranty of
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	486 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	487 GNU Affero General Public License for more details.
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	488 You should have received a copy of the GNU Affero General Public License
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: diff changeset	489 along with this program. If not, see <https://www.gnu.org/licenses/>.
2 b135c5908e8c "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: 0 diff changeset	490
b135c5908e8c "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: 0 diff changeset	491 ]]>
b135c5908e8c "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: 0 diff changeset	492 </help>
b135c5908e8c "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: 0 diff changeset	493 <expand macro="citations"/>
b135c5908e8c "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty" pimarin parents: 0 diff changeset	494 </tool>

Mercurial > repos > pimarin > recentrifuge

annotate recentrifuge.xml @ 2:b135c5908e8c draft