merqury: merqury.xml annotate

author	iuc
date	Sun, 18 Apr 2021 23:47:56 +0000
parents
children	39edec572bae

rev	line source
0 9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	1 <tool id="merqury" name="Merqury" version="@TOOL_VERSION@" profile="20.01">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	2 <description>evaluate the assembly quality</description>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	3 <macros>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	4 <import>macros.xml</import>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	5 </macros>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	6 <expand macro="edam_ontology"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	7 <expand macro="requirements"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	8 <version_command>merqury --version</version_command>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	10 mkdir -p output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	11 #if $mode.options == 'default'
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	12 && mkdir -p read-db.meryl
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	13 && tar -zxf ${mode.meryldb_F1} -C read-db.meryl --strip-components=1
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	14 #if $mode.assembly_options.number_assemblies == 'one'
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	15 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	16 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	17 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	18 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	19 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	20 && merqury.sh read-db.meryl assembly.fasta ${label}
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	21 && mv ${label}* output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	22 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 \| xargs -0r mv -t output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	23 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	24 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	25 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	26 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	27 && ln -s '$mode.assembly_options.assembly_01' assembly_01.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	28 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	29 #if $mode.assembly_options.assembly_02.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	30 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	31 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	32 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	33 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	34 && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta ${label}
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	35 && mv ${label}* output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	36 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 \| xargs -0r mv -t output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	37 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	38 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	39 && mkdir -p read-db.meryl pat.meryl mat.meryl
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	40 && tar -zxf ${mode.meryldb_F1} -C read-db.meryl --strip-components=1
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	41 && tar -zxf ${mode.meryldb_PAT} -C pat.meryl --strip-components=1
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	42 && tar -zxf ${mode.meryldb_MAT} -C mat.meryl --strip-components=1
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	43 #if $mode.assembly_options.number_assemblies == 'one'
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	44 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	45 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	46 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	47 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	48 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	49 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly.fasta ${label}
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	50 && mv ${label}* output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	51 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 \| xargs -0r mv -t output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	52 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	53 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	54 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	55 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	56 && ln -s '$mode.assembly_options.assembly_01' assembly_01.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	57 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	58 #if $mode.assembly_options.assembly_02.ext.endswith(".gz")
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	59 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	60 #else
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	61 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	62 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	63 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly_01.fasta assembly_02.fasta ${label}
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	64 && mv ${label}* output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	65 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 \| xargs -0r mv -t output_files
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	66 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	67 #end if
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	68 ]]> </command>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	69 <inputs>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	70 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	71 <param name="options" type="select"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	72 label="Evaluation mode" help="Merqury allows two operational modes: default and trio mode.">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	73 <option value="default">Default mode</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	74 <option value="trio">Trio mode</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	75 </param>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	76 <when value="default">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	77 <param name="meryldb_F1" type="data" format="meryldb"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	78 label="K-mer counts database"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	79 help="Select the k-mer counts of the read set."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	80 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	81 <param name="number_assemblies" type="select"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	82 label="Number of assemblies" help="Select the number of assemblies.">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	83 <option value="one">One assembly (pseudo-haplotype or mixed-haplotype)</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	84 <option value="two">Two assemblies (diploid)</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	85 </param>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	86 <when value="one">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	87 <param name="assembly_01" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	88 label="Genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	89 help="Select the assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	90 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	91 <when value="two">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	92 <param name="assembly_01" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	93 label="First genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	94 help="Select the first assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	95 <param name="assembly_02" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	96 label="Second genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	97 help="Select the second assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	98 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	99 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	100 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	101 <when value='trio'>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	102 <param name="meryldb_F1" type="data" format="meryldb"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	103 label="F1 k-mer counts"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	104 help="Select the k-mer counts of the read set (meryldb )."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	105 <param name="meryldb_PAT" type="data" format="meryldb"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	106 label="Paternal hap-mer database"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	107 help="K-mer counts of the paternal haplotype (meryldb)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	108 <param name="meryldb_MAT" type="data" format="meryldb"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	109 label="Maternal hap-mer database"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	110 help="K-mer counts of the maternal haplotype (meryldb)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	111 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	112 <param name="number_assemblies" type="select"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	113 label="Number of assemblies" help="Select the number of assemblies.">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	114 <option value="one">One assembly (pseudo-haplotype or mixed-haplotype)</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	115 <option value="two">Two assemblies (diploid)</option>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	116 </param>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	117 <when value="one">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	118 <param name="assembly_01" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	119 label="Genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	120 help="Select the assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	121 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	122 <when value="two">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	123 <param name="assembly_01" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	124 label="First genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	125 help="Select the first assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	126 <param name="assembly_02" type="data" format="fasta,fasta.gz"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	127 label="Second genome assembly"
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	128 help="Select the second assembled genome (FASTA)."/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	129 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	130 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	131 </when>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	132 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	133 <param name='label' type="text" value="output_merqury" label="Identification label" help="Assign an identification label.">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	134 <sanitizer invalid_char="">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	135 <valid initial="string.letters,string.digits">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	136 <add value="_" />
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	137 </valid>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	138 </sanitizer>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	139 </param>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	140 </inputs>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	141 <outputs>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	142 <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: bed">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	143 <discover_datasets pattern="(?P<name>.+)\.bed" format="bed" directory="output_files"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	144 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	145 <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: wig">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	146 <discover_datasets pattern="(?P<name>.+)\.wig" format="wig" directory="output_files"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	147 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	148 <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: qv">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	149 <discover_datasets pattern="(?P<name>.+)\.qv" format="tabular" directory="output_files"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	150 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	151 <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	152 <discover_datasets pattern="(?P<name>.+)\.png" format="png" directory="output_files"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	153 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	154 <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	155 <discover_datasets pattern="(?P<name>.+)\.sizes" format="tabular" directory="output_files"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	156 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	157 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	158 <discover_datasets pattern="(?P<name>.+)\.stats" format="tabular" directory="output_files"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	159 </collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	160 </outputs>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	161 <tests>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	162 <test>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	163 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	164 <param name="options" value="trio"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	165 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	166 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	167 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	168 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	169 <param name="number_assemblies" value="one"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	170 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	171 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	172 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	173 <param name="label" value="output_01"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	174 <output_collection name="png_files" type="list" count="3">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	175 <element name="output_01.assembly.mat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	176 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	177 <has_size value="2733" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	178 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	179 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	180 <element name="output_01.assembly.pat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	181 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	182 <has_size value="2733" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	183 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	184 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	185 <element name="output_01.hapmers.blob" file="output_01.hapmers.blob.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	186 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	187 <has_size value="10764" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	188 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	189 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	190 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	191 <output_collection name="stats_files" type="list" count="2">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	192 <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	193 <element name="output_01.completeness" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	194 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	195 <output_collection name="wig_files" type="list" count="2">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	196 <element name="output_01.assembly.pat" ftype="wig"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	197 <element name="output_01.assembly.mat" file="output_01.assembly.mat.wig" ftype="wig"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	198 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	199 <output_collection name="sizes_files" type="list" count="2">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	200 <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	201 <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	202 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	203 <output_collection name="bed_files" type="list" count="3">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	204 <element name="output_01.assembly.100_20000.phased_block" ftype="bed"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	205 <element name="output_01.assembly.100_20000.switch" ftype="bed"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	206 <element name="output_01.assembly.sort"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	207 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	208 </test>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	209 <test>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	210 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	211 <param name="options" value="default"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	212 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	213 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	214 <param name="number_assemblies" value="one"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	215 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	216 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	217 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	218 <param name="label" value="output_02"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	219 <output_collection name="png_files" type="list" count="6">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	220 <element name="output_02.assembly.spectra-cn.fl" file="output_02.assembly.spectra-cn.fl.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	221 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	222 <has_size value="58059" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	223 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	224 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	225 <element name="output_02.assembly.spectra-cn.ln" file="output_02.assembly.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	226 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	227 <has_size value="57763" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	228 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	229 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	230 <element name="output_02.assembly.spectra-cn.st" file="output_02.assembly.spectra-cn.st.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	231 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	232 <has_size value="61814" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	233 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	234 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	235 <element name="output_02.spectra-asm.fl" file="output_02.spectra-asm.fl.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	236 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	237 <has_size value="64445" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	238 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	239 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	240 <element name="output_02.spectra-asm.ln" file="output_02.spectra-asm.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	241 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	242 <has_size value="64795" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	243 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	244 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	245 <element name="output_02.spectra-asm.st" file="output_02.spectra-asm.st.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	246 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	247 <has_size value="66317" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	248 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	249 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	250 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	251 <output_collection name="stats_files" type="list" count="1">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	252 <element name="output_02.completeness" file="output_02.completeness.stats.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	253 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	254 <output_collection name="qv_files" type="list" count="2">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	255 <element name="output_02.assembly" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	256 <element name="output_02" file="output_02_qv.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	257 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	258 <output_collection name="wig_files" type="list" count="1">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	259 <element name="assembly_only" ftype="wig">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	260 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	261 <has_size value="29909811" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	262 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	263 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	264 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	265 <output_collection name="bed_files" type="list" count="1">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	266 <element name="assembly_only" ftype="bed">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	267 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	268 <has_size value="73516121" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	269 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	270 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	271 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	272 </test>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	273 <test>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	274 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	275 <param name="options" value="default"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	276 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	277 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	278 <param name="number_assemblies" value="two"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	279 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	280 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	281 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	282 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	283 <param name="label" value="output_03"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	284 <output_collection name="png_files" type="list" count="10">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	285 <element name="output_03.assembly_01.spectra-cn.fl" file="output_03.assembly_01.spectra-cn.fl.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	286 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	287 <has_size value="58059" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	288 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	289 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	290 <element name="output_03.assembly_01.spectra-cn.ln" file="output_03.assembly_01.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	291 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	292 <has_size value="57763" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	293 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	294 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	295 <element name="output_03.assembly_01.spectra-cn.st" file="output_03.assembly_01.spectra-cn.st.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	296 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	297 <has_size value="61814" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	298 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	299 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	300 <element name="output_03.assembly_02.spectra-cn.fl" file="output_03.assembly_02.spectra-cn.fl.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	301 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	302 <has_size value="61579" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	303 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	304 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	305 <element name="output_03.assembly_02.spectra-cn.ln" file="output_03.assembly_02.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	306 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	307 <has_size value="61538" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	308 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	309 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	310 <element name="output_03.assembly_02.spectra-cn.st" file="output_03.assembly_02.spectra-cn.st.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	311 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	312 <has_size value="67297" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	313 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	314 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	315 <element name="output_03.spectra-asm.ln" file="output_03.spectra-asm.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	316 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	317 <has_size value="2733" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	318 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	319 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	320 <element name="output_03.spectra-cn.fl" file="output_03.spectra-cn.fl.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	321 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	322 <has_size value="61397" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	323 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	324 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	325 <element name="output_03.spectra-cn.ln" file="output_03.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	326 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	327 <has_size value="61050" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	328 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	329 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	330 <element name="output_03.spectra-cn.st" file="output_03.spectra-cn.st.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	331 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	332 <has_size value="65243" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	333 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	334 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	335 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	336 <output_collection name="stats_files" type="list" count="1">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	337 <element name="output_03.completeness" file="output_03.completeness.stats.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	338 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	339 <output_collection name="qv_files" type="list" count="3">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	340 <element name="output_03.assembly_01" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	341 <element name="output_03.assembly_02" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	342 <element name="output_03" file="output_03_qv.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	343 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	344 </test>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	345 <test>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	346 <conditional name="mode">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	347 <param name="options" value="trio"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	348 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	349 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	350 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	351 <conditional name="assembly_options">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	352 <param name="number_assemblies" value="two"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	353 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	354 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	355 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	356 </conditional>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	357 <param name="label" value="output_04"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	358 <output_collection name="png_files" type="list" count="5">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	359 <element name="output_04.assembly_01.mat.spectra-cn.ln" file="output_04.assembly_01.mat.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	360 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	361 <has_size value="2733" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	362 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	363 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	364 <element name="output_04.assembly_01.pat.spectra-cn.ln" file="output_04.assembly_01.pat.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	365 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	366 <has_size value="2733" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	367 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	368 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	369 <element name="output_04.assembly_02.mat.spectra-cn.ln" file="output_04.assembly_02.mat.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	370 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	371 <has_size value="2733" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	372 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	373 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	374 <element name="output_04.assembly_02.pat.spectra-cn.ln" file="output_04.assembly_02.pat.spectra-cn.ln.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	375 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	376 <has_size value="2733" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	377 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	378 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	379 <element name="output_04.hapmers.blob" file="output_04.hapmers.blob.png" ftype="png">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	380 <assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	381 <has_size value="10764" delta="100"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	382 </assert_contents>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	383 </element>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	384 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	385 <output_collection name="stats_files" type="list" count="3">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	386 <element name="output_04.assembly_01.100_20000.phased_block" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	387 <element name="output_04.assembly_02.100_20000.phased_block" file="output_04.assembly_02.100_20000.phased_block.stats.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	388 <element name="output_04.completeness"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	389 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	390 <output_collection name="qv_files" type="list" count="1">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	391 <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	392 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	393 <output_collection name="wig_files" type="list" count="4">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	394 <element name="output_04.assembly_01.pat" ftype="wig"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	395 <element name="output_04.assembly_01.mat" ftype="wig"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	396 <element name="output_04.assembly_02.pat" ftype="wig"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	397 <element name="output_04.assembly_02.mat" ftype="wig"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	398 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	399 <output_collection name="sizes_files" type="list" count="4">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	400 <element name="output_04.assembly_01.100_20000.phased_block"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	401 <element name="output_04.assembly_01.contig" file="output_04.assembly_01.contig.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	402 <element name="output_04.assembly_02.100_20000.phased_block"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	403 <element name="output_04.assembly_02.contig" file="output_04.assembly_02.contig.tabular" ftype="tabular"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	404 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	405 <output_collection name="bed_files" type="list" count="6">
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	406 <element name="output_04.assembly_01.100_20000.phased_block" ftype="bed"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	407 <element name="output_04.assembly_01.100_20000.switch" file="output_04.assembly_01.100_20000.switch.bed" ftype="bed"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	408 <element name="output_04.assembly_01.sort" file="output_04.assembly_01.sort.bed" ftype="bed"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	409 <element name="output_04.assembly_02.100_20000.phased_block" ftype="bed"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	410 <element name="output_04.assembly_02.100_20000.switch" ftype="bed"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	411 <element name="output_04.assembly_02.sort" ftype="bed"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	412 </output_collection>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	413 </test>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	414 </tests>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	415 <help><![CDATA[
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	416 .. class:: infomark
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	417
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	418 Purpose
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	419
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	420 Merqury allows a reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	421 assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness.
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	422
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	423 For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors.
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	424
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	425 ----
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	426
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	427 .. class:: infomark
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	428
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	429 Input
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	430
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	431 Merqury requires two types of inputs: meryldbs and the genome assemblies.
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	432 There is no need to run merqury per-assemblies. If two assemblies areprovided, Merqury generates stats for each and combined.
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	433
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	434 ----
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	435
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	436 .. class:: infomark
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	437
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	438 Output
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	439
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	440 The generated metrics include consensus quality and k-mer completeness, and when parental genomic sequences are available (either assembled or unassembled), Merqury can output haplotype completeness, phase block statistics, switch error rates, and visual representations of phase consistency for the child’s genome. This includes TDF (or BED) features that can be displayed in a genome browser for visualizing the presence of k-mer classes across a genome (e.g., the k-mers inherited from a parental genome).
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	441
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	442 ]]> </help>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	443 <expand macro="citations"/>
9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd" iuc parents: diff changeset	444 </tool>

0

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

1 <tool id="merqury" name="Merqury" version="@TOOL_VERSION@" profile="20.01">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

2 <description>evaluate the assembly quality</description>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

3 <macros>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

4 <import>macros.xml</import>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

5 </macros>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

6 <expand macro="edam_ontology"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

7 <expand macro="requirements"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

8 <version_command>merqury --version</version_command>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

9 <command detect_errors="exit_code"><![CDATA[

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

10 mkdir -p output_files

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

11 #if $mode.options == 'default'

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

12 && mkdir -p read-db.meryl

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

13 && tar -zxf ${mode.meryldb_F1} -C read-db.meryl --strip-components=1

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

14 #if $mode.assembly_options.number_assemblies == 'one'

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

15 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

16 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

17 #else

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

18 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

19 #end if

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

20 && merqury.sh read-db.meryl assembly.fasta ${label}

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

21 && mv ${label}* output_files

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

22 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

23 #else

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

24 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

25 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

26 #else

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

27 && ln -s '$mode.assembly_options.assembly_01' assembly_01.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

28 #end if

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

29 #if $mode.assembly_options.assembly_02.ext.endswith(".gz")

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

30 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

31 #else

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

32 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

33 #end if

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

34 && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta ${label}

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

35 && mv ${label}* output_files

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

36 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

37 #end if

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

38 #else

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

39 && mkdir -p read-db.meryl pat.meryl mat.meryl

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

40 && tar -zxf ${mode.meryldb_F1} -C read-db.meryl --strip-components=1

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

41 && tar -zxf ${mode.meryldb_PAT} -C pat.meryl --strip-components=1

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

42 && tar -zxf ${mode.meryldb_MAT} -C mat.meryl --strip-components=1

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

43 #if $mode.assembly_options.number_assemblies == 'one'

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

44 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

45 && gunzip -c $mode.assembly_options.assembly_01 > assembly.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

46 #else

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

47 && ln -s '$mode.assembly_options.assembly_01' assembly.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

48 #end if

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

49 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly.fasta ${label}

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

50 && mv ${label}* output_files

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

51 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

52 #else

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

53 #if $mode.assembly_options.assembly_01.ext.endswith(".gz")

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

54 && gunzip -c $mode.assembly_options.assembly_01 > assembly_01.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

55 #else

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

56 && ln -s '$mode.assembly_options.assembly_01' assembly_01.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

57 #end if

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

58 #if $mode.assembly_options.assembly_02.ext.endswith(".gz")

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

59 && gunzip -c $mode.assembly_options.assembly_02 > assembly_02.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

60 #else

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

61 && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

62 #end if

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

63 && merqury.sh read-db.meryl pat.meryl mat.meryl assembly_01.fasta assembly_02.fasta ${label}

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

64 && mv ${label}* output_files

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

65 && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

66 #end if

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

67 #end if

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

68 ]]> </command>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

69 <inputs>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

70 <conditional name="mode">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

71 <param name="options" type="select"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

72 label="Evaluation mode" help="Merqury allows two operational modes: default and trio mode.">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

73 <option value="default">Default mode</option>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

74 <option value="trio">Trio mode</option>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

75 </param>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

76 <when value="default">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

77 <param name="meryldb_F1" type="data" format="meryldb"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

78 label="K-mer counts database"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

79 help="Select the k-mer counts of the read set."/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

80 <conditional name="assembly_options">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

81 <param name="number_assemblies" type="select"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

82 label="Number of assemblies" help="Select the number of assemblies.">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

83 <option value="one">One assembly (pseudo-haplotype or mixed-haplotype)</option>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

84 <option value="two">Two assemblies (diploid)</option>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

85 </param>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

86 <when value="one">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

87 <param name="assembly_01" type="data" format="fasta,fasta.gz"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

88 label="Genome assembly"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

89 help="Select the assembled genome (FASTA)."/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

90 </when>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

91 <when value="two">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

92 <param name="assembly_01" type="data" format="fasta,fasta.gz"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

93 label="First genome assembly"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

94 help="Select the first assembled genome (FASTA)."/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

95 <param name="assembly_02" type="data" format="fasta,fasta.gz"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

96 label="Second genome assembly"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

97 help="Select the second assembled genome (FASTA)."/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

98 </when>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

99 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

100 </when>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

101 <when value='trio'>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

102 <param name="meryldb_F1" type="data" format="meryldb"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

103 label="F1 k-mer counts"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

104 help="Select the k-mer counts of the read set (meryldb )."/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

105 <param name="meryldb_PAT" type="data" format="meryldb"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

106 label="Paternal hap-mer database"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

107 help="K-mer counts of the paternal haplotype (meryldb)."/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

108 <param name="meryldb_MAT" type="data" format="meryldb"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

109 label="Maternal hap-mer database"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

110 help="K-mer counts of the maternal haplotype (meryldb)."/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

111 <conditional name="assembly_options">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

112 <param name="number_assemblies" type="select"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

113 label="Number of assemblies" help="Select the number of assemblies.">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

114 <option value="one">One assembly (pseudo-haplotype or mixed-haplotype)</option>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

115 <option value="two">Two assemblies (diploid)</option>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

116 </param>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

117 <when value="one">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

118 <param name="assembly_01" type="data" format="fasta,fasta.gz"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

119 label="Genome assembly"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

120 help="Select the assembled genome (FASTA)."/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

121 </when>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

122 <when value="two">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

123 <param name="assembly_01" type="data" format="fasta,fasta.gz"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

124 label="First genome assembly"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

125 help="Select the first assembled genome (FASTA)."/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

126 <param name="assembly_02" type="data" format="fasta,fasta.gz"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

127 label="Second genome assembly"

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

128 help="Select the second assembled genome (FASTA)."/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

129 </when>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

130 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

131 </when>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

132 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

133 <param name='label' type="text" value="output_merqury" label="Identification label" help="Assign an identification label.">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

134 <sanitizer invalid_char="">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

135 <valid initial="string.letters,string.digits">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

136 <add value="_" />

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

137 </valid>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

138 </sanitizer>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

139 </param>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

140 </inputs>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

141 <outputs>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

142 <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: bed">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

143 <discover_datasets pattern="(?P<name>.+)\.bed" format="bed" directory="output_files"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

144 </collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

145 <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: wig">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

146 <discover_datasets pattern="(?P<name>.+)\.wig" format="wig" directory="output_files"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

147 </collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

148 <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: qv">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

149 <discover_datasets pattern="(?P<name>.+)\.qv" format="tabular" directory="output_files"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

150 </collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

151 <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

152 <discover_datasets pattern="(?P<name>.+)\.png" format="png" directory="output_files"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

153 </collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

154 <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

155 <discover_datasets pattern="(?P<name>.+)\.sizes" format="tabular" directory="output_files"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

156 </collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

157 <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

158 <discover_datasets pattern="(?P<name>.+)\.stats" format="tabular" directory="output_files"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

159 </collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

160 </outputs>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

161 <tests>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

162 <test>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

163 <conditional name="mode">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

164 <param name="options" value="trio"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

165 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

166 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

167 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

168 <conditional name="assembly_options">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

169 <param name="number_assemblies" value="one"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

170 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

171 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

172 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

173 <param name="label" value="output_01"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

174 <output_collection name="png_files" type="list" count="3">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

175 <element name="output_01.assembly.mat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

176 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

177 <has_size value="2733" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

178 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

179 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

180 <element name="output_01.assembly.pat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

181 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

182 <has_size value="2733" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

183 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

184 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

185 <element name="output_01.hapmers.blob" file="output_01.hapmers.blob.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

186 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

187 <has_size value="10764" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

188 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

189 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

190 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

191 <output_collection name="stats_files" type="list" count="2">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

192 <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

193 <element name="output_01.completeness" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

194 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

195 <output_collection name="wig_files" type="list" count="2">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

196 <element name="output_01.assembly.pat" ftype="wig"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

197 <element name="output_01.assembly.mat" file="output_01.assembly.mat.wig" ftype="wig"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

198 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

199 <output_collection name="sizes_files" type="list" count="2">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

200 <element name="output_01.assembly.100_20000.phased_block" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

201 <element name="output_01.assembly.contig" file="output_01.assembly.contig.tabular" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

202 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

203 <output_collection name="bed_files" type="list" count="3">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

204 <element name="output_01.assembly.100_20000.phased_block" ftype="bed"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

205 <element name="output_01.assembly.100_20000.switch" ftype="bed"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

206 <element name="output_01.assembly.sort"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

207 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

208 </test>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

209 <test>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

210 <conditional name="mode">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

211 <param name="options" value="default"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

212 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

213 <conditional name="assembly_options">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

214 <param name="number_assemblies" value="one"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

215 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

216 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

217 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

218 <param name="label" value="output_02"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

219 <output_collection name="png_files" type="list" count="6">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

220 <element name="output_02.assembly.spectra-cn.fl" file="output_02.assembly.spectra-cn.fl.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

221 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

222 <has_size value="58059" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

223 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

224 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

225 <element name="output_02.assembly.spectra-cn.ln" file="output_02.assembly.spectra-cn.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

226 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

227 <has_size value="57763" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

228 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

229 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

230 <element name="output_02.assembly.spectra-cn.st" file="output_02.assembly.spectra-cn.st.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

231 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

232 <has_size value="61814" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

233 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

234 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

235 <element name="output_02.spectra-asm.fl" file="output_02.spectra-asm.fl.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

236 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

237 <has_size value="64445" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

238 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

239 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

240 <element name="output_02.spectra-asm.ln" file="output_02.spectra-asm.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

241 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

242 <has_size value="64795" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

243 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

244 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

245 <element name="output_02.spectra-asm.st" file="output_02.spectra-asm.st.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

246 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

247 <has_size value="66317" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

248 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

249 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

250 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

251 <output_collection name="stats_files" type="list" count="1">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

252 <element name="output_02.completeness" file="output_02.completeness.stats.tabular" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

253 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

254 <output_collection name="qv_files" type="list" count="2">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

255 <element name="output_02.assembly" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

256 <element name="output_02" file="output_02_qv.tabular" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

257 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

258 <output_collection name="wig_files" type="list" count="1">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

259 <element name="assembly_only" ftype="wig">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

260 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

261 <has_size value="29909811" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

262 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

263 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

264 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

265 <output_collection name="bed_files" type="list" count="1">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

266 <element name="assembly_only" ftype="bed">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

267 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

268 <has_size value="73516121" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

269 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

270 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

271 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

272 </test>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

273 <test>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

274 <conditional name="mode">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

275 <param name="options" value="default"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

276 <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

277 <conditional name="assembly_options">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

278 <param name="number_assemblies" value="two"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

279 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

280 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

281 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

282 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

283 <param name="label" value="output_03"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

284 <output_collection name="png_files" type="list" count="10">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

285 <element name="output_03.assembly_01.spectra-cn.fl" file="output_03.assembly_01.spectra-cn.fl.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

286 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

287 <has_size value="58059" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

288 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

289 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

290 <element name="output_03.assembly_01.spectra-cn.ln" file="output_03.assembly_01.spectra-cn.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

291 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

292 <has_size value="57763" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

293 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

294 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

295 <element name="output_03.assembly_01.spectra-cn.st" file="output_03.assembly_01.spectra-cn.st.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

296 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

297 <has_size value="61814" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

298 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

299 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

300 <element name="output_03.assembly_02.spectra-cn.fl" file="output_03.assembly_02.spectra-cn.fl.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

301 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

302 <has_size value="61579" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

303 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

304 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

305 <element name="output_03.assembly_02.spectra-cn.ln" file="output_03.assembly_02.spectra-cn.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

306 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

307 <has_size value="61538" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

308 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

309 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

310 <element name="output_03.assembly_02.spectra-cn.st" file="output_03.assembly_02.spectra-cn.st.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

311 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

312 <has_size value="67297" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

313 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

314 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

315 <element name="output_03.spectra-asm.ln" file="output_03.spectra-asm.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

316 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

317 <has_size value="2733" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

318 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

319 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

320 <element name="output_03.spectra-cn.fl" file="output_03.spectra-cn.fl.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

321 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

322 <has_size value="61397" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

323 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

324 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

325 <element name="output_03.spectra-cn.ln" file="output_03.spectra-cn.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

326 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

327 <has_size value="61050" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

328 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

329 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

330 <element name="output_03.spectra-cn.st" file="output_03.spectra-cn.st.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

331 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

332 <has_size value="65243" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

333 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

334 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

335 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

336 <output_collection name="stats_files" type="list" count="1">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

337 <element name="output_03.completeness" file="output_03.completeness.stats.tabular" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

338 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

339 <output_collection name="qv_files" type="list" count="3">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

340 <element name="output_03.assembly_01" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

341 <element name="output_03.assembly_02" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

342 <element name="output_03" file="output_03_qv.tabular" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

343 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

344 </test>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

345 <test>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

346 <conditional name="mode">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

347 <param name="options" value="trio"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

348 <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

349 <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

350 <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

351 <conditional name="assembly_options">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

352 <param name="number_assemblies" value="two"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

353 <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

354 <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

355 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

356 </conditional>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

357 <param name="label" value="output_04"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

358 <output_collection name="png_files" type="list" count="5">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

359 <element name="output_04.assembly_01.mat.spectra-cn.ln" file="output_04.assembly_01.mat.spectra-cn.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

360 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

361 <has_size value="2733" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

362 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

363 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

364 <element name="output_04.assembly_01.pat.spectra-cn.ln" file="output_04.assembly_01.pat.spectra-cn.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

365 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

366 <has_size value="2733" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

367 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

368 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

369 <element name="output_04.assembly_02.mat.spectra-cn.ln" file="output_04.assembly_02.mat.spectra-cn.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

370 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

371 <has_size value="2733" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

372 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

373 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

374 <element name="output_04.assembly_02.pat.spectra-cn.ln" file="output_04.assembly_02.pat.spectra-cn.ln.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

375 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

376 <has_size value="2733" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

377 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

378 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

379 <element name="output_04.hapmers.blob" file="output_04.hapmers.blob.png" ftype="png">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

380 <assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

381 <has_size value="10764" delta="100"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

382 </assert_contents>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

383 </element>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

384 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

385 <output_collection name="stats_files" type="list" count="3">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

386 <element name="output_04.assembly_01.100_20000.phased_block" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

387 <element name="output_04.assembly_02.100_20000.phased_block" file="output_04.assembly_02.100_20000.phased_block.stats.tabular" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

388 <element name="output_04.completeness"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

389 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

390 <output_collection name="qv_files" type="list" count="1">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

391 <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

392 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

393 <output_collection name="wig_files" type="list" count="4">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

394 <element name="output_04.assembly_01.pat" ftype="wig"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

395 <element name="output_04.assembly_01.mat" ftype="wig"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

396 <element name="output_04.assembly_02.pat" ftype="wig"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

397 <element name="output_04.assembly_02.mat" ftype="wig"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

398 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

399 <output_collection name="sizes_files" type="list" count="4">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

400 <element name="output_04.assembly_01.100_20000.phased_block"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

401 <element name="output_04.assembly_01.contig" file="output_04.assembly_01.contig.tabular" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

402 <element name="output_04.assembly_02.100_20000.phased_block"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

403 <element name="output_04.assembly_02.contig" file="output_04.assembly_02.contig.tabular" ftype="tabular"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

404 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

405 <output_collection name="bed_files" type="list" count="6">

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

406 <element name="output_04.assembly_01.100_20000.phased_block" ftype="bed"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

407 <element name="output_04.assembly_01.100_20000.switch" file="output_04.assembly_01.100_20000.switch.bed" ftype="bed"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

408 <element name="output_04.assembly_01.sort" file="output_04.assembly_01.sort.bed" ftype="bed"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

409 <element name="output_04.assembly_02.100_20000.phased_block" ftype="bed"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

410 <element name="output_04.assembly_02.100_20000.switch" ftype="bed"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

411 <element name="output_04.assembly_02.sort" ftype="bed"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

412 </output_collection>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

413 </test>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

414 </tests>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

415 <help><![CDATA[

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

416 .. class:: infomark

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

417

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

418 **Purpose**

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

419

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

420 Merqury allows a reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

421 assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness.

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

422

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

423 For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors.

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

424

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

425 ----

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

426

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

427 .. class:: infomark

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

428

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

429 **Input**

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

430

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

431 Merqury requires two types of inputs: meryldbs and the genome assemblies.

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

432 There is no need to run merqury per-assemblies. If two assemblies areprovided, Merqury generates stats for each and combined.

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

433

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

434 ----

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

435

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

436 .. class:: infomark

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

437

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

438 **Output**

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

439

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

440 The generated metrics include consensus quality and k-mer completeness, and when parental genomic sequences are available (either assembled or unassembled), Merqury can output haplotype completeness, phase block statistics, switch error rates, and visual representations of phase consistency for the child’s genome. This includes TDF (or BED) features that can be displayed in a genome browser for visualizing the presence of k-mer classes across a genome (e.g., the k-mers inherited from a parental genome).

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

441

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

442 ]]> </help>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

443 <expand macro="citations"/>

9d79beb19ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 561c3bcec49ecef9384b565861ccee11a377f7cd"

iuc

parents:

diff changeset

444 </tool>

Mercurial > repos > iuc > merqury

annotate merqury.xml @ 0:9d79beb19ac3 draft