shasta: shasta.xml annotate

annotate shasta.xml @ 0:60573349e9ae draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"

author	iuc
date	Wed, 11 Nov 2020 21:54:51 +0000
parents
children

rev	line source
0 60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	1 <?xml version="1.0"?>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	2 <tool id="shasta" name="Shasta" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	3 <description>De novo assembly of long read sequencing data</description>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	4 <macros>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	5 <import>macros.xml</import>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	6 </macros>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	7
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	8 <expand macro="requirements"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	9
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	10 <expand macro="version_command"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	11
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	12 <command detect_errors="exit_code"><![CDATA[
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	13 ### Initialize input reads (either unzip or symlink to have the right file extensions for shasta)
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	14
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	15 @INIT_INPUT_READS@
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	16
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	17 shasta --threads \${GALAXY_SLOTS:-4}
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	18
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	19 #if $use_config.use_config_select == "yes":
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	20 --config '${__tool_directory__}/configs/${use_config.config_select}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	21 #elif $use_config.use_config_select == "file":
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	22 --config '$in_config'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	23 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	24
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	25 --assemblyDirectory shasta_out
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	26 --command assemble
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	27
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	28 ######################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	29 ### Reads Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	30 ######################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	31
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	32 #if str($reads.min_read_length):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	33 --Reads.minReadLength '${reads.min_read_length}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	34 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	35 #if str($reads.desired_coverage):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	36 --Reads.desiredCoverage '${reads.desired_coverage}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	37 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	38
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	39 #######################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	40 ### Reads.palindromicReads Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	41 #######################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	42
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	43 #if $reads.palindromic_reads.skip_flagging:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	44 --Reads.palindromicReads.skipFlagging '${reads.palindromic_reads.skip_flagging}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	45 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	46 #if str($reads.palindromic_reads.max_skip):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	47 --Reads.palindromicReads.maxSkip '${reads.palindromic_reads.max_skip}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	48 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	49 #if str($reads.palindromic_reads.max_drift):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	50 --Reads.palindromicReads.maxDrift '${reads.palindromic_reads.max_drift}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	51 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	52 #if str($reads.palindromic_reads.max_marker_frequency):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	53 --Reads.palindromicReads.maxMarkerFrequency '${reads.palindromic_reads.max_marker_frequency}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	54 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	55 #if str($reads.palindromic_reads.aligned_fraction_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	56 --Reads.palindromicReads.alignedFractionThreshold '${reads.palindromic_reads.aligned_fraction_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	57 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	58 #if str($reads.palindromic_reads.near_diagonal_fraction_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	59 --Reads.palindromicReads.nearDiagonalFractionThreshold '${reads.palindromic_reads.near_diagonal_fraction_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	60 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	61 #if str($reads.palindromic_reads.delta_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	62 --Reads.palindromicReads.deltaThreshold '${reads.palindromic_reads.delta_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	63 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	64
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	65 ######################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	66 ### Kmers Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	67 ######################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	68
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	69 #if $kmers.generation_method:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	70 --Kmers.generationMethod '${kmers.generation_method}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	71 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	72 #if str($kmers.k):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	73 --Kmers.k '${kmers.k}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	74 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	75 #if str($kmers.probability):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	76 --Kmers.probability '${kmers.probability}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	77 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	78 #if str($kmers.enrichment_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	79 --Kmers.enrichmentThreshold '${kmers.enrichment_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	80 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	81 #if $kmers.file:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	82 --Kmers.file '${kmers.file}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	83 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	84
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	85 ########################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	86 ### MinHash Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	87 ########################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	88
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	89 #if $minhash.version:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	90 --MinHash.version '${minhash.version}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	91 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	92 #if str($minhash.m):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	93 --MinHash.m '${minhash.m}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	94 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	95 #if str($minhash.hash_fraction):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	96 --MinHash.hashFraction '${minhash.hash_fraction}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	97 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	98 #if str($minhash.min_hash_iteration_count):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	99 --MinHash.minHashIterationCount '${minhash.min_hash_iteration_count}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	100 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	101 #if str($minhash.alignment_candidates_per_read):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	102 --MinHash.alignmentCandidatesPerRead '${minhash.alignment_candidates_per_read}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	103 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	104 #if str($minhash.min_bucket_size):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	105 --MinHash.minBucketSize '${minhash.min_bucket_size}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	106 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	107 #if str($minhash.max_bucket_size):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	108 --MinHash.maxBucketSize '${minhash.max_bucket_size}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	109 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	110 #if str($minhash.min_frequency):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	111 --MinHash.minFrequency '${minhash.min_frequency}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	112 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	113 #if $minhash.all_pairs:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	114 ${minhash.all_pairs}
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	115 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	116
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	117 ######################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	118 ### Align Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	119 ######################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	120
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	121 #if $align.align_method:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	122 --Align.alignMethod '${align.align_method}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	123 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	124 #if str($align.max_skip):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	125 --Align.maxSkip '${align.max_skip}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	126 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	127 #if str($align.max_drift):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	128 --Align.maxDrift '${align.max_drift}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	129 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	130 #if str($align.max_trim):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	131 --Align.maxTrim '${align.max_trim}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	132 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	133 #if str($align.max_marker_frequency):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	134 --Align.maxMarkerFrequency '${align.max_marker_frequency}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	135 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	136 #if str($align.min_aligned_marker_count):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	137 --Align.minAlignedMarkerCount '${align.min_aligned_marker_count}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	138 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	139 #if str($align.min_aligned_fraction):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	140 --Align.minAlignedFraction '${align.min_aligned_fraction}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	141 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	142 #if str($align.match_score):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	143 --Align.matchScore '${align.match_score}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	144 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	145 #if str($align.mismatch_score):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	146 --Align.mismatchScore '${align.mismatch_score}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	147 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	148 #if str($align.gap_score):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	149 --Align.gapScore '${align.gap_score}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	150 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	151 #if str($align.downsampling_factor):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	152 --Align.downsamplingFactor '${align.downsampling_factor}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	153 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	154 #if str($align.band_extend):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	155 --Align.bandExtend '${align.band_extend}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	156 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	157 #if str($align.max_band):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	158 --Align.maxBand '${align.max_band}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	159 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	160 #if $align.suppress_containments:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	161 ${align.suppress_containments}
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	162 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	163
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	164 ###############################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	165 ### Align.sameChannelReadAlignment Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	166 ###############################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	167
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	168 #if str($align.same_channel_read_alignment.suppress_delta_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	169 --Align.sameChannelReadAlignment.suppressDeltaThreshold '${align.same_channel_read_alignment.suppress_delta_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	170 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	171
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	172 ##########################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	173 ### ReadGraph Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	174 ##########################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	175
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	176 #if $read_graph.creation_method:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	177 --ReadGraph.creationMethod '${read_graph.creation_method}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	178 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	179 #if str($read_graph.max_alignment_count):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	180 --ReadGraph.maxAlignmentCount '${read_graph.max_alignment_count}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	181 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	182 #if str($read_graph.max_chimeric_read_distance):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	183 --ReadGraph.maxChimericReadDistance '${read_graph.max_chimeric_read_distance}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	184 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	185 #if str($read_graph.cross_strand_max_distance):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	186 --ReadGraph.crossStrandMaxDistance '${read_graph.cross_strand_max_distance}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	187 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	188 #if str($read_graph.contained_neighbor_count):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	189 --ReadGraph.containedNeighborCount '${read_graph.contained_neighbor_count}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	190 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	191 #if str($read_graph.uncontained_neighbor_count_per_direction):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	192 --ReadGraph.uncontainedNeighborCountPerDirection '${read_graph.uncontained_neighbor_count_per_direction}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	193 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	194 #if str($read_graph.marker_count_percentile):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	195 --ReadGraph.markerCountPercentile '${read_graph.marker_count_percentile}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	196 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	197 #if str($read_graph.aligned_fraction_percentile):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	198 --ReadGraph.alignedFractionPercentile '${read_graph.aligned_fraction_percentile}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	199 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	200 #if str($read_graph.max_skip_percentile):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	201 --ReadGraph.maxSkipPercentile '${read_graph.max_skip_percentile}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	202 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	203 #if str($read_graph.max_drift_percentile):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	204 --ReadGraph.maxDriftPercentile '${read_graph.max_drift_percentile}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	205 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	206 #if str($read_graph.max_trim_percentile):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	207 --ReadGraph.maxTrimPercentile '${read_graph.max_trim_percentile}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	208 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	209
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	210 ############################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	211 ### MarkerGraph Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	212 ############################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	213
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	214 #if str($marker_graph.min_coverage):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	215 --MarkerGraph.minCoverage '${marker_graph.min_coverage}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	216 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	217 #if str($marker_graph.max_coverage):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	218 --MarkerGraph.maxCoverage '${marker_graph.max_coverage}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	219 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	220 #if str($marker_graph.min_coverage_per_strand):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	221 --MarkerGraph.minCoveragePerStrand '${marker_graph.min_coverage_per_strand}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	222 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	223 #if str($marker_graph.low_coverage_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	224 --MarkerGraph.lowCoverageThreshold '${marker_graph.low_coverage_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	225 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	226 #if str($marker_graph.high_coverage_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	227 --MarkerGraph.highCoverageThreshold '${marker_graph.high_coverage_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	228 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	229 #if str($marker_graph.max_distance):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	230 --MarkerGraph.maxDistance '${marker_graph.max_distance}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	231 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	232 #if str($marker_graph.edge_marker_skip_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	233 --MarkerGraph.edgeMarkerSkipThreshold '${marker_graph.edge_marker_skip_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	234 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	235 #if str($marker_graph.prune_iteration_count):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	236 --MarkerGraph.pruneIterationCount '${marker_graph.prune_iteration_count}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	237 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	238 #if str($marker_graph.simplifiy_max_length):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	239 --MarkerGraph.simplifyMaxLength '${marker_graph.simplifiy_max_length}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	240 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	241 #if str($marker_graph.cross_edge_coverage_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	242 --MarkerGraph.crossEdgeCoverageThreshold '${marker_graph.cross_edge_coverage_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	243 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	244 #if str($marker_graph.refine_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	245 --MarkerGraph.refineThreshold '${marker_graph.refine_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	246 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	247 #if $marker_graph.reverse_transitive_reduction:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	248 ${marker_graph.reverse_transitive_reduction}
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	249 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	250
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	251 #######################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	252 ### MarkerGraph.peakFinder Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	253 #######################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	254
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	255 #if str($marker_graph.peak_finder.min_area_fraction):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	256 --MarkerGraph.peakFinder.minAreaFraction '${marker_graph.peak_finder.min_area_fraction}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	257 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	258 #if str($marker_graph.peak_finder.area_start_index):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	259 --MarkerGraph.peakFinder.areaStartIndex '${marker_graph.peak_finder.area_start_index}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	260 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	261
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	262 #########################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	263 ### Assembly Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	264 #########################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	265
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	266 #if str($assembly.marker_graph_edge_length_threshold_for_consensus):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	267 --Assembly.markerGraphEdgeLengthThresholdForConsensus '${assembly.marker_graph_edge_length_threshold_for_consensus}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	268 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	269 #if str($assembly.consensus_caller.consensus_caller_select) == "custom":
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	270 --Assembly.consensusCaller 'Bayesian:${assembly.consensus_caller.consensus_caller_conf_file}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	271 #elif str($assembly.consensus_caller.consensus_caller_select) != "default":
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	272 --Assembly.consensusCaller ${assembly.consensus_caller.consensus_caller_select}
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	273 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	274 ## ## The below option only can be meaningfully set with memoryMode set to filesystem, which requires root access. Therefore, removing this param
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	275 ## #if str($assembly.store_coverage_data_csv_length_threshold):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	276 ## --Assembly.storeCoverageDataCsvLengthThreshold '${assembly.store_coverage_data_csv_length_threshold}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	277 ## #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	278 ${assembly.write_reads_by_assembled_segment}
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	279
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	280 ##################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	281 ### Assembly.detangle Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	282 ##################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	283
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	284 #if $assembly.detangle.detangle_method:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	285 --Assembly.detangleMethod '${assembly.detangle.detangle_method}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	286 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	287 #if str($assembly.detangle.diagonal_read_count_min):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	288 --Assembly.detangle.diagonalReadCountMin '${assembly.detangle.diagonal_read_count_min}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	289 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	290 #if str($assembly.detangle.off_diagonal_read_count_max):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	291 --Assembly.detangle.offDiagonalReadCountMax '${assembly.detangle.off_diagonal_read_count_max}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	292 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	293 #if str($assembly.detangle.off_diagonal_ratio):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	294 --Assembly.detangle.offDiagonalRatio '${assembly.detangle.off_diagonal_ratio}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	295 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	296
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	297 ###################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	298 ### Assembly.iterative Options: ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	299 ###################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	300
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	301 #if $assembly.iterative.iterative:
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	302 $assembly.iterative.iterative
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	303 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	304 #if str($assembly.iterative.iteration_count):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	305 --Assembly.iterative.iterationCount '${assembly.iterative.iteration_count}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	306 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	307 #if str($assembly.iterative.pseudo_path_align_match_score):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	308 --Assembly.iterative.pseudoPathAlignMatchScore '${assembly.iterative.pseudo_path_align_match_score}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	309 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	310 #if str($assembly.iterative.pseudo_path_align_mismatch_score):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	311 --Assembly.iterative.pseudoPathAlignMismatchScore '${assembly.iterative.pseudo_path_align_mismatch_score}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	312 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	313 #if str($assembly.iterative.pseudo_path_align_gap_score):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	314 --Assembly.iterative.pseudoPathAlignGapScore '${assembly.iterative.pseudo_path_align_gap_score}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	315 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	316 #if str($assembly.iterative.mismatch_square_factor):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	317 --Assembly.iterative.mismatchSquareFactor '${assembly.iterative.mismatch_square_factor}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	318 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	319 #if str($assembly.iterative.min_score):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	320 --Assembly.iterative.minScore '${assembly.iterative.min_score}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	321 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	322 #if str($assembly.iterative.max_alignment_count):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	323 --Assembly.iterative.maxAlignmentCount '${assembly.iterative.max_alignment_count}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	324 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	325 #if str($assembly.iterative.bridge_removal_iteration_count):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	326 --Assembly.iterative.bridgeRemovalIterationCount '${assembly.iterative.bridge_removal_iteration_count}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	327 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	328 #if str($assembly.iterative.bridge_removal_max_distance):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	329 --Assembly.iterative.bridgeRemovalMaxDistance '${assembly.iterative.bridge_removal_max_distance}'
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	330 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	331
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	332 ################################################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	333 ### List input files with their corresponding file extension ###
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	334 ################################################################
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	335
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	336 --input
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	337 #for $counter, $input in enumerate($in_data):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	338 #if $input.is_of_type("fasta","fasta.gz"):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	339 #set $ext = "fasta"
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	340 #elif $input.is_of_type("fastq","fastqsanger","fastq.gz","fastqsanger.gz"):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	341 #set $ext = "fastq"
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	342 #end if
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	343 ./input_${counter}.${ext}
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	344 #end for
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	345 \| tee '$out_log' 1>&2
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	346 ]]></command>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	347 <inputs>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	348 <expand macro="input_reads"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	349 <conditional name="use_config">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	350 <param name="use_config_select" type="select" label="Config file options" help="If you use a config file and specify any conflicting values in the other options, the values specified in the other options will take precedence.">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	351 <option value="yes" selected="true">Select a packaged config file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	352 <option value="file">Provide my own config file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	353 <option value="no">Do not provide config file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	354 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	355 <when value="yes">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	356 <expand macro="config_selection"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	357 </when>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	358 <when value="file">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	359 <param name="in_config" type="data" format="txt" label="Config file"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	360 </when>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	361 <when value="no">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	362 </when>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	363 </conditional>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	364 <section name="outputs" expanded="true" title="Output options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	365 <param name="report_graphical_fragment_assembly" type="boolean" label="Report graphical fragment assembly?" checked="true" help="The graphical fragment assembly file describes the assembly and how contigs in the assembly relate to one another in the assembly graph"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	366 <param name="report_config" type="boolean" label="Report configuration file" checked="true" help="The configuration file contains all of the parameters used by shasta based on the options selected."/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	367 <param name="report_log" type="boolean" label="Report log file?" checked="true" help="Log file contains basic information about the run"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	368 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	369 <section name="reads" expanded="true" title="Reads options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	370 <param argument="--Reads.minReadLength" name="min_read_length" optional="true" type="integer" label="MinReadLength" help="Read length cutoff. Shorter reads are discarded" min="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	371 <param argument="--Reads.desiredCoverage" name="desired_coverage" optional="true" type="text" label="Desired coverage" help="Reduce coverage to desired value. If not zero, specifies desired coverage (number of bases). The read length cutoff specified via --Reads.minReadLength is increased to reduce coverage to the specified value. Power of 10 multipliers can be used, for example 120Gb to request 120 Gb of coverage">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	372 <validator type="regex" message="Desired coverage must be an integer, optionally followed by the a unit prefix (KMG)">^([0-9]*)?([KMG]bp?)?$</validator>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	373 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	374 <!-- Decided not to expose the below parameter, can revisit this later if we change our minds on this-->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	375 <!-- <param name="no_cache" optional="true" type="boolean" /> -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	376
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	377 <section name="palindromic_reads" expanded="true" title="Palindromic reads options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	378 <param argument="--Reads.palindromicReads.skipFlagging" name="skip_flagging" optional="true" type="select" label="Skip flagging palindromic reads?" help="Oxford Nanopore reads should be flagged for better results.">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	379 <option value="">Do not skip flagging palindromic reads unless otherwise specified in provided config file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	380 <option value="--Reads.palindromicReads.skipFlagging">Skip flagging of palindromic reads</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	381 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	382 <param argument="--Reads.palindromicReads.maxSkip" name="max_skip" optional="true" type="integer" label="maxSkip for palindromic read detection" min="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	383 <param argument="--Reads.palindromicReads.maxDrift" name="max_drift" optional="true" type="integer" label="maxDrift for palindromic read detection" min="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	384 <param argument="--Reads.palindromicReads.maxMarkerFrequency" name="max_marker_frequency" optional="true" type="integer" label="maxMarkerFrequency for palindromic read detection" min="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	385 <param argument="--Reads.palindromicReads.alignedFractionThreshold" name="aligned_fraction_threshold" optional="true" type="float" label="alignedFractionThreshold for palindromic read detection"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	386 <param argument="--Reads.palindromicReads.nearDiagonalFractionThreshold" name="near_diagonal_fraction_threshold" optional="true" type="float" label="nearDiagonalFractionThreshold for palindromic read detection"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	387 <param argument="--Reads.palindromicReads.deltaThreshold" name="delta_threshold" optional="true" type="integer" label="deltaThreshold for palindromic read detection"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	388 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	389
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	390 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	391 <section name="kmers" expanded="true" title="Kmers options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	392 <param argument="--Kmers.generationMethod" name="generation_method" optional="true" type="select" label="Method to generate marker k-mers">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	393 <option value="0">Random</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	394 <option value="1">Random, excluding globally overenriched</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	395 <option value="2">Random, excluding overenriched even in a single read</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	396 <option value="3">Read from file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	397 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	398 <param argument="--Kmers.k" name="k" optional="true" type="integer" label="Length of marker k-mers (In run length space)"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	399 <param argument="--Kmers.probability" name="probability" optional="true" type="float" label="Fraction k-mers used as a marker"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	400 <param argument="--Kmers.enrichmentThreshold" name="enrichment_threshold" optional="true" type="float" label="Enrichment threshold for defining cutoff in Kmers.generationMethod that select based on enrichment"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	401 <param argument="--Kmers.file" name="file" optional="true" type="data" format="txt" label="The file containing the k-mers to be used as markers, one kmer per line. Only used if the Kmers.generationMethod is 'Read from file'"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	402 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	403 <section name="minhash" expanded="true" title="MinHash options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	404 <param argument="--MinHash.version" name="version" optional="true" type="select" label="Version of the LowHash algorithm to use">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	405 <option value="0">Default</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	406 <option value="1">Experimental</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	407 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	408 <param argument="--MinHash.m" name="m" optional="true" type="integer" label="The number of consecutive markers that define a MinHash/LowHash feature"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	409 <param argument="--MinHash.hashFraction" name="hash_fraction" optional="true" type="float" label="Defines how low a hash has to be to be used with the LowHash algorithm"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	410 <param argument="--MinHash.minHashIterationCount" name="min_hash_iteration_count" optional="true" type="integer" label="The number of MinHash/LowHash iterations" help="Set to 0 to let --MinHash.alignmentCandidatesPerRead control the number of iterations"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	411 <param argument="--MinHash.alignmentCandidatesPerRead" name="alignment_candidates_per_read" optional="true" type="float" label="If --MinHash.minHashIterationCount is 0, Min hash iteration is stopped when the average number of alignment candidates that each read is involved in reaches this value." help="If --MinHash.minHashIterationCount is not 0, this is not used"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	412 <param argument="--MinHash.minBucketSize" name="min_bucket_size" optional="true" type="integer" label="The minimum bucket size to be used by the LowHash algorithm"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	413 <param argument="--MinHash.maxBucketSize" name="max_bucket_size" optional="true" type="integer" label="The maximum bucket size to be used by the LowHash algorithm"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	414 <param argument="--MinHash.minFrequency" name="min_frequency" optional="true" type="integer" label="The minimum number of times a pair of reads must be found by the MinHash/LowHash algorithm in order to be considered a candidate alignment"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	415 <param argument="--MinHash.allPairs" name="all_pairs" optional="true" type="select" label="Skip the MinHash algorithm and mark all pairs of reads as alignment candidates with both orientation?" help="This should only be used for experimentation on very small runs because it is very time consuming">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	416 <option value="">Do not skip the MinHash algorithm unless otherwise specified in provided config file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	417 <option value="--MinHash.allPairs">Skip the MinHash algorithm and mark all pairs of reads as alignment candidates with both orientation</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	418 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	419 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	420 <section name="align" expanded="true" title="Align options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	421 <param argument="--Align.alignMethod" name="align_method" optional="true" type="select" label="Alignment method" help="The alignment method to be used to create the read graph and the marker graph.">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	422 <option value="0">Old Shasta method</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	423 <option value="1">SeqAn (slow)</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	424 <option value="3">Banded SeqAn</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	425 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	426 <param argument="--Align.maxSkip" name="max_skip" optional="true" type="integer" label="The maximum number of markers that an alignment is allowed to skip"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	427 <param argument="--Align.maxDrift" name="max_drift" optional="true" type="integer" label="The maximum amount of marker drift that an alignment is allowed to tolerate"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	428 <param argument="--Align.maxTrim" name="max_trim" optional="true" type="integer" label="The maximum number of unaligned markers tolerated at the beginning and end of an alignment"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	429 <param argument="--Align.maxMarkerFrequency" name="max_marker_frequency" optional="true" type="integer" label="Marker frequency threshold" help="Markers more frequent than this value in either of two oriented reads being aligned are discarded and not used to compute the alignment."/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	430 <param argument="--Align.minAlignedMarkerCount" name="min_aligned_marker_count" optional="true" type="integer" label="The minimum number of aligned markers for an alignment to be used"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	431 <param argument="--Align.minAlignedFraction" name="min_aligned_fraction" optional="true" type="float" label="The minimum fraction of aligned markers for an alignment to be used"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	432 <param argument="--Align.matchScore" name="match_score" optional="true" type="integer" label="Match score for marker alignments" help="Only used for 'SeqAn' and 'Banded SeqAn' alignment methods"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	433 <param argument="--Align.mismatchScore" name="mismatch_score" optional="true" type="integer" label="Mismatch score for marker alignments" help="Only used for 'SeqAn' and 'Banded SeqAn' alignment methods"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	434 <param argument="--Align.gapScore" name="gap_score" optional="true" type="integer" label="Gap score for marker alignments" help="Only used for 'SeqAn' and 'Banded SeqAn' alignment methods"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	435 <param argument="--Align.downsamplingFactor" name="downsampling_factor" optional="true" type="float" label="Downsampling factor" help="Only used for 'Banded SeqAn' alignment method"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	436 <param argument="--Align.bandExtend" name="band_extend" optional="true" type="integer" label="Amount to extend the downsampled band" help="Only used for 'Banded SeqAn' alignment method"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	437 <param argument="--Align.maxBand" name="max_band" optional="true" type="integer" label="Maximum alignment band" help="Only used for 'Banded SeqAn' alignment method"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	438
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	439 <param argument="--Align.suppressContainments" name="suppress_containments" optional="true" type="select" label="Suppress containment alignments?" help="Containment alignments are alignments in which one read is entirely contained in another read, except possibly for up to maxTrim markers at the beggining and end">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	440 <option value="">Do not suppress containment alignments, unless otherwise specified in provided config file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	441 <option value="--Align.suppressContainments">Suppress containment alignments</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	442 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	443
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	444 <section name="same_channel_read_alignment" expanded="true" title="Same channel read alignment options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	445 <param argument="--Align.sameChannelReadAlignment.suppressDeltaThreshold" name="suppress_delta_threshold" optional="true" type="integer" label="Supress delta threshold" help="If not zero, alignments between reads from the same nanopore channel and close in time are suppressed. The 'read' meta data fields from the FASTA or FASTQ header are checked. If their difference, in absolute value, is less than the value of this option, the alignment is suppressed. This can help avoid assembly artifact. This check is only done if the two reads have identical meta data fields 'runid', 'sampleid', and 'ch'. If any of these metadata fields are missing this check is suppressed and this option has no effect."/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	446 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	447 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	448 <section name="read_graph" expanded="true" title="ReadGraph options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	449 <param argument="--ReadGraph.creationMethod" name="creation_method" optional="true" type="select" label="The method used to create the read graph">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	450 <option value="0">Default</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	451 <option value="1">Experimental version 1</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	452 <option value="2">Experimental version 2</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	453 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	454 <param argument="--ReadGraph.maxAlignmentCount" name="max_alignment_count" optional="true" type="integer" label="The maximum number of alignments to be kept for each read"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	455 <!--The below parameter is currently ignored per the command line help, don't bother exposing it-->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	456 <!-- <param argument="ReadGraph.minComponentSize" name="min_component_size" optional="true" type="integer" label="The minimum size (number of oriented reads) of a connected component of the read graph to be kept. This is currently ignored."/> -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	457 <param argument="--ReadGraph.maxChimericReadDistance" name="max_chimeric_read_distance" optional="true" type="integer" label="Max chimeric read distance" help="Used for chimeric read detection"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	458 <param argument="--ReadGraph.crossStrandMaxDistance" name="cross_strand_max_distance" optional="true" type="integer" label="Maximum distance (edges) for flagCrossStrandReadGraphEdges" help="Set this to zero to entirely suppress flagCrossStrandReadGraphEdges"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	459 <param argument="--ReadGraph.containedNeighborCount" name="contained_neighbor_count" optional="true" type="integer" label="Maximum number of alignments to be kept for each contained read" help="Only used when creation method for the read graph is Experimental version 1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	460 <param argument="--ReadGraph.uncontainedNeighborCountPerDirection" name="uncontained_neighbor_count_per_direction" optional="true" type="integer" label="Maximum number of alignments to be kept in each direction (forward, backward) for each uncontained read" help="Only used when creation method for the read graph is Experimental version 1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	461 <!--The below parameter is currently experimental and advised not to be used, dont bother exposing it-->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	462 <!-- <param argument="ReadGraph.removeConflicts" name="remove_conflicts" optional="true" type="select"/> -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	463 <param argument="--ReadGraph.markerCountPercentile" name="marker_count_percentile" optional="true" type="float" label="Percentile for marker Count" help="Only used when creation method for the read graph is Experimental version 2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	464 <param argument="--ReadGraph.alignedFractionPercentile" name="aligned_fraction_percentile" optional="true" type="float" label="Percentile for alignedFraction" help="Only used when creation method for the read graph is Experimental version 2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	465 <param argument="--ReadGraph.maxSkipPercentile" name="max_skip_percentile" optional="true" type="float" label="Percentile for maxSkip" help="Only used when creation method for the read graph is Experimental version 2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	466 <param argument="--ReadGraph.maxDriftPercentile" name="max_drift_percentile" optional="true" type="float" label="Percentile for maxDrift" help="Only used when creation method for the read graph is Experimental version 2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	467 <param argument="--ReadGraph.maxTrimPercentile" name="max_trim_percentile" optional="true" type="float" label="Percentile for maxTrim" help="Only used when creation method for the read graph is Experimental version 2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	468 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	469 <section name="marker_graph" expanded="true" title="MarkerGraph options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	470 <param argument="--MarkerGraph.minCoverage" name="min_coverage" optional="true" type="integer" label="Minimum coverage (number of supporting oriented reads) for a marker graph vertex to be created." help="Specifying 0 causes a suitable value of this parameter to be selected automatically"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	471 <param argument="--MarkerGraph.maxCoverage" name="max_coverage" optional="true" type="integer" label="Maximum coverage (number of supporting oriented reads) for a marker graph vertex"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	472 <param argument="--MarkerGraph.minCoveragePerStrand" name="min_coverage_per_strand" optional="true" type="integer" label="Minimum coverage (number of supporting oriented reads) for each strand for a marker graph vertex"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	473 <param argument="--MarkerGraph.lowCoverageThreshold" name="low_coverage_threshold" optional="true" type="integer" label="Low coverage threshold" help="Used during approximate transitive reduction. Marker graph edges with coverage lower than this value are always marked as removed regardless of reachability"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	474 <param argument="--MarkerGraph.highCoverageThreshold" name="high_coverage_threshold" optional="true" type="integer" label="High coverage threshold" help="Used during approximate transitive reduction. Marker graph edges with coverage higher than this value are never marked as removed regardless of reachability"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	475 <param argument="--MarkerGraph.maxDistance" name="max_distance" optional="true" type="integer" label="Max distance" help="Used during approximate transitive reduction"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	476 <param argument="--MarkerGraph.edgeMarkerSkipThreshold" name="edge_marker_skip_threshold" optional="true" type="integer" label="Edge marker skip threshold" help="Used during approximate transitive reduction"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	477 <param argument="--MarkerGraph.pruneIterationCount" name="prune_iteration_count" optional="true" type="integer" label="Number of prune iterations"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	478 <param argument="--MarkerGraph.simplifyMaxLength" name="simplifiy_max_length" optional="true" type="text" label="Simplify max length" help="Maximum lengths (in markers) used at each iteration of simplifyMarkerGraph. Ex.) 10,100,1000">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	479 <validator type="regex" message="Must be a comma separated list of integers">^[0-9]+(,[0-9]+)*$</validator>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	480 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	481 <param argument="--MarkerGraph.crossEdgeCoverageThreshold" name="cross_edge_coverage_threshold" optional="true" type="float" label="Cross edge coverage threshold" help="Experimental. If this is not zero, assembly graph cross-edges with average edge coverage less than this value are removed, together with the corresponding marker graph edges. A cross edge is defined as an edge v0=>v1 with out-degree(v0)>1, in-degree(v1)>1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	482 <param argument="--MarkerGraph.refineThreshold" name="refine_threshold" optional="true" type="integer" label="Refine threshold" help="Length threshold, in markers, for the marker graph refinement step, or 0 to turn off refinement step"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	483 <param argument="--MarkerGraph.reverseTransitiveReduction" name="reverse_transitive_reduction" optional="true" type="select" label="Perform reverse transitive reduction?">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	484 <option value="">Don't perform appproximate reverse transitive reduction of the marker graph unless otherwise specified in provided config file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	485 <option value="--MarkerGraph.reverseTransitiveReduction">Perform appproximate reverse transitive reduction of the marker graph</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	486 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	487
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	488 <section name="peak_finder" expanded="true" title="Peak Finder options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	489 <param argument="--MarkerGraph.peakFinder.minAreaFraction" name="min_area_fraction" optional="true" type="float" label="Peak finding min area fraction" help="Used in the automatic selection of --MarkerGraph.minCoverage when --MarkerGraph.minCoverage is set to 0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	490 <param argument="--MarkerGraph.peakFinder.areaStartIndex" name="area_start_index" optional="true" type="integer" label="Peak finding area start index" help="Used in the automatic selection of --MarkerGraph.minCoverage when --MarkerGraph.minCoverage is set to 0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	491 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	492
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	493 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	494 <section name="assembly" expanded="true" title="Assembly options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	495 <param argument="--Assembly.crossEdgeCoverageThreshold" name="cross_edge_coverage_threshold" optional="true" type="integer" label="Maximum average edge coverage for a cross edge of the assembly graph to be removed"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	496 <param argument="--Assembly.markerGraphEdgeLengthThresholdForConsensus" name="marker_graph_edge_length_threshold_for_consensus" optional="true" type="integer" label="Marker graph edge length threshold for consensus" help="Controls assembly of long marker graph edges"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	497 <conditional name="consensus_caller">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	498 <param argument="--Assembly.consensusCaller" name="consensus_caller_select" type="select" label="Consensus caller for repeat counts">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	499 <option value="default" selected="true">Default or caller in provided config file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	500 <option value="Modal"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	501 <option value="Median"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	502 <option value="Bayesian:guppy-2.3.1-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	503 <option value="Bayesian:guppy-2.3.5-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	504 <option value="Bayesian:guppy-3.0.5-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	505 <option value="Bayesian:guppy-3.4.4-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	506 <option value="Bayesian:guppy-3.6.0-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	507 <option value="Bayesian:r10-guppy-3.4.8-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	508 <option value="custom">Custom config file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	509 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	510 <when value="default"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	511 <when value="Modal"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	512 <when value="Median"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	513 <when value="Bayesian:guppy-2.3.1-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	514 <when value="Bayesian:guppy-2.3.5-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	515 <when value="Bayesian:guppy-3.0.5-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	516 <when value="Bayesian:guppy-3.4.4-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	517 <when value="Bayesian:guppy-3.6.0-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	518 <when value="Bayesian:r10-guppy-3.4.8-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	519 <when value="custom">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	520 <param name="consensus_caller_conf_file" type="data" format="csv" label="Custom config file for consensus caller"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	521 </when>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	522 </conditional>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	523 <!--TODO - param below outputs coverage data in a binary format, but that format is not specified anywhere in the Shasta documentation so I don't know what format I'd assign it in Galaxy. For now, don't expose this parameter and look into changing this later-->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	524 <!-- <param argument="Assembly.storeCoverageData" name="store_coverage_data" type="boolean" label="Store coverage data in binary format?" checked="false" truevalue="Assembly.storeCoverageData" falsevalue=""/> -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	525 <!-- The below option only can be meaningfully set with memoryMode set to filesystem, which requires root access. Therefore, removing this param-->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	526 <!-- <param argument="Assembly.storeCoverageDataCsvLengthThreshold" name="store_coverage_data_csv_length_threshold" optional="true" type="integer" label="CSV coverage data length threshold" help="Used to specify the minimum length of an assembled segment for which coverage data in csv format shold be stored. If 0, no coverage data in csv format is stored"/> -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	527 <param argument="--Assembly.writeReadsByAssembledSegment" name="write_reads_by_assembled_segment" optional="true" type="boolean" label="Write the reads that contributed to assembling each segment?" checked="false" truevalue="--Assembly.writeReadsByAssembledSegment" falsevalue=""/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	528
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	529 <section name="detangle" expanded="true" title="Detangle options">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	530 <param argument="--Assembly.detangleMethod" name="detangle_method" optional="true" type="select" label="Method used to detangle the assembly graph" help="Controlled by Assembly.detangle.* options (experimental)">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	531 <option value="0">No detangling</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	532 <option value="1">Strict detangling</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	533 <option value="2">Less strict detangling</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	534 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	535 <param argument="--Assembly.detangle.diagonalReadCountMin" name="diagonal_read_count_min" optional="true" type="integer" label="Minimum number of reads on detangle matrix diagonal elements required for detangling"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	536 <param argument="--Assembly.detangle.offDiagonalReadCountMax" name="off_diagonal_read_count_max" optional="true" type="integer" label="Maximum number of reads on detangle matrix off-diagonal elements allowed for detangling"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	537 <param argument="--Assembly.detangle.offDiagonalRatio" name="off_diagonal_ratio" optional="true" type="float" label="Maximum ratio of total off-diagonal elements over diagonal element allowed for detangling"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	538 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	539
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	540 <section name="iterative" expanded="false" title="Iterative assembly options (experimental)">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	541 <param argument="--Assembly.iterative" name="iterative" optional="true" type="select" label="Request iterative assembly? (experimental)">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	542 <option value="">Do not perform iterative assembly unless otherwise specified in provided config file</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	543 <option value="--Assembly.iterative">Perform iterative assembly</option>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	544 </param>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	545 <param argument="--Assembly.iterative.iterationCount" name="iteration_count" optional="true" type="integer" label="Number of iterations for iterative assembly (experimental)"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	546 <param argument="--Assembly.iterative.pseudoPathAlignMatchScore" name="pseudo_path_align_match_score" optional="true" type="integer" label="Psuedopath alignment match score for iterative assembly (experimental)"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	547 <param argument="--Assembly.iterative.pseudoPathAlignMismatchScore" name="pseudo_path_align_mismatch_score" optional="true" type="integer" label="Psuedopath alignment mismatch score for iterative assembly (experimental)"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	548 <param argument="--Assembly.iterative.pseudoPathAlignGapScore" name="pseudo_path_align_gap_score" optional="true" type="integer" label="Psuedopath alignment gap score for iterative assembly (experimental)"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	549 <param argument="--Assembly.iterative.mismatchSquareFactor" name="mismatch_square_factor" optional="true" type="float" label="Mismatch square factor for iterative assembly (experimental)"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	550 <param argument="--Assembly.iterative.minScore" name="min_score" optional="true" type="float" label="Minimum psuedo-alignment score for iterative assembly (experimental)"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	551 <param argument="--Assembly.iterative.maxAlignmentCount" name="max_alignment_count" optional="true" type="integer" label="Maximum number of read graph neighbors for iterative assembly (experimental)"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	552 <param argument="--Assembly.iterative.bridgeRemovalIterationCount" name="bridge_removal_iteration_count" optional="true" type="integer" label="Number of read graph bridge removal iterations for iterative assembly (experimental)"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	553 <param argument="--Assembly.iterative.bridgeRemovalMaxDistance" name="bridge_removal_max_distance" optional="true" type="integer" label="Maximum distance for reag graph bridge removal for iterative assembly (experimental)"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	554 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	555
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	556 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	557 </inputs>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	558 <outputs>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	559 <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="shasta_out/Assembly.gfa">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	560 <filter>outputs["report_graphical_fragment_assembly"]</filter>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	561 </data>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	562 <data name="out_conf" format="txt" label="${tool.name} on ${on_string} (Config file)" from_work_dir="shasta_out/shasta.conf">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	563 <filter>outputs["report_config"]</filter>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	564 </data>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	565 <data name="out_log" format="txt" label="${tool.name} on ${on_string} (Log file)">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	566 <filter>outputs["report_log"]</filter>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	567 </data>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	568 <!-- The below output collection only can be meaningfully produced with memoryMode set to filesystem, which requires root access. Therefore, removing this output-->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	569 <!-- <collection name="out_coverage_csvs" type="list" label="${tool.name} on ${on_string} (Coverage CSVs)">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	570 <discover_datasets directory="shasta_out/Coverage" pattern="__name_and_ext__" format="csv" visible="false"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	571 <filter>not ( assembly["store_coverage_data_csv_length_threshold"] == 0 or assembly["store_coverage_data_csv_length_threshold"] == "" )</filter>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	572 </collection> -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	573 <data name="out_reads_csv" format="csv" label="${tool.name} on ${on_string} (Reads by assembled segment)" from_work_dir="shasta_out/ReadsBySegment.csv">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	574 <filter>assembly["write_reads_by_assembled_segment"]</filter>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	575 </data>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	576 <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)" from_work_dir="shasta_out/Assembly.fasta"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	577 </outputs>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	578 <tests>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	579 <!--
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	580 Test full run, all outputs
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	581 -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	582 <test expect_num_outputs="5">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	583 <param name="in_data" ftype="fasta.gz" value="nanopore.fasta.gz"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	584 <conditional name="use_config">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	585 <param name="use_config_select" value="yes"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	586 <param name="config_select" value="Nanopore-Dec2019.conf"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	587 </conditional>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	588 <section name="assembly">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	589 <!-- The below option only can be meaningfully set with memoryMode set to filesystem, which requires root access. Therefore, removing this param-->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	590 <!-- <param name="store_coverage_data_csv_length_threshold" value="1000"/> -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	591 <param name="write_reads_by_assembled_segment" value="true"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	592 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	593 <output name="out_fasta" file="out_fasta.fasta">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	594 <assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	595 <has_n_lines n="2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	596 </assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	597 </output>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	598 <output name="out_gfa" file="out_gfa.gfa1">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	599 <assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	600 <has_n_lines n="2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	601 </assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	602 </output>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	603 <output name="out_log"> <!--Log file has timestamps and mac specific outputs. Can't compare vs known file.-->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	604 <assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	605 <has_line line="Input files: ./input_0.fasta "/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	606 <has_line line="assemblyDirectory = shasta_out"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	607 </assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	608 </output>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	609 <output name="out_conf" file="out_config.txt">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	610 <assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	611 <has_n_lines n="100"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	612 </assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	613 </output>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	614 <output name="out_reads_csv" file="out_reads.csv">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	615 <assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	616 <has_n_lines n="59"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	617 </assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	618 </output>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	619 <!-- The below output collection only can be meaningfully produced with memoryMode set to filesystem, which requires root access. Therefore, removing this output-->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	620 <!-- <output_collection name="out_coverage_csvs" type="list">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	621 <element name="0" ftype="csv">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	622 <assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	623 <has_n_lines n="11714"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	624 </assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	625 </element>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	626 </output_collection> -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	627 </test>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	628 <!--
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	629 Test ability to disable outputs
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	630 -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	631 <test expect_num_outputs="1">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	632 <param name="in_data" ftype="fasta.gz" value="nanopore.fasta.gz"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	633 <conditional name="use_config">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	634 <param name="use_config_select" value="yes"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	635 <param name="config_select" value="Nanopore-Dec2019.conf"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	636 </conditional>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	637 <section name="outputs">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	638 <param name="report_graphical_fragment_assembly" value="false"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	639 <param name="report_config" value="false"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	640 <param name="report_log" value="false"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	641 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	642 <output name="out_fasta" file="out_fasta.fasta">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	643 <assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	644 <has_n_lines n="2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	645 </assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	646 </output>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	647 </test>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	648 <!--
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	649 Test ability to use passed config file
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	650 -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	651 <test expect_num_outputs="1">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	652 <param name="in_data" ftype="fasta.gz" value="nanopore.fasta.gz"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	653 <conditional name="use_config">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	654 <param name="use_config_select" value="file"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	655 <param name="in_config" ftype="txt" value="out_config2.txt"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	656 </conditional>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	657 <section name="outputs">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	658 <param name="report_graphical_fragment_assembly" value="false"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	659 <param name="report_config" value="false"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	660 <param name="report_log" value="false"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	661 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	662 <output name="out_fasta" file="out_fasta.fasta">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	663 <assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	664 <has_n_lines n="2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	665 </assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	666 </output>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	667 </test>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	668 <!--
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	669 Test ability to not provide config and pass equivalent options through the parameters.
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	670 -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	671 <test expect_num_outputs="2">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	672 <param name="in_data" ftype="fasta.gz" value="nanopore.fasta.gz"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	673 <conditional name="use_config">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	674 <param name="use_config_select" value="no"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	675 </conditional>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	676 <section name="outputs">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	677 <param name="report_graphical_fragment_assembly" value="false"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	678 <param name="report_config" value="true"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	679 <param name="report_log" value="false"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	680 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	681 <section name="reads">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	682 <param name="min_read_length" value="10000"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	683 <param name="desired_coverage" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	684 <section name="palindromic_reads">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	685 <param name="skip_flagging" value=""/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	686 <param name="max_skip" value="100"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	687 <param name="max_drift" value="100"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	688 <param name="max_marker_frequency" value="10"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	689 <param name="aligned_fraction_threshold" value="0.1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	690 <param name="near_diagonal_fraction_threshold" value="0.1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	691 <param name="delta_threshold" value="100"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	692 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	693 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	694 <section name="kmers">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	695 <param name="generation_method" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	696 <param name="k" value="10"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	697 <param name="probability" value="0.1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	698 <param name="enrichmentThreshold" value="100"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	699 <!-- <param name="file" value=""/> -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	700 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	701 <section name="minhash">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	702 <param name="version" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	703 <param name="m" value="4"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	704 <param name="hash_fraction" value="0.01"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	705 <param name="min_hash_iteration_count" value="10"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	706 <param name="alignment_candidates_per_read" value="20"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	707 <param name="min_bucket_size" value="5"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	708 <param name="max_bucket_size" value="30"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	709 <param name="min_frequency" value="5"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	710 <param name="all_pairs" value=""/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	711 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	712 <section name="align">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	713 <param name="align_method" value="3"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	714 <param name="max_skip" value="30"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	715 <param name="max_drift" value="30"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	716 <param name="max_trim" value="30"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	717 <param name="max_marker_frequency" value="10"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	718 <param name="min_aligned_marker_count" value="100"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	719 <param name="min_aligned_fraction" value="0.4"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	720 <param name="match_score" value="6"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	721 <param name="mismatch_score" value="-1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	722 <param name="gap_score" value="-1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	723 <param name="downsampling_factor" value="0.1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	724 <param name="band_extend" value="10"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	725 <param name="max_band" value="1000"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	726 <param name="suppress_containments" value=""/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	727 <section name="same_channel_read_alignment">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	728 <param name="suppress_delta_threshold" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	729 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	730 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	731 <section name="read_graph">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	732 <param name="creation_method" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	733 <param name="max_alignment_count" value="6"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	734 <param name="max_chimeric_read_distance" value="2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	735 <param name="cross_strand_max_distance" value="6"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	736 <param name="contained_neighbor_count" value="6"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	737 <param name="uncontained_neighbor_count_per_direction" value="3"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	738 <param name="marker_count_percentile" value="0.015"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	739 <param name="aligned_fraction_percentile" value="0.12"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	740 <param name="max_skip_percentile" value="0.12"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	741 <param name="max_drift_percentile" value="0.12"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	742 <param name="max_trim_percentile" value="0.015"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	743 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	744 <section name="marker_graph">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	745 <param name="min_coverage" value="10"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	746 <param name="max_coverage" value="100"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	747 <param name="min_coverage_per_strand" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	748 <param name="low_coverage_threshold" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	749 <param name="high_coverage_threshold" value="256"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	750 <param name="max_distance" value="30"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	751 <param name="edge_marker_skip_threshold" value="100"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	752 <param name="prune_iteration_count" value="6"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	753 <param name="simplifiy_max_length" value="10,100,1000"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	754 <param name="cross_edge_coverage_threshold" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	755 <param name="refine_threshold" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	756 <param name="reverse_transitive_reduction" value=""/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	757 <section name="peak_finder">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	758 <param name="min_area_fraction" value="0.08"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	759 <param name="area_start_index" value="2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	760 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	761 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	762 <section name="assembly">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	763 <param name="cross_edge_coverage_threshold" value="3"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	764 <param name="marker_graph_edge_length_threshold_for_consensus" value="1000"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	765 <conditional name="consensus_caller">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	766 <param name="consensus_caller_select" value="Bayesian:guppy-3.0.5-a"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	767 </conditional>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	768 <!-- The below option only can be meaningfully set with memoryMode set to filesystem, which requires root access. Therefore, removing this param-->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	769 <!-- <param name="store_coverage_data_csv_length_threshold" value="0"/> -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	770 <param name="write_reads_by_assembled_segment" value="false"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	771 <section name="detangle">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	772 <param name="detangle_method" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	773 <param name="diagonal_read_count_min" value="1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	774 <param name="off_diagonal_read_count_max" value="2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	775 <param name="off_diagonal_ratio" value="0.3"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	776 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	777 <section name="iterative">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	778 <param name="iterative" value=""/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	779 <param name="iteration_count" value="3"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	780 <param name="pseudo_path_align_match_score" value="1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	781 <param name="pseudo_path_align_mismatch_score" value="-1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	782 <param name="pseudo_path_align_gap_score" value="-1"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	783 <param name="mismatch_square_factor" value="3"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	784 <param name="min_score" value="0"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	785 <param name="max_alignment_count" value="6"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	786 <param name="bridge_removal_iteration_count" value="3"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	787 <param name="bridge_removal_max_distance" value="2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	788 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	789 </section>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	790 <output name="out_fasta" file="out_fasta.fasta">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	791 <assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	792 <has_n_lines n="2"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	793 </assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	794 </output>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	795 <output name="out_conf" file="out_config2.txt">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	796 <assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	797 <has_n_lines n="100"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	798 </assert_contents>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	799 </output>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	800 </test>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	801 </tests>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	802 <help><![CDATA[
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	803 .. class:: infomark
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	804
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	805 What it does
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	806
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	807 @WID@
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	808
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	809 Input
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	810
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	811 - fasta / fastq data
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	812
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	813 - config file (optional)
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	814
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	815
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	816 Example config files can be found `here <https://github.com/chanzuckerberg/shasta/tree/master/conf>`_ (these files correspond to the packaged config files available for this tool).
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	817
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	818 Output
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	819
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	820 - Assembled genome (FASTA)
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	821 - Graphical fragment assembly (optional) (.gfa1)
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	822 - Log file (optional) (.txt)
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	823 - Config file (optional) (.txt)
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	824 - Read CSV detailing which reads align to which assembly fragments (optional) (.csv)
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	825 - Coverage CSV List (optional) (list:.csv)
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	826
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	827 References
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	828
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	829 @REFERENCES@
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	830 ]]></help>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	831 <expand macro="citations"/>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74" iuc parents: diff changeset	832 </tool>

Mercurial > repos > iuc > shasta

annotate shasta.xml @ 0:60573349e9ae draft default tip