paralyzer: paralyzer.xml annotate

annotate paralyzer.xml @ 0:d4d72f60e8d6 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"

author	rnateam
date	Wed, 23 Oct 2019 19:07:59 -0400
parents
children

rev	line source
0 d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	1 <tool id="paralyzer" name="PARalyzer" version="1.5">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	2 <description>A method to map interaction sites between RNA-binding proteins
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	3 and their targets</description>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	4 <requirements>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	5 <!-- conda dependency -->
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	6 <requirement type="package" version="1.5">paralyzer</requirement>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	7 <requirement type="package" version="324">ucsc-fatotwobit</requirement>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	8 </requirements>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	9 <command detect_errors="aggressive"><![CDATA[
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	10
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	11 #if $refGenomeSource.genomeSource == "history":
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	12 faToTwoBit '$refGenomeSource.ownFile' ownFile.2bit
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	13 &&
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	14 #end if
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	15
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	16 ## execute paralyzer
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	17 ## note the 2nd argument is the memory parameter
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	18 ## the parameter can be override in job_conf.xml e.g.
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	19 ## <env id="_JAVA_OPTIONS">-Xmx12G</env>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	20 PARalyzer 2G $input_ini
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	21
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	22 ]]>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	23 </command>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	24 <configfiles>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	25 <configfile name="input_ini">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	26 ## genome source
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	27 #if $refGenomeSource.genomeSource == "history":
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	28 GENOME_2BIT_FILE=ownFile.2bit
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	29 #else
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	30 GENOME_2BIT_FILE=$refGenomeSource.builtin.fields.path
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	31 #end if
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	32
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	33 SAM_FILE=$input_sam$collapse
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	34
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	35 #if $methods.choice == "ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL":
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	36 ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL=$methods.max_num
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	37 #else:
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	38 $methods.choice
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	39 #end if
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	40
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	41 #if $conversion.selection == "custom":
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	42 CONVERSION=$conversion.character_from>$conversion.character_to
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	43 #end if
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	44
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	45 ## required parameters
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	46 #if $params.settingsType == "custom":
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	47 BANDWIDTH=$params.BANDWIDTH
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	48 MINIMUM_READ_COUNT_PER_GROUP=$params.min_read_group
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	49 MINIMUM_READ_COUNT_PER_CLUSTER=$params.min_read_cluster
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	50 MINIMUM_READ_COUNT_FOR_KDE=$params.min_read_kde
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	51 MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=$params.min_read_cluster_inc
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	52 MINIMUM_CLUSTER_SIZE=$params.min_cluster_size
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	53 MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=$params.min_conv_loc_cluster
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	54 MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=$params.min_conv_cluster
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	55 MINIMUM_READ_LENGTH=$params.min_read_len
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	56 MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=$params.max_num_conv_mis
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	57 #end if
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	58
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	59 OUTPUT_DISTRIBUTIONS_FILE=out.distribution
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	60 OUTPUT_GROUPS_FILE=out.groups
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	61 OUTPUT_CLUSTERS_FILE=out.clusters
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	62 </configfile>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	63 </configfiles>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	64 <inputs>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	65 <param name="input_sam" type="data"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	66 format="sam" label="Alignment"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	67 help="The sam file containing alignment of the read data."/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	68
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	69 <param name="collapse" type="boolean" truevalue="=COLLAPSED"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	70 falsevalue="" checked="True"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	71 label="Incorporate the read copy number"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	72 help="If reads were collapse before alignment and you want
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	73 to incorporate the read copy number, please select Yes,
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	74 otherwise select No" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	75
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	76 <!-- Genome source. -->
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	77 <conditional name="refGenomeSource">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	78 <param name="genomeSource" type="select"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	79 label="Will you select a reference genome from your
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	80 history or use a built-in genome?"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	81 help="The version of genome against which the reads were aligned.">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	82 <option value="2bit" selected="True">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	83 Use a built-in genome</option>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	84 <option value="history">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	85 Use a genome from my current history</option>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	86 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	87 <when value="2bit">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	88 <param name="builtin" type="select"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	89 label="Select a reference genome">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	90 <options from_data_table="lastz_seqs">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	91 <filter type="sort_by" column="1" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	92 <validator type="no_options"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	93 message="A built-in reference genome is not available
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	94 for the build associated with the selected input file"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	95 </options>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	96 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	97 </when>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	98 <when value="history">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	99 <param name="ownFile" type="data" format="fasta"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	100 label="Select the reference genome" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	101 </when>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	102 </conditional>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	103
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	104 <conditional name="methods">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	105 <param name="choice" type="select"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	106 label="Please select one of the approaches"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	107 help="">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	108 <option value="EXTEND_BY_READ">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	109 EXTEND_BY_READ
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	110 </option>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	111 <option value="HAFFNER_APPROACH">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	112 HAFFNER_APPROACH
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	113 </option>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	114 <option value="ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	115 ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	116 </option>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	117 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	118 <when value="EXTEND_BY_READ" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	119 <when value="HAFFNER_APPROACH" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	120 <when value="ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	121 <param name="max_num" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	122 value="0" label="The maximum number"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	123 help="
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	124 The maximum number of reads to extend beyond the positive
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	125 signal in each direction (default 0) the cluster is defined
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	126 ">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	127 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	128 message="Minimum allowed value is 0" min="0"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	129 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	130 </when>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	131 </conditional>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	132
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	133 <conditional name="conversion">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	134 <param name="selection" type="select"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	135 label="Conversion"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	136 help="Please specify characters">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	137 <option value="default">Use defaults: T to C</option>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	138 <option value="custom">Specify other characters</option>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	139 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	140 <when value="default" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	141 <when value="custom">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	142 <param name="character_from" type="text"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	143 size="1" value="T" label="Character from"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	144 help="Character representing the modified ribonucleotide
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	145 (default 'T')">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	146 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	147 <param name="character_to" type="text"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	148 size="1" value="C" label="Character to"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	149 help="Character representing what the modified ribonucleotide
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	150 is read as by rTranscriptase (default 'C')">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	151 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	152 </when>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	153 </conditional>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	154
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	155 <!-- optional parameters -->
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	156 <conditional name="params">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	157 <param name="settingsType" type="select"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	158 label="Required parameters"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	159 help="You can use the default settings or
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	160 set custom values for any of paralyzer's parameters.">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	161 <option value="default">Use defaults</option>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	162 <option value="custom">Full parameter list</option>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	163 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	164 <when value="default" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	165 <!-- Full/advanced params. -->
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	166 <when value="custom">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	167 <param name="BANDWIDTH" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	168 value="3" label="BANDWIDTH"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	169 help="Size of bandwidth for KDE calculation (default 3)">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	170 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	171 message="Minimum allowed value is 1" min="1"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	172 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	173
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	174 <param name="min_read_group" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	175 value="5" label="MINIMUM_READ_COUNT_PER_GROUP"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	176 help="Minimum number of reads required to call a group (default 5)">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	177 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	178 message="Minimum allowed value is 1" min="1"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	179 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	180
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	181 <param name="min_read_cluster" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	182 value="2" label="MINIMUM_READ_COUNT_PER_CLUSTER"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	183 help="Minimum number of reads required to call a cluster (default 2)">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	184 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	185 message="Minimum allowed value is 1" min="1"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	186 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	187
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	188 <param name="min_read_kde" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	189 value="3" label="MINIMUM_READ_COUNT_FOR_KDE"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	190 help="Minimum read depth at a location to
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	191 make a KDE estimate (default 3)">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	192 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	193 message="Minimum allowed value is 1" min="1"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	194 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	195
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	196 <param name="min_read_cluster_inc" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	197 value="1" label="MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	198 help="Minimum read depth for a location to be included
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	199 within a cluster (default 1)">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	200 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	201 message="Minimum allowed value is 1" min="1"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	202 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	203
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	204 <param name="min_cluster_size" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	205 value="11" label="MINIMUM_CLUSTER_SIZE"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	206 help="Minimum length required for a cluster
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	207 to be reported (default 11)">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	208 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	209 message="Minimum allowed value is 1" min="1"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	210 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	211
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	212 <param name="min_conv_loc_cluster" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	213 value="2" label="MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	214 help="Minimum number of separate locations to have a
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	215 reported conversion for a cluster to be
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	216 reported (default 2)">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	217 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	218 message="Minimum allowed value is 1" min="1"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	219 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	220
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	221 <param name="min_conv_cluster" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	222 value="2" label="MINIMUM_CONVERSION_COUNT_FOR_CLUSTER"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	223 help="Minimum number of conversion events within a
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	224 region to report a cluster (default 2)">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	225 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	226 message="Minimum allowed value is 1" min="1"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	227 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	228
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	229 <param name="min_read_len" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	230 value="20" label="MINIMUM_READ_LENGTH"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	231 help="Minimum length of mapped read to be included
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	232 in the analysis (default 20)">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	233 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	234 message="Minimum allowed value is 1" min="1"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	235 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	236
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	237 <param name="max_num_conv_mis" type="integer"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	238 value="1" label="MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	239 help="Maximum number of non-conversion mismatches of
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	240 a mapped read to be included in the analysis (default 1)">
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	241 <validator type="in_range"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	242 message="Minimum allowed value is 1" min="1"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	243 </param>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	244 </when> <!-- full -->
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	245 </conditional>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	246 </inputs>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	247 <outputs>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	248 <data name="distribution" format="txt"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	249 from_work_dir="out.distribution"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	250 label="${tool.name} on ${on_string}: DISTRIBUTIONS"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	251
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	252 <data name="groups" format="txt"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	253 from_work_dir="out.groups"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	254 label="${tool.name} on ${on_string}: GROUPS"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	255
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	256 <data name="clusters" format="txt"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	257 from_work_dir="out.clusters"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	258 label="${tool.name} on ${on_string}: CLUSTERS"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	259
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	260 <!--
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	261 <data name="PARalyzer_Utilized" format="sam"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	262 from_work_dir="out_PARalyzer_Utilized.sam"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	263 label="${tool.name} on ${on_string}: PARalyzer_Utilized.sam"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	264 -->
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	265 </outputs>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	266 <tests>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	267 <test>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	268 <param name="input_sam" value="input.sam" ftype="sam" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	269 <param name="genomeSource" value="history" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	270 <param name="ownFile" value="input.fa" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	271 <param name="choice" value="EXTEND_BY_READ" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	272 <param name="selection" value="custom" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	273 <param name="character_from" value="T" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	274 <param name="character_to" value="C" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	275 <param name="settingsType" value="custom" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	276 <param name="$BANDWIDTH" value="3" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	277 <param name="min_read_group" value="5" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	278 <param name="min_read_cluster" value="2" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	279 <param name="min_read_kde" value="3" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	280 <param name="min_read_cluster_inc" value="1" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	281 <param name="min_cluster_size" value="11" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	282 <param name="min_conv_loc_cluster" value="2" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	283 <param name="min_conv_cluster" value="2" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	284 <param name="min_read_len" value="20" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	285 <param name="max_num_conv_mis" value="1" />
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	286 <output name="distribution" file="out.distribution"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	287 ftype="txt"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	288 <output name="groups" file="out.groups"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	289 ftype="txt"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	290 <output name="clusters" file="out.clusters"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	291 ftype="txt"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	292 <!--
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	293 <output name="PARalyzer_Utilized" file="out_PARalyzer_Utilized.sam"
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	294 ftype="sam"/>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	295 -->
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	296 </test>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	297 </tests>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	298 <help>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	299 <![CDATA[
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	300 .. class:: infomark
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	301
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	302 What it does
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	303
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	304 `paralyzer`_ is an algorithm to generate a high resolution
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	305 map of interaction sites between RNA-binding proteins and their targets. The
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	306 algorithm utilizes the deep sequencing reads generated by `PAR-CLIP`_
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	307 (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	308 Immunoprecipitation) protocol.The use of photoactivatable nucleotides in the
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	309 PAR-CLIP protocol results in more efficient crosslinking between the
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	310 RNA-binding protein and its target relative to other CLIP methods; in addition
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	311 a nucleotide substitution occurs at the site of crosslinking, providing for
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	312 single-nucleotide resolution binding information. PARalyzer utilizes this
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	313 nucleotide substition in a kernel density estimate classifier to generate
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	314 the high resolution set of Protein-RNA interaction sites.
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	315
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	316 .. _paralyzer: https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	317 .. _PAR-CLIP: http://www.ncbi.nlm.nih.gov/pubmed/20371350
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	318
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	319 .. class:: infomark
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	320
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	321 Approaches
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	322
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	323 ``EXTEND_BY_READ``: including this line means that the cluster will be extended
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	324 beyond the signal to include a region such that it extends to
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	325 the end of any read that falls within the cluster and contained
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	326 a conversion, or until the minimum read depth
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	327 (MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION parameter) is no longer met
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	328
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	329 ``HAFNER_APPROACH``: identifies the location with the largest number of conversion
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	330 events and extends the cluster up to
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	331 ( parameter ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL)nt
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	332 in each direction from that point, or until the minimum
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	333 read depth (MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION parameter) is no longer met
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	334
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	335 ``ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL``: the maximum number of reads to
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	336 extend beyond the positive signal in each direction (default 0)
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	337 the cluster is defined as the region where the conversion KDE is above
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	338 the background KDE and then extended up to #integer#, or until the minimum
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	339 read depth (MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION parameter) is no longer met
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	340
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	341 .. class:: infomark
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	342
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	343 Outputs
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	344
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	345 DISTRIBUTIONS: contains the signal KDE, background KDE, read count & conversion for all locations within each group
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	346 * The data will be in blocks of four lines for each group
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	347 * groups on the reverse strand do not need to be reversed; the values always equal nucleotdies from GroupStart to GroupEnd, regardless of Strand
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	348 * First Column = Chromosome = chromosome on which the group resides
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	349 * Second Column = Strand = orientation in which the group resides
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	350 * Third Column = GroupStart = beginning coordinate on the chromosome of the group
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	351 * Fourth Column = GroupEnd = ending coordinate on the chromosome of the group
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	352 * Fifth Column = GroupID = unique ID for the group
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	353 * Sixth Column = Information = reports if the current line contains the Signal, Background, Conversion Percent, or ReadCount
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	354 * All nucleotides that do not have any possibility of having a conversion event are given a value of -1
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	355 * All Subsequent Columns: the values for each nucleotide from GroupStart until GroupEnd
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	356
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	357
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	358 GROUPS: a comma separated file containing the information about the resulting groups
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	359 * Chromosome = chromosome on which the group resides
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	360 * Strand = orientation in which the group resides
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	361 * GroupStart = beginning coordinate on the chromosome of the group
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	362 * GroupEnd = ending coordinate on the chromosome of the group
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	363 * GroupID = unique ID for the group
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	364 * ReadCount = number of reads within the group
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	365
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	366 CLUSTERS: a comma separated file containing the information about the resulting clusters
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	367 * Chromosome = chromosome on which the cluster resides
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	368 * Strand = orientation in which the cluster resides
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	369 * ClusterStart = beginning coordinate on the chromosome of the cluster
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	370 * ClusterEnd = ending coordinate on the chromosome of the cluster
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	371 * ClusterID = unique ID for the cluster
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	372 * ClusterSequence = sequence of the cluster
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	373 * ReadCount = number of reads that overlap the cluster by at least 1 nucleotide
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	374 * ModeLocation = coordinate of the location with the highest signal / (signal + background) value
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	375 * ModeScore = score of the highest signal / (signal + background) value
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	376 * ConversionLocationCount = number of unique location where at least 1 conversion occurred
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	377 * ConversionEventCount = total number of conversions that occurred within the cluster
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	378 * NonConversionEventCount = total number of possible conversion events that did not occur
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	379
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	380 ]]></help>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	381 <citations>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	382 <citation type="doi">10.1186/gb-2011-12-8-r79</citation>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	383 </citations>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244" rnateam parents: diff changeset	384 </tool>

Mercurial > repos > rnateam > paralyzer

annotate paralyzer.xml @ 0:d4d72f60e8d6 draft default tip