music_deconvolution: music-deconvolution.xml.orig annotate

author	bgruening
date	Mon, 28 Oct 2024 17:32:19 +0000
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6 fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	1 <tool id="music_deconvolution" name="MuSiC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	2 profile="21.09" license="GPL-3.0-or-later" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	3 <description>estimate cell type proportions in bulk RNA-seq data</description>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	4 <macros>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	5 <import>macros.xml</import>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	6 </macros>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	7 <expand macro="requirements" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	8 <command detect_errors="exit_code" ><![CDATA[
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	9 mkdir report_data &&
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	10 Rscript --vanilla '$__tool_directory__/scripts/${do.method}.R' '$conf'
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	11 ]]></command>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	12 <configfiles>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	13 <configfile name="conf" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	14
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	15 null_str_vec = function(gstr){
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	16 tokens = unlist(as.vector(strsplit(gstr, split=",")))
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	17 if (length(tokens) == 0){
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	18 return(NULL)
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	19 }
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	20 if (length(tokens) == 1){
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	21 return(tokens[[1]])
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	22 }
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	23 return(tokens)
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	24 }
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	25
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	26 bulk_eset = readRDS('$bulk_eset')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	27 scrna_eset = readRDS('$scrna_eset')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	28 use_disease_factor = FALSE
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	29 maxyscale = NA
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	30
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	31 #if str($do.method) == "estimateprops":
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	32
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	33 maxyscale = as.numeric('$do.maxyscale') ## yields "NA" if blank
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	34 phenotype_factors = null_str_vec('$do.phenotype_factors')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	35 phenotype_factors_always_exclude = null_str_vec('$do.phenotype_factors_always_exclude')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	36 celltypes_label = null_str_vec('$do.celltypes_label')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	37 samples_label = null_str_vec('$do.samples_label')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	38 celltypes = null_str_vec('$do.celltypes')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	39 methods = c("MuSiC", "NNLS")
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	40
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	41 #if str($do.disease_factor.use) == "yes":
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	42 use_disease_factor = TRUE
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	43 <<<<<<< HEAD
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	44 phenotype_scrna_target = null_str_vec('$do.disease_factor.phenotype_scrna_target')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	45 =======
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	46 >>>>>>> 768a6e5b (v3 update:)
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	47 phenotype_target = null_str_vec('$do.disease_factor.phenotype_target')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	48 phenotype_target_threshold = as.numeric('$do.disease_factor.phenotype_target_threshold')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	49 sample_disease_group = null_str_vec('$do.disease_factor.sample_disease_group')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	50 sample_disease_group_scale = as.integer('$do.disease_factor.sample_disease_group_scale')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	51 <<<<<<< HEAD
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	52 =======
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	53 compare_title = null_str_vec('$do.disease_factor.compare_title')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	54 >>>>>>> 768a6e5b (v3 update:)
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	55 #end if
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	56
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	57 outfile_pdf='$out_pdf'
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	58
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	59 #elif str($do.method) == "dendrogram":
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	60
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	61 celltypes_label = null_str_vec('$do.celltypes_label')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	62 clustertype_label = null_str_vec('$do.clustertype_label')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	63 samples_label = null_str_vec('$do.samples_label')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	64 celltypes = null_str_vec('$do.celltypes')
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	65
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	66 data.to.use = list(
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	67 #for $i, $repeat in enumerate( $do.cluster_groups )
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	68 #if $i == 0:
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	69 $repeat.cluster_id = list(cell.types = null_str_vec('$repeat.celltypes'),
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	70 marker.names = null_str_vec('$repeat.marker_name'),
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	71 marker.list = read_list('$repeat.marker_list'))
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	72 #else
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	73 , $repeat.cluster_id = list(cell.types = null_str_vec('$repeat.celltypes'),
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	74 marker.names = null_str_vec('$repeat.marker_name'),
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	75 marker.list = read_list('$repeat.marker_list'))
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	76 #end if
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	77 #end for
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	78 )
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	79
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	80 outfile_pdf='$out_pdf'
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	81 outfile_tab='$out_tab'
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	82
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	83 #else
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	84 stop("No such option")
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	85 #end if
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	86
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	87 </configfile>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	88 </configfiles>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	89 <inputs>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	90 <param name="scrna_eset" label="scRNA Dataset" type="data" format="@RDATATYPE@" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	91 <param name="bulk_eset" label="Bulk RNA Dataset" type="data" format="@RDATATYPE@" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	92 <conditional name="do" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	93 <param name="method" type="select" label="Purpose" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	94 <!-- The values here correspond to script names in the scripts folder
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	95 and must remain so -->
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	96 <option value="estimateprops">Estimate Proportions</option>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	97 <option value="dendrogram">Compute Dendrogram</option>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	98 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	99 <when value="estimateprops" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	100 <param name="celltypes_label" type="text" value="cellType"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	101 label="Cell Types Label from scRNA dataset" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	102 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	103 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	104 <param name="samples_label" type="text" value="sampleID"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	105 label="Samples Identifier from scRNA dataset" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	106 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	107 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	108 <expand macro="celltypes_macro" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	109 <param name="phenotype_factors" type="text"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	110 label="Phenotype factors"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	111 help="List of phenotypes factors to be used in the linear regression. Please make sure that each factor has more than one unique value. Names correspond to column names in the bulk RNA dataset phenotype table. If blank, then treat all bulk phenotype columns as factors." >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	112 <expand macro="validator_index_identifiers" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	113 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	114 <param name="phenotype_factors_always_exclude" type="text"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	115 label="Excluded phenotype factors"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	116 help="List of phenotype factors to always exclude in the analysis"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	117 value="sampleID,SubjectName" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	118 <expand macro="validator_index_identifiers" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	119 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	120 <conditional name="disease_factor" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	121 <param name="use" type="select" label="Show proportions of a disease factor?" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	122 <option value="no" selected="true" >No</option>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	123 <option value="yes" >Yes</option>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	124 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	125 <when value="no" ></when>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	126 <when value="yes" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	127 <<<<<<< HEAD
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	128 <param name="phenotype_scrna_target" type="text" label="scRNA Phenotype Cell Target"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	129 help="The name of a target scRNA cell type to select in the phenotype comparison." >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	130 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	131 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	132 <param name="phenotype_target" type="text" label="Bulk Phenotype Target"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	133 help="MUST exist in the bulk RNA datasets phenotype factors as above." >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	134 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	135 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	136 <param name="phenotype_target_threshold" type="float" label="Bulk Phenotype Target Threshold"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	137 value="-99"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	138 help="The (%) threshold at which the phenotype target manifests. Leave at -99 to select all." >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	139 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	140 <param name="sample_disease_group" type="text" label="scRNA Sample Disease Group"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	141 help="Name for target disease group, ideally a value from the scRNA phenotype factor data" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	142 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	143 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	144 <param name="sample_disease_group_scale" type="integer"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	145 label="scRNA Sample Disease Group (Scale)" value="5"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	146 help="Used to accentutate certain features in the plots. Increase this number to reduce the effect." />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	147 =======
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	148 <param name="phenotype_target" type="text" label="Phenotype Target"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	149 help="MUST exist in the bulk RNA datasets phenotype factors as above." >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	150 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	151 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	152 <param name="phenotype_target_threshold" type="float" label="Phenotype Target Threshold"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	153 value="-99"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	154 help="The (%) threshold at which the phenotype target manifests. Leave at -99 to select all." >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	155 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	156 <param name="sample_disease_group" type="text" label="Sample Disease Group"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	157 help="MUST exist in the sample_groups above." >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	158 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	159 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	160 <param name="sample_disease_group_scale" type="integer"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	161 label="Sample Disease Group (Scale)" value="5"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	162 help="Used to accentutate certain features in the plots. Increase this number to reduce the effect." />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	163 <param name="compare_title" type="text" label="Plot Title" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	164 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	165 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	166 >>>>>>> 768a6e5b (v3 update:)
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	167 </when>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	168 </conditional>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	169 <param name="maxyscale" type="float" min="0" value="" optional="true"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	170 label="Scale all Y-axes to max limit" help="Leave blank to autoscale each plot."/>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	171 </when>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	172 <when value="dendrogram" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	173 <param name="celltypes_label" type="text" value="cellType"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	174 label="Cell Types Label from scRNA dataset" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	175 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	176 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	177 <param name="clustertype_label" type="text" value="clusterType"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	178 label="Cluster Types Label from scRNA dataset" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	179 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	180 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	181 <param name="samples_label" type="text" value="sampleID"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	182 label="Samples Identifier from scRNA dataset" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	183 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	184 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	185 <expand macro="celltypes_macro" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	186 <repeat name="cluster_groups" title="Cluster Groups" min="0"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	187 help="Insert cell cluster groups based on a previous clustering." >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	188 <param name="cluster_id" label="Cluster ID" type="text" value=""
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	189 help="e.g. C1 or Cluster1, etc." />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	190 <expand macro="celltypes_macro" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	191 <param name="marker_name" label="Marker Gene Group Name" type="text"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	192 optional="true" value=""
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	193 help="Name of the list of gene markers used to describe the marker list supplied below." >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	194 <expand macro="validator_text" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	195 </param>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	196 <param name="marker_list" label="List of Gene Markers" type="data" format="txt,tabular"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	197 optional="true"
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	198 help="A single column of marker genes" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	199 </repeat>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	200 </when>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	201 </conditional>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	202 </inputs>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	203 <outputs>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	204 <data name="out_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF Plots" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	205 <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Cell Proportions by Sample" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	206 <filter>do["method"] == "dendrogram" and len(do["cluster_groups"]) >0</filter>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	207 </data>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	208 <collection name="props" type="list" label="${tool.name} on ${on_string}: Proportion Matrices" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	209 <filter>do["method"] == "estimateprops"</filter>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	210 <discover_datasets pattern="prop_(?P<designation>.+)\.tabular" format="tabular" directory="report_data" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	211 </collection>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	212 <collection name="summaries" type="list" label="${tool.name} on ${on_string}: Summaries and Logs">
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	213 <filter>do["method"] == "estimateprops" and do["disease_factor"]["use"] == "yes"</filter>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	214 <discover_datasets pattern="summ_(?P<designation>.+)\.txt" format="txt" directory="report_data" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	215 <discover_datasets pattern="varprop_(?P<designation>.+)\.tabular" format="tabular" directory="report_data" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	216 <discover_datasets pattern="rsquared_(?P<designation>.+)\.tabular" format="tabular" directory="report_data" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	217 <discover_datasets pattern="weightgene_(?P<designation>.+)\.tabular" format="tabular" directory="report_data" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	218 </collection>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	219 </outputs>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	220 <tests>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	221 <test expect_num_outputs="1" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	222 <!-- Dendrogram test 1 -->
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	223 <param name="bulk_eset" value="Mousebulkeset.rds" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	224 <param name="scrna_eset" value="Mousesubeset.degenesonly2.half.rds" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	225 <conditional name="do" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	226 <param name="method" value="dendrogram" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	227 <param name="celltypes_label" value="cellType" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	228 <param name="samples_label" value="sampleID" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	229 <param name="celltypes" value="Endo,Podo,PT,LOH,DCT,CD-PC,CD-IC,Fib,Macro,Neutro,B lymph,T lymph,NK" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	230 </conditional>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	231 <output name="out_pdf" value="dendro_1.pdf" compare="sim_size" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	232 </test>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	233 <test expect_num_outputs="2" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	234 <!-- Dendrogram test 2 -->
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	235 <param name="bulk_eset" value="Mousebulkeset.rds" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	236 <param name="scrna_eset" value="Mousesubeset.degenesonly2.half.rds" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	237 <conditional name="do" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	238 <param name="method" value="dendrogram" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	239 <param name="celltypes_label" value="cellType" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	240 <param name="samples_label" value="sampleID" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	241 <param name="celltypes" value="Endo,Podo,PT,LOH,DCT,CD-PC,CD-IC,Fib,Macro,Neutro,B lymph,T lymph,NK" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	242 <repeat name="cluster_groups" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	243 <param name="cluster_id" value="C1" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	244 <param name="celltypes" value="Neutro" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	245 </repeat>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	246 <repeat name="cluster_groups" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	247 <param name="cluster_id" value="C2" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	248 <param name="celltypes" value="Podo" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	249 </repeat>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	250 <repeat name="cluster_groups" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	251 <param name="cluster_id" value="C3" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	252 <param name="celltypes" value="Endo,CD-PC,LOH,CD-IC,DCT,PT" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	253 <param name="marker_name" value="Epithelial" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	254 <param name="marker_list" value="epith.markers" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	255 </repeat>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	256 <repeat name="cluster_groups" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	257 <param name="cluster_id" value="C4" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	258 <param name="celltypes" value="Macro,Fib,B lymph,NK,T lymph" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	259 <param name="marker_name" value="Immune" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	260 <param name="marker_list" value="immune.markers" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	261 </repeat>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	262 </conditional>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	263 <output name="out_pdf" value="dendro.pdf" compare="sim_size" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	264 <output name="out_tab">
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	265 <assert_contents>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	266 <has_text_matching expression="^\s+Neutro\s+Podo\s+Endo" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	267 <has_text text="APOL1.GNA78M"/>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	268 </assert_contents>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	269 </output>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	270 </test>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	271 <test expect_num_outputs="2" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	272 <!-- Estimate Proportions: no disease factor, no fitting reports -->
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	273 <param name="bulk_eset" value="GSE50244bulkeset.subset.rds" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	274 <param name="scrna_eset" value="EMTABesethealthy.subset.rds" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	275 <conditional name="do" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	276 <param name="method" value="estimateprops" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	277 <param name="celltypes_label" value="cellType" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	278 <param name="samples_label" value="sampleID" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	279 <param name="disease_factor" value="no" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	280 </conditional>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	281 <output name="out_pdf" value="default_output_no_disease.pdf" compare="sim_size" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	282 </test>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	283 <test expect_num_outputs="3" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	284 <!-- Estimate Proportions: no disease factor -->
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	285 <param name="bulk_eset" value="GSE50244bulkeset.subset.rds" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	286 <param name="scrna_eset" value="EMTABesethealthy.subset.rds" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	287 <conditional name="do" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	288 <param name="method" value="estimateprops" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	289 <param name="celltypes_label" value="cellType" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	290 <param name="samples_label" value="sampleID" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	291 <param name="disease_factor" value="no" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	292 </conditional>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	293 <output name="out_pdf" value="default_output_no_disease.pdf" compare="sim_size" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	294 <output_collection name="summaries" count="5">
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	295 <element name="Log of MuSiC fitting" ftype="txt">
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	296 <assert_contents>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	297 <has_text text="Residual standard error: 0.1734 on 72 degrees of freedom"/>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	298 </assert_contents>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	299 </element>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	300 <element name="Log of NNLS fitting" ftype="txt">
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	301 <assert_contents>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	302 <has_text text="Residual standard error: 0.2687 on 72 degrees of freedom"/>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	303 </assert_contents>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	304 </element>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	305 </output_collection>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	306 </test>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	307 <test expect_num_outputs="3" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	308 <!-- Estimate Proportions test -->
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	309 <param name="bulk_eset" value="GSE50244bulkeset.subset.rds" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	310 <param name="scrna_eset" value="EMTABesethealthy.subset.rds" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	311 <conditional name="do" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	312 <param name="method" value="estimateprops" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	313 <param name="celltypes_label" value="cellType" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	314 <param name="samples_label" value="sampleID" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	315 <param name="celltypes" value="alpha,beta,delta,gamma,acinar,ductal" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	316 <conditional name="disease_factor" >
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	317 <param name="use" value="yes" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	318 <<<<<<< HEAD
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	319 <param name="phenotype_scrna_target" value="beta" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	320 =======
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	321 >>>>>>> 768a6e5b (v3 update:)
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	322 <param name="phenotype_factors" value="age,bmi,hba1c,gender" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	323 <param name="phenotype_target" value="hba1c" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	324 <param name="phenotype_target_threshold" value="6.5" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	325 <param name="sample_disease_group" value="T2D" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	326 <param name="sample_disease_group_scale" value="5" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	327 <<<<<<< HEAD
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	328 =======
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	329 <param name="compare_title" value="HbA1c vs Beta Cell Type Proportion" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	330 >>>>>>> 768a6e5b (v3 update:)
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	331 </conditional>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	332 </conditional>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	333 <output name="out_pdf" value="default_output.pdf" compare="sim_size" />
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	334 <output_collection name="summaries" count="5">
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	335 <element name="Log of MuSiC fitting" ftype="txt">
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	336 <assert_contents>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	337 <has_text text="Residual standard error: 0.1704 on 72 degrees of freedom"/>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	338 </assert_contents>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	339 </element>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	340 <element name="Log of NNLS fitting" ftype="txt">
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	341 <assert_contents>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	342 <has_text text="Residual standard error: 0.0645 on 72 degrees of freedom"/>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	343 </assert_contents>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	344 </element>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	345 </output_collection>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	346 </test>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	347 </tests>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	348 <help><![CDATA[
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	349 MuSiC utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another.
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	350
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	351 Solid tissues often contain closely related cell types which leads to collinearity. To deal with collinearity, MuSiC employs a tree-guided procedure that recursively zooms in on closely related cell types. Briefly, we first group similar cell types into the same cluster and estimate cluster proportions, then recursively repeat this procedure within each cluster.
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	352
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	353 ]]></help>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	354 <citations>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	355 <citation type="doi">https://doi.org/10.1038/s41467-018-08023-x</citation>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	356 </citations>
fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50 bgruening parents: diff changeset	357 </tool>

6

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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1 <tool id="music_deconvolution" name="MuSiC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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2 profile="21.09" license="GPL-3.0-or-later" >

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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3 <description>estimate cell type proportions in bulk RNA-seq data</description>

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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4 <macros>

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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5 <import>macros.xml</import>

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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6 </macros>

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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7 <expand macro="requirements" />

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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9 mkdir report_data &&

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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10 Rscript --vanilla '$__tool_directory__/scripts/${do.method}.R' '$conf'

fb36f390cc52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d5c7ca22af1d4f0eaa7a607886554bebb95e8c50

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11 ]]></command>

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12 <configfiles>

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13 <configfile name="conf" >

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14

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15 null_str_vec = function(gstr){

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16 tokens = unlist(as.vector(strsplit(gstr, split=",")))

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17 if (length(tokens) == 0){

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18 return(NULL)

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19 }

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20 if (length(tokens) == 1){

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21 return(tokens[[1]])

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22 }

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23 return(tokens)

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24 }

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25

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26 bulk_eset = readRDS('$bulk_eset')

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27 scrna_eset = readRDS('$scrna_eset')

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28 use_disease_factor = FALSE

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29 maxyscale = NA

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30

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31 #if str($do.method) == "estimateprops":

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32

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33 maxyscale = as.numeric('$do.maxyscale') ## yields "NA" if blank

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34 phenotype_factors = null_str_vec('$do.phenotype_factors')

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35 phenotype_factors_always_exclude = null_str_vec('$do.phenotype_factors_always_exclude')

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36 celltypes_label = null_str_vec('$do.celltypes_label')

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37 samples_label = null_str_vec('$do.samples_label')

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38 celltypes = null_str_vec('$do.celltypes')

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39 methods = c("MuSiC", "NNLS")

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40

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41 #if str($do.disease_factor.use) == "yes":

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42 use_disease_factor = TRUE

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43 <<<<<<< HEAD

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44 phenotype_scrna_target = null_str_vec('$do.disease_factor.phenotype_scrna_target')

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45 =======

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46 >>>>>>> 768a6e5b (v3 update:)

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47 phenotype_target = null_str_vec('$do.disease_factor.phenotype_target')

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48 phenotype_target_threshold = as.numeric('$do.disease_factor.phenotype_target_threshold')

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49 sample_disease_group = null_str_vec('$do.disease_factor.sample_disease_group')

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50 sample_disease_group_scale = as.integer('$do.disease_factor.sample_disease_group_scale')

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51 <<<<<<< HEAD

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52 =======

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53 compare_title = null_str_vec('$do.disease_factor.compare_title')

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54 >>>>>>> 768a6e5b (v3 update:)

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55 #end if

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56

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57 outfile_pdf='$out_pdf'

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58

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59 #elif str($do.method) == "dendrogram":

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60

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61 celltypes_label = null_str_vec('$do.celltypes_label')

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62 clustertype_label = null_str_vec('$do.clustertype_label')

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63 samples_label = null_str_vec('$do.samples_label')

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64 celltypes = null_str_vec('$do.celltypes')

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65

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66 data.to.use = list(

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67 #for $i, $repeat in enumerate( $do.cluster_groups )

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68 #if $i == 0:

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69 $repeat.cluster_id = list(cell.types = null_str_vec('$repeat.celltypes'),

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70 marker.names = null_str_vec('$repeat.marker_name'),

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71 marker.list = read_list('$repeat.marker_list'))

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72 #else

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73 , $repeat.cluster_id = list(cell.types = null_str_vec('$repeat.celltypes'),

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74 marker.names = null_str_vec('$repeat.marker_name'),

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75 marker.list = read_list('$repeat.marker_list'))

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76 #end if

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77 #end for

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78 )

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79

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80 outfile_pdf='$out_pdf'

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81 outfile_tab='$out_tab'

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82

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83 #else

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84 stop("No such option")

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85 #end if

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86

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87 </configfile>

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88 </configfiles>

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89 <inputs>

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90 <param name="scrna_eset" label="scRNA Dataset" type="data" format="@RDATATYPE@" />

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91 <param name="bulk_eset" label="Bulk RNA Dataset" type="data" format="@RDATATYPE@" />

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92 <conditional name="do" >

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93 <param name="method" type="select" label="Purpose" >

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94 <!-- The values here correspond to script names in the scripts folder

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95 and must remain so -->

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96 <option value="estimateprops">Estimate Proportions</option>

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97 <option value="dendrogram">Compute Dendrogram</option>

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98 </param>

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99 <when value="estimateprops" >

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100 <param name="celltypes_label" type="text" value="cellType"

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101 label="Cell Types Label from scRNA dataset" >

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102 <expand macro="validator_text" />

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103 </param>

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104 <param name="samples_label" type="text" value="sampleID"

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105 label="Samples Identifier from scRNA dataset" >

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106 <expand macro="validator_text" />

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107 </param>

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108 <expand macro="celltypes_macro" />

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109 <param name="phenotype_factors" type="text"

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110 label="Phenotype factors"

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111 help="List of phenotypes factors to be used in the linear regression. Please make sure that each factor has more than one unique value. Names correspond to column names in the bulk RNA dataset phenotype table. If blank, then treat all bulk phenotype columns as factors." >

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112 <expand macro="validator_index_identifiers" />

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113 </param>

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114 <param name="phenotype_factors_always_exclude" type="text"

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115 label="Excluded phenotype factors"

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116 help="List of phenotype factors to always exclude in the analysis"

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117 value="sampleID,SubjectName" >

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118 <expand macro="validator_index_identifiers" />

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119 </param>

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120 <conditional name="disease_factor" >

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121 <param name="use" type="select" label="Show proportions of a disease factor?" >

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122 <option value="no" selected="true" >No</option>

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123 <option value="yes" >Yes</option>

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124 </param>

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125 <when value="no" ></when>

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126 <when value="yes" >

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127 <<<<<<< HEAD

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128 <param name="phenotype_scrna_target" type="text" label="scRNA Phenotype Cell Target"

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129 help="The name of a target scRNA cell type to select in the phenotype comparison." >

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130 <expand macro="validator_text" />

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131 </param>

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132 <param name="phenotype_target" type="text" label="Bulk Phenotype Target"

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133 help="MUST exist in the bulk RNA datasets phenotype factors as above." >

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134 <expand macro="validator_text" />

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135 </param>

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136 <param name="phenotype_target_threshold" type="float" label="Bulk Phenotype Target Threshold"

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137 value="-99"

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138 help="The (%) threshold at which the phenotype target manifests. Leave at -99 to select all." >

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139 </param>

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140 <param name="sample_disease_group" type="text" label="scRNA Sample Disease Group"

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141 help="Name for target disease group, ideally a value from the scRNA phenotype factor data" >

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142 <expand macro="validator_text" />

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143 </param>

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144 <param name="sample_disease_group_scale" type="integer"

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145 label="scRNA Sample Disease Group (Scale)" value="5"

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146 help="Used to accentutate certain features in the plots. Increase this number to reduce the effect." />

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147 =======

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148 <param name="phenotype_target" type="text" label="Phenotype Target"

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149 help="MUST exist in the bulk RNA datasets phenotype factors as above." >

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150 <expand macro="validator_text" />

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151 </param>

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152 <param name="phenotype_target_threshold" type="float" label="Phenotype Target Threshold"

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153 value="-99"

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154 help="The (%) threshold at which the phenotype target manifests. Leave at -99 to select all." >

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155 </param>

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156 <param name="sample_disease_group" type="text" label="Sample Disease Group"

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157 help="MUST exist in the sample_groups above." >

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158 <expand macro="validator_text" />

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159 </param>

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160 <param name="sample_disease_group_scale" type="integer"

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161 label="Sample Disease Group (Scale)" value="5"

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162 help="Used to accentutate certain features in the plots. Increase this number to reduce the effect." />

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163 <param name="compare_title" type="text" label="Plot Title" >

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164 <expand macro="validator_text" />

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165 </param>

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166 >>>>>>> 768a6e5b (v3 update:)

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167 </when>

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168 </conditional>

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169 <param name="maxyscale" type="float" min="0" value="" optional="true"

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170 label="Scale all Y-axes to max limit" help="Leave blank to autoscale each plot."/>

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171 </when>

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172 <when value="dendrogram" >

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173 <param name="celltypes_label" type="text" value="cellType"

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174 label="Cell Types Label from scRNA dataset" >

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175 <expand macro="validator_text" />

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176 </param>

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177 <param name="clustertype_label" type="text" value="clusterType"

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178 label="Cluster Types Label from scRNA dataset" >

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179 <expand macro="validator_text" />

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180 </param>

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181 <param name="samples_label" type="text" value="sampleID"

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182 label="Samples Identifier from scRNA dataset" >

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183 <expand macro="validator_text" />

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184 </param>

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185 <expand macro="celltypes_macro" />

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186 <repeat name="cluster_groups" title="Cluster Groups" min="0"

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187 help="Insert cell cluster groups based on a previous clustering." >

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188 <param name="cluster_id" label="Cluster ID" type="text" value=""

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189 help="e.g. C1 or Cluster1, etc." />

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190 <expand macro="celltypes_macro" />

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191 <param name="marker_name" label="Marker Gene Group Name" type="text"

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192 optional="true" value=""

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193 help="Name of the list of gene markers used to describe the marker list supplied below." >

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194 <expand macro="validator_text" />

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195 </param>

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196 <param name="marker_list" label="List of Gene Markers" type="data" format="txt,tabular"

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197 optional="true"

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198 help="A single column of marker genes" />

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199 </repeat>

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200 </when>

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201 </conditional>

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202 </inputs>

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203 <outputs>

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204 <data name="out_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF Plots" />

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205 <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Cell Proportions by Sample" >

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206 <filter>do["method"] == "dendrogram" and len(do["cluster_groups"]) >0</filter>

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207 </data>

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208 <collection name="props" type="list" label="${tool.name} on ${on_string}: Proportion Matrices" >

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209 <filter>do["method"] == "estimateprops"</filter>

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210 <discover_datasets pattern="prop_(?P<designation>.+)\.tabular" format="tabular" directory="report_data" />

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211 </collection>

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212 <collection name="summaries" type="list" label="${tool.name} on ${on_string}: Summaries and Logs">

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213 <filter>do["method"] == "estimateprops" and do["disease_factor"]["use"] == "yes"</filter>

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214 <discover_datasets pattern="summ_(?P<designation>.+)\.txt" format="txt" directory="report_data" />

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215 <discover_datasets pattern="varprop_(?P<designation>.+)\.tabular" format="tabular" directory="report_data" />

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216 <discover_datasets pattern="rsquared_(?P<designation>.+)\.tabular" format="tabular" directory="report_data" />

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217 <discover_datasets pattern="weightgene_(?P<designation>.+)\.tabular" format="tabular" directory="report_data" />

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218 </collection>

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219 </outputs>

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220 <tests>

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221 <test expect_num_outputs="1" >

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222

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223 <param name="bulk_eset" value="Mousebulkeset.rds" />

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224 <param name="scrna_eset" value="Mousesubeset.degenesonly2.half.rds" />

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225 <conditional name="do" >

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226 <param name="method" value="dendrogram" />

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227 <param name="celltypes_label" value="cellType" />

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228 <param name="samples_label" value="sampleID" />

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229 <param name="celltypes" value="Endo,Podo,PT,LOH,DCT,CD-PC,CD-IC,Fib,Macro,Neutro,B lymph,T lymph,NK" />

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230 </conditional>

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231 <output name="out_pdf" value="dendro_1.pdf" compare="sim_size" />

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232 </test>

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233 <test expect_num_outputs="2" >

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234

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235 <param name="bulk_eset" value="Mousebulkeset.rds" />

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236 <param name="scrna_eset" value="Mousesubeset.degenesonly2.half.rds" />

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237 <conditional name="do" >

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238 <param name="method" value="dendrogram" />

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239 <param name="celltypes_label" value="cellType" />

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240 <param name="samples_label" value="sampleID" />

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241 <param name="celltypes" value="Endo,Podo,PT,LOH,DCT,CD-PC,CD-IC,Fib,Macro,Neutro,B lymph,T lymph,NK" />

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242 <repeat name="cluster_groups" >

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243 <param name="cluster_id" value="C1" />

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244 <param name="celltypes" value="Neutro" />

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245 </repeat>

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246 <repeat name="cluster_groups" >

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247 <param name="cluster_id" value="C2" />

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248 <param name="celltypes" value="Podo" />

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249 </repeat>

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250 <repeat name="cluster_groups" >

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251 <param name="cluster_id" value="C3" />

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252 <param name="celltypes" value="Endo,CD-PC,LOH,CD-IC,DCT,PT" />

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253 <param name="marker_name" value="Epithelial" />

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254 <param name="marker_list" value="epith.markers" />

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255 </repeat>

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256 <repeat name="cluster_groups" >

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257 <param name="cluster_id" value="C4" />

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258 <param name="celltypes" value="Macro,Fib,B lymph,NK,T lymph" />

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259 <param name="marker_name" value="Immune" />

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260 <param name="marker_list" value="immune.markers" />

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261 </repeat>

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262 </conditional>

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263 <output name="out_pdf" value="dendro.pdf" compare="sim_size" />

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264 <output name="out_tab">

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265 <assert_contents>

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266 <has_text_matching expression="^\s+Neutro\s+Podo\s+Endo" />

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267 <has_text text="APOL1.GNA78M"/>

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268 </assert_contents>

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269 </output>

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270 </test>

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271 <test expect_num_outputs="2" >

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272

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273 <param name="bulk_eset" value="GSE50244bulkeset.subset.rds" />

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274 <param name="scrna_eset" value="EMTABesethealthy.subset.rds" />

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275 <conditional name="do" >

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276 <param name="method" value="estimateprops" />

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277 <param name="celltypes_label" value="cellType" />

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278 <param name="samples_label" value="sampleID" />

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279 <param name="disease_factor" value="no" />

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280 </conditional>

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281 <output name="out_pdf" value="default_output_no_disease.pdf" compare="sim_size" />

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282 </test>

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283 <test expect_num_outputs="3" >

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284

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285 <param name="bulk_eset" value="GSE50244bulkeset.subset.rds" />

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286 <param name="scrna_eset" value="EMTABesethealthy.subset.rds" />

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287 <conditional name="do" >

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288 <param name="method" value="estimateprops" />

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289 <param name="celltypes_label" value="cellType" />

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290 <param name="samples_label" value="sampleID" />

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291 <param name="disease_factor" value="no" />

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292 </conditional>

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293 <output name="out_pdf" value="default_output_no_disease.pdf" compare="sim_size" />

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294 <output_collection name="summaries" count="5">

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295 <element name="Log of MuSiC fitting" ftype="txt">

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296 <assert_contents>

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297 <has_text text="Residual standard error: 0.1734 on 72 degrees of freedom"/>

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298 </assert_contents>

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299 </element>

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300 <element name="Log of NNLS fitting" ftype="txt">

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301 <assert_contents>

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302 <has_text text="Residual standard error: 0.2687 on 72 degrees of freedom"/>

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303 </assert_contents>

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304 </element>

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305 </output_collection>

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306 </test>

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307 <test expect_num_outputs="3" >

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308

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309 <param name="bulk_eset" value="GSE50244bulkeset.subset.rds" />

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310 <param name="scrna_eset" value="EMTABesethealthy.subset.rds" />

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311 <conditional name="do" >

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312 <param name="method" value="estimateprops" />

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313 <param name="celltypes_label" value="cellType" />

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314 <param name="samples_label" value="sampleID" />

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315 <param name="celltypes" value="alpha,beta,delta,gamma,acinar,ductal" />

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316 <conditional name="disease_factor" >

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317 <param name="use" value="yes" />

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318 <<<<<<< HEAD

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319 <param name="phenotype_scrna_target" value="beta" />

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320 =======

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321 >>>>>>> 768a6e5b (v3 update:)

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322 <param name="phenotype_factors" value="age,bmi,hba1c,gender" />

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323 <param name="phenotype_target" value="hba1c" />

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324 <param name="phenotype_target_threshold" value="6.5" />

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325 <param name="sample_disease_group" value="T2D" />

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326 <param name="sample_disease_group_scale" value="5" />

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327 <<<<<<< HEAD

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328 =======

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329 <param name="compare_title" value="HbA1c vs Beta Cell Type Proportion" />

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330 >>>>>>> 768a6e5b (v3 update:)

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331 </conditional>

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332 </conditional>

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333 <output name="out_pdf" value="default_output.pdf" compare="sim_size" />

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334 <output_collection name="summaries" count="5">

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335 <element name="Log of MuSiC fitting" ftype="txt">

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336 <assert_contents>

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337 <has_text text="Residual standard error: 0.1704 on 72 degrees of freedom"/>

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338 </assert_contents>

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339 </element>

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340 <element name="Log of NNLS fitting" ftype="txt">

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341 <assert_contents>

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342 <has_text text="Residual standard error: 0.0645 on 72 degrees of freedom"/>

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343 </assert_contents>

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344 </element>

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345 </output_collection>

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346 </test>

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347 </tests>

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348 <help><![CDATA[

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349 MuSiC utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another.

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350

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351 Solid tissues often contain closely related cell types which leads to collinearity. To deal with collinearity, MuSiC employs a tree-guided procedure that recursively zooms in on closely related cell types. Briefly, we first group similar cell types into the same cluster and estimate cluster proportions, then recursively repeat this procedure within each cluster.

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352

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353 ]]></help>

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354 <citations>

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355 <citation type="doi">https://doi.org/10.1038/s41467-018-08023-x</citation>

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356 </citations>

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357 </tool>

Mercurial > repos > bgruening > music_deconvolution

annotate music-deconvolution.xml.orig @ 6:fb36f390cc52 draft