Mercurial > repos > bgruening > music_deconvolution

annotate music-deconvolution.xml @ 0:224721e76869 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
author bgruening
date Sun, 12 Sep 2021 19:48:48 +0000
parents
children 3ca0132c182a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
1 <tool id="music_deconvolution" name="MuSiC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
2 profile="20.05" license="GPL-3.0-or-later" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
3 <description>estimate cell type proportions in bulk RNA-seq data</description>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
4 <macros>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
5 <import>macros.xml</import>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
6 </macros>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
7 <expand macro="requirements" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
9 mkdir report_data &&
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
10 Rscript --vanilla '$__tool_directory__/scripts/${do.method}.R' '$conf'
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
11 ]]></command>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
12 <configfiles>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
13 <configfile name="conf" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
14
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
15 null_str_vec = function(gstr){
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
16 tokens = unlist(as.vector(strsplit(gstr, split=",")))
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
17 if (length(tokens) == 0){
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
18 return(NULL)
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
19 }
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
20 if (length(tokens) == 1){
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
21 return(tokens[[1]])
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
22 }
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
23 return(tokens)
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
24 }
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
25
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
26 bulk_eset = readRDS('$bulk_eset')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
27 scrna_eset = readRDS('$scrna_eset')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
28
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
29 #if str($do.method) == "estimateprops":
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
30
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
31 phenotype_factors = null_str_vec('$do.phenotype_factors')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
32 celltypes_label = null_str_vec('$do.celltypes_label')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
33 samples_label = null_str_vec('$do.samples_label')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
34 celltypes = null_str_vec('$do.celltypes')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
35 methods = null_str_vec('$do.methods')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
36 phenotype_gene = null_str_vec('$do.phenotype_gene')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
37 sample_groups = null_str_vec('$do.sample_groups')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
38 sample_disease_group = null_str_vec('$do.sample_disease_group')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
39 sample_disease_group_scale = as.integer('$do.sample_disease_group_scale')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
40 healthy_phenotype = null_str_vec('$do.healthy_phenotype')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
41 compare_title = null_str_vec('$do.compare_title')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
42 outfile_pdf='$out_pdf'
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
43
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
44 #elif str($do.method) == "dendrogram":
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
45
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
46 celltypes_label = null_str_vec('$do.celltypes_label')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
47 clustertype_label = null_str_vec('$do.clustertype_label')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
48 samples_label = null_str_vec('$do.samples_label')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
49 celltypes = null_str_vec('$do.celltypes')
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
50
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
51 data.to.use = list(
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
52 #for $i, $repeat in enumerate( $do.cluster_groups )
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
53 #if $i == 0:
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
54 $repeat.cluster_id = list(cell.types = null_str_vec('$repeat.celltypes'),
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
55 marker.names = null_str_vec('$repeat.marker_name'),
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
56 marker.list = read_list('$repeat.marker_list'))
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
57 #else
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
58 , $repeat.cluster_id = list(cell.types = null_str_vec('$repeat.celltypes'),
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
59 marker.names = null_str_vec('$repeat.marker_name'),
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
60 marker.list = read_list('$repeat.marker_list'))
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
61 #end if
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
62 #end for
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
63 )
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
64
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
65 outfile_pdf='$out_pdf'
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
66 outfile_tab='$out_tab'
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
67
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
68 #else
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
69 stop("No such option")
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
70 #end if
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
71
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
72 </configfile>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
73 </configfiles>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
74 <inputs>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
75 <param name="scrna_eset" label="scRNA Dataset" type="data" format="rdata.eset" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
76 <param name="bulk_eset" label="Bulk RNA Dataset" type="data" format="rdata.eset" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
77 <conditional name="do" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
78 <param name="method" type="select" label="Purpose" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
79 <!-- The values here correspond to script names in the scripts folder
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
80 and must remain so -->
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
81 <option value="estimateprops">Estimate Proportions</option>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
82 <option value="dendrogram">Compute Dendrogram</option>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
83 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
84 <when value="estimateprops" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
85 <param name="celltypes_label" type="text" value="cellType"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
86 label="Cell Types Label from scRNA dataset" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
87 <expand macro="validator_text" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
88 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
89 <param name="samples_label" type="text" value="sampleID"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
90 label="Samples Identifier from scRNA dataset" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
91 <expand macro="validator_text" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
92 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
93 <expand macro="celltypes_macro" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
94 <param name="methods" multiple="true" type="select" display="checkboxes" label="Cell Proportion Method" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
95 <option value="MuSiC" selected="true" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
96 <option value="NNLS" selected="true" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
97 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
98 <param name="phenotype_factors" type="text"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
99 label="List of phenotypes factors" help="If blank, then use all phenotypes." >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
100 <expand macro="validator_index_identifiers" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
101 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
102 <param name="phenotype_gene" type="text" label="Causative Gene"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
103 help="MUST exist in the phenotype factors above." >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
104 <expand macro="validator_text" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
105 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
106 <param name="sample_groups" type="text" label="List of Sample Groups" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
107 <expand macro="validator_index_identifiers" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
108 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
109 <param name="sample_disease_group" type="text" label="Sample Disease Group"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
110 help="MUST exist in the sample_groups above." >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
111 <expand macro="validator_text" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
112 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
113 <param name="sample_disease_group_scale" type="integer"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
114 label="Sample Disease Group (Scale)" value="5"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
115 help="Used to accentutate certain features in the plots. Increase this number to reduce the effect." />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
116 <param name="healthy_phenotype" type="text" label="Healthy Phenotype" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
117 <expand macro="validator_text" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
118 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
119 <param name="compare_title" type="text" label="Plot Title" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
120 <expand macro="validator_text" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
121 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
122 </when>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
123 <when value="dendrogram" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
124 <param name="celltypes_label" type="text" value="cellType"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
125 label="Cell Types Label from scRNA dataset" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
126 <expand macro="validator_text" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
127 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
128 <param name="clustertype_label" type="text" value="clusterType"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
129 label="Cell Types Label from scRNA dataset" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
130 <expand macro="validator_text" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
131 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
132 <param name="samples_label" type="text" value="sampleID"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
133 label="Samples Identifier from scRNA dataset" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
134 <expand macro="validator_text" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
135 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
136 <expand macro="celltypes_macro" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
137 <repeat name="cluster_groups" title="Cluster Groups" min="2" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
138 <param name="cluster_id" label="Cluster ID" type="text" value=""
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
139 help="e.g. C1 or Cluster1, etc." />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
140 <expand macro="celltypes_macro" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
141 <param name="marker_name" label="Marker Gene Group Name" type="text"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
142 optional="true" value=""
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
143 help="Name of the list of geme markers used to describe the marker list supplied below." >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
144 <expand macro="validator_text" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
145 </param>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
146 <param name="marker_list" label="List of Gene Markers" type="data" format="txt,tabular"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
147 optional="true"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
148 help="A single column of marker genes" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
149 </repeat>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
150 </when>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
151 </conditional>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
152 </inputs>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
153 <outputs>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
154 <data name="out_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF Plots" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
155 <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Cell Proportions by Sample" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
156 <filter>do["method"] == "dendrogram"</filter>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
157 </data>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
158 <collection name="summaries" type="list" label="${tool.name} on ${on_string}: Method Summaries">
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
159 <filter>do["method"] == "estimateprops"</filter>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
160 <discover_datasets pattern="summ_(?P&lt;designation&gt;.+)\.txt" format="txt"
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
161 directory="report_data" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
162 </collection>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
163 </outputs>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
164 <tests>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
165 <test expect_num_outputs="2" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
166 <!-- Dendrogram test -->
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
167 <param name="bulk_eset" value="Mousebulkeset.rds" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
168 <param name="scrna_eset" value="Mousesubeset.degenesonly2.half.rds" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
169 <conditional name="do" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
170 <param name="method" value="dendrogram" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
171 <param name="celltypes_label" value="cellType" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
172 <param name="samples_label" value="sampleID" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
173 <param name="celltypes" value="Endo,Podo,PT,LOH,DCT,CD-PC,CD-IC,Fib,Macro,Neutro,B lymph,T lymph,NK" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
174 <repeat name="cluster_groups" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
175 <param name="cluster_id" value="C1" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
176 <param name="celltypes" value="Neutro" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
177 </repeat>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
178 <repeat name="cluster_groups" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
179 <param name="cluster_id" value="C2" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
180 <param name="celltypes" value="Podo" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
181 </repeat>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
182 <repeat name="cluster_groups" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
183 <param name="cluster_id" value="C3" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
184 <param name="celltypes" value="Endo,CD-PC,LOH,CD-IC,DCT,PT" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
185 <param name="marker_name" value="Epithelial" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
186 <param name="marker_list" value="epith.markers" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
187 </repeat>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
188 <repeat name="cluster_groups" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
189 <param name="cluster_id" value="C4" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
190 <param name="celltypes" value="Macro,Fib,B lymph,NK,T lymph" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
191 <param name="marker_name" value="Immune" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
192 <param name="marker_list" value="immune.markers" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
193 </repeat>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
194 </conditional>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
195 <output name="out_pdf" value="dendro.pdf" compare="sim_size" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
196 <output name="out_tab">
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
197 <assert_contents>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
198 <has_text_matching expression="^\s+Est\.prop\.weighted\.cluster\.Neutro\s+Est\.prop\.weighted\.cluster\.Podo\s+Est\.prop\.weighted\.cluster\.Endo" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
199 <has_text text="APOL1.GNA78M"/>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
200 </assert_contents>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
201 </output>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
202 </test>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
203 <test expect_num_outputs="2" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
204 <!-- Estimate Proportions test -->
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
205 <param name="bulk_eset" value="GSE50244bulkeset.subset.rds" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
206 <param name="scrna_eset" value="EMTABesethealthy.subset.rds" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
207 <conditional name="do" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
208 <param name="method" value="estimateprops" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
209 <param name="celltypes_label" value="cellType" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
210 <param name="samples_label" value="sampleID" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
211 <param name="celltypes" value="alpha,beta,delta,gamma,acinar,ductal" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
212 <param name="methods" value="MuSiC,NNLS" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
213 <param name="phenotype_factors" value="age,bmi,hba1c,gender" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
214 <param name="phenotype_gene" value="hba1c" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
215 <param name="sample_groups" value="Normal,T2D" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
216 <param name="sample_disease_group" value="T2D" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
217 <param name="sample_disease_group_scale" value="5" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
218 <param name="healthy_phenotype" value="Normal" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
219 <param name="compare_title" value="HbA1c vs Beta Cell Type Proportion" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
220 </conditional>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
221 <output name="out_pdf" value="default_output.pdf" compare="sim_size" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
222 <output_collection name="summaries" count="2">
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
223 <element name="MuSiC" ftype="txt">
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
224 <assert_contents>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
225 <has_text text="Residual standard error: 0.1662 on 72 degrees of freedom"/>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
226 </assert_contents>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
227 </element>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
228 <element name="NNLS" ftype="txt">
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
229 <assert_contents>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
230 <has_text text="Residual standard error: 0.06561 on 72 degrees of freedom"/>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
231 </assert_contents>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
232 </element>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
233 </output_collection>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
234 </test>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
235 </tests>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
236 <help><![CDATA[
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
237 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.
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
238
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
239 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.
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
240
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
241 .. image:: https://xuranw.github.io/MuSiC/articles/images/FigureMethod.jpg
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
242 ]]></help>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
243 <citations>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
244 <citation type="doi">https://doi.org/10.1038/s41467-018-08023-x</citation>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
245 </citations>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
246 </tool>