Mercurial > repos > bgruening > music_deconvolution

annotate music-deconvolution.xml @ 1:3ca0132c182a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
author bgruening
date Fri, 26 Nov 2021 15:54:51 +0000
parents 224721e76869
children 1c4cf4b7debe
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1 <tool id="music_deconvolution" name="MuSiC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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2 profile="21.09" license="GPL-3.0-or-later" >
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3 <description>estimate cell type proportions in bulk RNA-seq data</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code" ><![CDATA[
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9 mkdir report_data &&
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10 Rscript --vanilla '$__tool_directory__/scripts/${do.method}.R' '$conf'
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11 ]]></command>
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12 <configfiles>
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13 <configfile name="conf" >
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15 null_str_vec = function(gstr){
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16 tokens = unlist(as.vector(strsplit(gstr, split=",")))
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17 if (length(tokens) == 0){
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18 return(NULL)
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19 }
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20 if (length(tokens) == 1){
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21 return(tokens[[1]])
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22 }
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23 return(tokens)
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24 }
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26 bulk_eset = readRDS('$bulk_eset')
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27 scrna_eset = readRDS('$scrna_eset')
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29 #if str($do.method) == "estimateprops":
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31 phenotype_factors = null_str_vec('$do.phenotype_factors')
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32 phenotype_factors_always_exclude = null_str_vec('$do.phenotype_factors_always_exclude')
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33 celltypes_label = null_str_vec('$do.celltypes_label')
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34 samples_label = null_str_vec('$do.samples_label')
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35 celltypes = null_str_vec('$do.celltypes')
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36 methods = c("MuSiC", "NNLS")
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37 phenotype_target = null_str_vec('$do.phenotype_target')
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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38 phenotype_target_threshold = as.numeric('$do.phenotype_target_threshold')
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39 sample_disease_group = null_str_vec('$do.sample_disease_group')
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40 sample_disease_group_scale = as.integer('$do.sample_disease_group_scale')
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41 compare_title = null_str_vec('$do.compare_title')
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42
0
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43 outfile_pdf='$out_pdf'
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44
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45 #elif str($do.method) == "dendrogram":
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46
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47 celltypes_label = null_str_vec('$do.celltypes_label')
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48 clustertype_label = null_str_vec('$do.clustertype_label')
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49 samples_label = null_str_vec('$do.samples_label')
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50 celltypes = null_str_vec('$do.celltypes')
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51
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52 data.to.use = list(
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53 #for $i, $repeat in enumerate( $do.cluster_groups )
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54 #if $i == 0:
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55 $repeat.cluster_id = list(cell.types = null_str_vec('$repeat.celltypes'),
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56 marker.names = null_str_vec('$repeat.marker_name'),
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57 marker.list = read_list('$repeat.marker_list'))
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58 #else
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59 , $repeat.cluster_id = list(cell.types = null_str_vec('$repeat.celltypes'),
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60 marker.names = null_str_vec('$repeat.marker_name'),
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61 marker.list = read_list('$repeat.marker_list'))
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62 #end if
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63 #end for
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64 )
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65
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66 outfile_pdf='$out_pdf'
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67 outfile_tab='$out_tab'
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68
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69 #else
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70 stop("No such option")
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71 #end if
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72
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73 </configfile>
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74 </configfiles>
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75 <inputs>
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76 <param name="scrna_eset" label="scRNA Dataset" type="data" format="rdata.eset" />
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77 <param name="bulk_eset" label="Bulk RNA Dataset" type="data" format="rdata.eset" />
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78 <conditional name="do" >
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79 <param name="method" type="select" label="Purpose" >
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80 <!-- The values here correspond to script names in the scripts folder
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81 and must remain so -->
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82 <option value="estimateprops">Estimate Proportions</option>
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83 <option value="dendrogram">Compute Dendrogram</option>
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84 </param>
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85 <when value="estimateprops" >
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86 <param name="celltypes_label" type="text" value="cellType"
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87 label="Cell Types Label from scRNA dataset" >
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88 <expand macro="validator_text" />
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89 </param>
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90 <param name="samples_label" type="text" value="sampleID"
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91 label="Samples Identifier from scRNA dataset" >
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92 <expand macro="validator_text" />
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93 </param>
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94 <expand macro="celltypes_macro" />
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95 <param name="phenotype_factors" type="text"
1
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96 label="Phenotype factors"
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97 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." >
0
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98 <expand macro="validator_index_identifiers" />
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99 </param>
1
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100 <param name="phenotype_factors_always_exclude" type="text"
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101 label="Excluded phenotype factors"
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102 help="List of phenotype factors to always exclude in the analysis"
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103 value="sampleID,SubjectName" >
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104 <expand macro="validator_index_identifiers" />
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105 </param>
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106 <param name="phenotype_target" type="text" label="Phenotype Target"
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107 help="MUST exist in the bulk RNA datasets phenotype factors, as above." >
0
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108 <expand macro="validator_text" />
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109 </param>
1
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110 <param name="phenotype_target_threshold" type="float" label="Phenotype Target Threshold"
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111 value="-99"
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112 help="The (%) threshold at which the phenotype target manifests. Leave at -99 to select all." >
0
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113 </param>
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114 <param name="sample_disease_group" type="text" label="Sample Disease Group"
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115 help="MUST exist in the sample_groups above." >
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116 <expand macro="validator_text" />
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117 </param>
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118 <param name="sample_disease_group_scale" type="integer"
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119 label="Sample Disease Group (Scale)" value="5"
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120 help="Used to accentutate certain features in the plots. Increase this number to reduce the effect." />
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121 <param name="compare_title" type="text" label="Plot Title" >
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122 <expand macro="validator_text" />
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123 </param>
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124 </when>
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125 <when value="dendrogram" >
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126 <param name="celltypes_label" type="text" value="cellType"
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127 label="Cell Types Label from scRNA dataset" >
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128 <expand macro="validator_text" />
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129 </param>
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130 <param name="clustertype_label" type="text" value="clusterType"
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131 label="Cluster Types Label from scRNA dataset" >
0
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132 <expand macro="validator_text" />
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133 </param>
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134 <param name="samples_label" type="text" value="sampleID"
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135 label="Samples Identifier from scRNA dataset" >
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136 <expand macro="validator_text" />
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137 </param>
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138 <expand macro="celltypes_macro" />
1
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139 <repeat name="cluster_groups" title="Cluster Groups" min="0"
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140 help="Insert cell cluster groups based on a previous clustering." >
0
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141 <param name="cluster_id" label="Cluster ID" type="text" value=""
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142 help="e.g. C1 or Cluster1, etc." />
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143 <expand macro="celltypes_macro" />
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144 <param name="marker_name" label="Marker Gene Group Name" type="text"
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145 optional="true" value=""
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146 help="Name of the list of gene markers used to describe the marker list supplied below." >
0
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147 <expand macro="validator_text" />
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148 </param>
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149 <param name="marker_list" label="List of Gene Markers" type="data" format="txt,tabular"
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150 optional="true"
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151 help="A single column of marker genes" />
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152 </repeat>
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153 </when>
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154 </conditional>
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155 </inputs>
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156 <outputs>
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157 <data name="out_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF Plots" />
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158 <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: Cell Proportions by Sample" >
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159 <filter>do["method"] == "dendrogram" and len(do["cluster_groups"]) > 0</filter>
0
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160 </data>
1
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161 <collection name="props" type="list" label="${tool.name} on ${on_string}: Proportion Matrices" >
0
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162 <filter>do["method"] == "estimateprops"</filter>
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163 <discover_datasets pattern="prop_(?P&lt;designation&gt;.+)\.tabular" format="tabular" directory="report_data" />
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164 </collection>
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165 <collection name="summaries" type="list" label="${tool.name} on ${on_string}: Summaries and Logs">
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166 <filter>do["method"] == "estimateprops"</filter>
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167 <discover_datasets pattern="summ_(?P&lt;designation&gt;.+)\.txt" format="txt" directory="report_data" />
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168 <discover_datasets pattern="varprop_(?P&lt;designation&gt;.+)\.tabular" format="tabular" directory="report_data" />
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
169 <discover_datasets pattern="rsquared_(?P&lt;designation&gt;.+)\.tabular" format="tabular" directory="report_data" />
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
170 <discover_datasets pattern="weightgene_(?P&lt;designation&gt;.+)\.tabular" format="tabular" directory="report_data" />
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
171 </collection>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
172 </outputs>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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173 <tests>
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
174 <test expect_num_outputs="1" >
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
175 <!-- Dendrogram test 1 -->
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
176 <param name="bulk_eset" value="Mousebulkeset.rds" />
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
177 <param name="scrna_eset" value="Mousesubeset.degenesonly2.half.rds" />
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
178 <conditional name="do" >
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
179 <param name="method" value="dendrogram" />
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
180 <param name="celltypes_label" value="cellType" />
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
181 <param name="samples_label" value="sampleID" />
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
182 <param name="celltypes" value="Endo,Podo,PT,LOH,DCT,CD-PC,CD-IC,Fib,Macro,Neutro,B lymph,T lymph,NK" />
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
183 </conditional>
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
184 <output name="out_pdf" value="dendro_1.pdf" compare="sim_size" />
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
185 </test>
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
186 <test expect_num_outputs="2" >
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
187 <!-- Dendrogram test 2 -->
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
188 <param name="bulk_eset" value="Mousebulkeset.rds" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
189 <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"
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parents:
diff changeset
190 <conditional name="do" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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parents:
diff changeset
191 <param name="method" value="dendrogram" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
192 <param name="celltypes_label" value="cellType" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
193 <param name="samples_label" value="sampleID" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
194 <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"
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diff changeset
195 <repeat name="cluster_groups" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
196 <param name="cluster_id" value="C1" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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197 <param name="celltypes" value="Neutro" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
198 </repeat>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
199 <repeat name="cluster_groups" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
200 <param name="cluster_id" value="C2" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
201 <param name="celltypes" value="Podo" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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parents:
diff changeset
202 </repeat>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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parents:
diff changeset
203 <repeat name="cluster_groups" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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204 <param name="cluster_id" value="C3" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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parents:
diff changeset
205 <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"
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diff changeset
206 <param name="marker_name" value="Epithelial" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
207 <param name="marker_list" value="epith.markers" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
208 </repeat>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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parents:
diff changeset
209 <repeat name="cluster_groups" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
210 <param name="cluster_id" value="C4" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
211 <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"
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diff changeset
212 <param name="marker_name" value="Immune" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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diff changeset
213 <param name="marker_list" value="immune.markers" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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214 </repeat>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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215 </conditional>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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216 <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"
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diff changeset
217 <output name="out_tab">
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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218 <assert_contents>
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
219 <has_text_matching expression="^\s+Neutro\s+Podo\s+Endo" />
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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220 <has_text text="APOL1.GNA78M"/>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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221 </assert_contents>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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222 </output>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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223 </test>
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
224 <test expect_num_outputs="3" >
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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225 <!-- Estimate Proportions test -->
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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226 <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"
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diff changeset
227 <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"
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228 <conditional name="do" >
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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229 <param name="method" value="estimateprops" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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230 <param name="celltypes_label" value="cellType" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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231 <param name="samples_label" value="sampleID" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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232 <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"
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233 <param name="phenotype_factors" value="age,bmi,hba1c,gender" />
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
234 <param name="phenotype_target" value="hba1c" />
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
235 <param name="phenotype_target_threshold" value="6.5" />
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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236 <param name="sample_disease_group" value="T2D" />
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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237 <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"
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238 <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"
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239 </conditional>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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240 <output name="out_pdf" value="default_output.pdf" compare="sim_size" />
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
241 <output_collection name="summaries" count="5">
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
242 <element name="Log of MuSiC fitting" ftype="txt">
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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243 <assert_contents>
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
244 <has_text text="Residual standard error: 0.1704 on 72 degrees of freedom"/>
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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245 </assert_contents>
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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246 </element>
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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diff changeset
247 <element name="Log of NNLS fitting" ftype="txt">
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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248 <assert_contents>
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
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parents: 0
diff changeset
249 <has_text text="Residual standard error: 0.0645 on 72 degrees of freedom"/>
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
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250 </assert_contents>
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251 </element>
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252 </output_collection>
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253 </test>
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254 </tests>
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255 <help><![CDATA[
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256 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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257
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258 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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259
1
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260 .. image:: $PATH_TO_IMAGES/FigureMethod.jpg
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261
0
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262 ]]></help>
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263 <citations>
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264 <citation type="doi">https://doi.org/10.1038/s41467-018-08023-x</citation>
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265 </citations>
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266 </tool>