Mercurial > repos > iuc > raceid_inspectclusters

annotate macros_trajectory.xml @ 3:0fa80752a314 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit d94b3b8a4c7cf8c604279eb1eea24d32b3868922
author iuc
date Mon, 15 Apr 2019 17:55:46 -0400
parents 9fec5dd8fbb9
children
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9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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1 <macros>
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2 <macro name="trajectory_inputs" >
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3 <param name="inputrds" type="data" format="rdata" label="Input RDS" help="This is the output RData file given by the Cluster stage" />
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4 <section name="projcell" title="Compute transcriptome entropy of each cell" expanded="true" >
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5 <param name="knn" type="integer" min="0" value="3" label="KNN" help="Number of nearest neighbours to consider." />
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6 <param name="cthr" type="integer" min="0" value="5" label="Cluster Threshold" help="Clusters to be included in the StemID analysis must have more than this number of cells" />
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7 <expand macro="use_defaults_no" >
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8 <param name="nmode" type="boolean" checked="true" label="Neighbour Mode" help="Assign a cell of a given cluster to the cluster with the smallest average distance of the knn nearest neighbours within this cluster." />
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9 <param name="fr" type="boolean" checked="false" label="F-R layout?" help="Use Fruchterman-Rheigold layout instead of t-SNE" />
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10 </expand>
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11 </section>
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12 <section name="projback" title="Compute Cell Projections for Randomized Background Distribution" expanded="true" >
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13 <param name="pdishuf" type="integer" min="100" value="2000" label="Shuffle Projections" help="Number of randomizations of cell positions for which to compute projections of cells on inter-cluster links" />
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14 <expand macro="use_defaults_no" >
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15 <param name="fast" type="boolean" checked="false" label="Use a fast approximate background model to infer links" />
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16 <param name="rseed" type="integer" value="17000" label="Random seed" />
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17 </expand>
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18 </section>
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19 <section name="comppval" title="Computing P-values for Link Significance" expanded="true" >
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20 <param name="pthr" type="float" value="0.01" label="P-value cutoff" help="Cutoff for link significance. This threshold is applied for the calculation of link scores reflecting how uniformly a link is occupied by cells." />
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21 <param name="sensitive" type="boolean" checked="false" label="Sensitivity" help="All cells on the most highly significant link are and the link itself are disregard to test significance of the remaining links with a binomial p-value" />
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22 </section>
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23 <section name="plotgraph" title="StemID2 Lineage Graph" expanded="true" >
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24 <param name="showcells" type="boolean" checked="false" label="Show Cells" help="Projections of cells are shown in the plot" />
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25 <param name="scthr" type="float" min="0" max="1" value="0" label="Score Threshold" help="Score threshold for links to be shown in the graph" />
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26 <expand macro="use_defaults_no">
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27 <param name="showtsne" type="boolean" checked="true" label="Show tSNE" help="Show transparent t-SNE map of cells in the background" />
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28 <param name="tp" type="float" min="0" max="1" value="0.5" label="Transparency" help="Level of transparency of t-SNE map" />
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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29 </expand>
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30 </section>
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31 <section name="compscore" title="Compute StemID2 score" expanded="true" >
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32 <param name="nn" type="integer" min="0" value="1" label="Number of Neighbours" help="Number of higher order neighbours to be included for the determination of links" />
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33 <param name="scthr" type="float" min="0" max="1" value="0" label="Score Threshold" help="Score threshold for links to be included in the calculation" />
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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34 </section>
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35 </macro>
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36 <macro name="trajectory_tests" >
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37 <test>
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38 <!-- All defaults -->
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39 <param name="inputrds" value="out_cluster_default.rdat" />
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40 <output name="outpdf" value="out_traject_default.pdf" compare="sim_size" delta="15" />
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41 <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="15" />
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42 </test>
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43 <test>
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44 <!-- Manually specify the defaults: should ideally give same output as above test -->
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45 <param name="inputrds" value="out_cluster_default.rdat" />
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46 <section name="projcell" >
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47 <param name="knn" value="3" />
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48 <param name="cthr" value="5" />
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49 <expand macro="test_nondef" >
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50 <param name="nmode" value="true" />
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51 <param name="fr" value="false" />
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52 </expand>
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53 </section>
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54 <section name="projback" >
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55 <param name="pdishuf" value="2000" />
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56 <expand macro="test_nondef" >
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57 <param name="fast" value="false" />
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58 <param name="rseed" value="17000" />
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59 </expand>
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60 </section>
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61 <section name="comppval" >
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62 <param name="pthr" value="0.01" />
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63 <param name="sensitive" value="false" />
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64 </section>
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65 <section name="plotgraph" >
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66 <param name="showcells" value="false" />
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67 <param name="scthr" value="0" />
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68 <expand macro="test_nondef" >
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69 <param name="showtsne" value="true" />
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70 <param name="tp" value="0.5" />
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71 </expand>
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72 </section>
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73 <section name="compscore" >
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74 <param name="nn" value="1" />
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75 <param name="scthr" value="0" />
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76 </section>
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77 <output name="outpdf" value="out_traject_default.pdf" compare="sim_size" delta="15" />
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78 <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="15" />
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79 </test>
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80 <test>
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81 <!-- Non-defaults -->
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82 <param name="inputrds" value="out_cluster_default.rdat" />
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83 <section name="projcell">
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84 <param name="knn" value="4" />
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85 <param name="cthr" value="4" />
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86 <expand macro="test_nondef" >
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87 <param name="nmode" value="false" />
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88 <param name="fr" value="true" />
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89 </expand>
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90 </section>
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91 <section name="projback">
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92 <param name="pdishuf" value="1500" />
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93 <expand macro="test_nondef" >
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94 <param name="fast" value="true" />
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95 <param name="rseed" value="1500" />
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96 </expand>
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97 </section>
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98 <section name="comppval">
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99 <param name="pthr" value="0.05" />
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100 <param name="sensitive" value="true" />
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101 </section>
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102 <section name="plotgraph">
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103 <param name="showcells" value="true" />
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104 <param name="scthr" value="0.5" />
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105 <expand macro="test_nondef" >
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106 <param name="showtsne" value="false" />
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107 <param name="tp" value="0.25" />
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108 </expand>
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109 </section>
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110 <section name="compscore">
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111 <param name="nn" value="2" />
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112 <param name="scthr" value="0.5" />
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113 </section>
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114 <output name="outpdf" value="out_traject_adv_nondef.pdf" compare="sim_size" delta="15" />
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115 </test>
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116 </macro>
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117 <token name="@TRAJECTORY_CHEETAH@"><![CDATA[
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118
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119 in.rdat = readRDS('${inputrds}')
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120
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121 pstc.projc = formals(projcells)
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122 pstc.projc\$knn = as.integer( '$projcell.knn' )
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123 pstc.projc\$cthr = as.integer( '$projcell.cthr' )
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124 #if str($projcell.use.def) == "no":
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125 pstc.projc\$nmode = as.logical( '$projcell.use.nmode' )
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126 pstc.projc\$fr = as.logical( '$projcell.use.fr' )
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127 #end if
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128
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129 pstc.projb = formals(projback)
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130 pstc.projb\$pdishuf = as.integer( '$projback.pdishuf' )
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131 #if str($projback.use.def) == "no":
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132 pstc.projb\$fast = as.logical( '$projback.use.fast' )
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133 pstc.projb\$rseed = as.integer( '$projback.use.rseed' )
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134 #end if
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135
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136 pstc.comppval = formals(comppvalue)
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137 pstc.comppval\$pthr = as.numeric( '$comppval.pthr' )
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138 pstc.comppval\$sensitive = as.logical( '$comppval.sensitive' )
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139
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140 pstc.plotgraph = formals(plotgraph)
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141 pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' )
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142 pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' )
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143 #if str($plotgraph.use.def) == "no":
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144 pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' )
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145 pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' )
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146 #end if
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147
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148 pstc.compscore = formals(compscore)
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149 pstc.compscore\$nn = as.integer( '$compscore.nn' )
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150 pstc.compscore\$scthr = as.numeric( '$compscore.scthr' )
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151
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152 out.pdf='${outpdf}'
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153 out.rdat='${outrdat}'
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154 ]]>
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155 </token>
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156 </macros>