Mercurial > repos > iuc > raceid_inspectclusters
comparison macros_trajectory.xml @ 0:9fec5dd8fbb9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
author | iuc |
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date | Thu, 22 Nov 2018 04:45:41 -0500 |
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-1:000000000000 | 0:9fec5dd8fbb9 |
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1 <macros> | |
2 <macro name="trajectory_inputs" > | |
3 <param name="inputrds" type="data" format="rdata" label="Input RDS" help="This is the output RData file given by the Cluster stage" /> | |
4 <section name="projcell" title="Compute transcriptome entropy of each cell" expanded="true" > | |
5 <param name="knn" type="integer" min="0" value="3" label="KNN" help="Number of nearest neighbours to consider." /> | |
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" /> | |
7 <expand macro="use_defaults_no" > | |
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." /> | |
9 <param name="fr" type="boolean" checked="false" label="F-R layout?" help="Use Fruchterman-Rheigold layout instead of t-SNE" /> | |
10 </expand> | |
11 </section> | |
12 <section name="projback" title="Compute Cell Projections for Randomized Background Distribution" expanded="true" > | |
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" /> | |
14 <expand macro="use_defaults_no" > | |
15 <param name="fast" type="boolean" checked="false" label="Use a fast approximate background model to infer links" /> | |
16 <param name="rseed" type="integer" value="17000" label="Random seed" /> | |
17 </expand> | |
18 </section> | |
19 <section name="comppval" title="Computing P-values for Link Significance" expanded="true" > | |
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." /> | |
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" /> | |
22 </section> | |
23 <section name="plotgraph" title="StemID2 Lineage Graph" expanded="true" > | |
24 <param name="showcells" type="boolean" checked="false" label="Show Cells" help="Projections of cells are shown in the plot" /> | |
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" /> | |
26 <expand macro="use_defaults_no"> | |
27 <param name="showtsne" type="boolean" checked="true" label="Show tSNE" help="Show transparent t-SNE map of cells in the background" /> | |
28 <param name="tp" type="float" min="0" max="1" value="0.5" label="Transparency" help="Level of transparency of t-SNE map" /> | |
29 </expand> | |
30 </section> | |
31 <section name="compscore" title="Compute StemID2 score" expanded="true" > | |
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" /> | |
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" /> | |
34 </section> | |
35 </macro> | |
36 <macro name="trajectory_tests" > | |
37 <test> | |
38 <!-- All defaults --> | |
39 <param name="inputrds" value="out_cluster_default.rdat" /> | |
40 <output name="outpdf" value="out_traject_default.pdf" compare="sim_size" delta="15" /> | |
41 <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="15" /> | |
42 </test> | |
43 <test> | |
44 <!-- Manually specify the defaults: should ideally give same output as above test --> | |
45 <param name="inputrds" value="out_cluster_default.rdat" /> | |
46 <section name="projcell" > | |
47 <param name="knn" value="3" /> | |
48 <param name="cthr" value="5" /> | |
49 <expand macro="test_nondef" > | |
50 <param name="nmode" value="true" /> | |
51 <param name="fr" value="false" /> | |
52 </expand> | |
53 </section> | |
54 <section name="projback" > | |
55 <param name="pdishuf" value="2000" /> | |
56 <expand macro="test_nondef" > | |
57 <param name="fast" value="false" /> | |
58 <param name="rseed" value="17000" /> | |
59 </expand> | |
60 </section> | |
61 <section name="comppval" > | |
62 <param name="pthr" value="0.01" /> | |
63 <param name="sensitive" value="false" /> | |
64 </section> | |
65 <section name="plotgraph" > | |
66 <param name="showcells" value="false" /> | |
67 <param name="scthr" value="0" /> | |
68 <expand macro="test_nondef" > | |
69 <param name="showtsne" value="true" /> | |
70 <param name="tp" value="0.5" /> | |
71 </expand> | |
72 </section> | |
73 <section name="compscore" > | |
74 <param name="nn" value="1" /> | |
75 <param name="scthr" value="0" /> | |
76 </section> | |
77 <output name="outpdf" value="out_traject_default.pdf" compare="sim_size" delta="15" /> | |
78 <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="15" /> | |
79 </test> | |
80 <test> | |
81 <!-- Non-defaults --> | |
82 <param name="inputrds" value="out_cluster_default.rdat" /> | |
83 <section name="projcell"> | |
84 <param name="knn" value="4" /> | |
85 <param name="cthr" value="4" /> | |
86 <expand macro="test_nondef" > | |
87 <param name="nmode" value="false" /> | |
88 <param name="fr" value="true" /> | |
89 </expand> | |
90 </section> | |
91 <section name="projback"> | |
92 <param name="pdishuf" value="1500" /> | |
93 <expand macro="test_nondef" > | |
94 <param name="fast" value="true" /> | |
95 <param name="rseed" value="1500" /> | |
96 </expand> | |
97 </section> | |
98 <section name="comppval"> | |
99 <param name="pthr" value="0.05" /> | |
100 <param name="sensitive" value="true" /> | |
101 </section> | |
102 <section name="plotgraph"> | |
103 <param name="showcells" value="true" /> | |
104 <param name="scthr" value="0.5" /> | |
105 <expand macro="test_nondef" > | |
106 <param name="showtsne" value="false" /> | |
107 <param name="tp" value="0.25" /> | |
108 </expand> | |
109 </section> | |
110 <section name="compscore"> | |
111 <param name="nn" value="2" /> | |
112 <param name="scthr" value="0.5" /> | |
113 </section> | |
114 <output name="outpdf" value="out_traject_adv_nondef.pdf" compare="sim_size" delta="15" /> | |
115 </test> | |
116 </macro> | |
117 <token name="@TRAJECTORY_CHEETAH@"><![CDATA[ | |
118 | |
119 in.rdat = readRDS('${inputrds}') | |
120 | |
121 pstc.projc = formals(projcells) | |
122 pstc.projc\$knn = as.integer( '$projcell.knn' ) | |
123 pstc.projc\$cthr = as.integer( '$projcell.cthr' ) | |
124 #if str($projcell.use.def) == "no": | |
125 pstc.projc\$nmode = as.logical( '$projcell.use.nmode' ) | |
126 pstc.projc\$fr = as.logical( '$projcell.use.fr' ) | |
127 #end if | |
128 | |
129 pstc.projb = formals(projback) | |
130 pstc.projb\$pdishuf = as.integer( '$projback.pdishuf' ) | |
131 #if str($projback.use.def) == "no": | |
132 pstc.projb\$fast = as.logical( '$projback.use.fast' ) | |
133 pstc.projb\$rseed = as.integer( '$projback.use.rseed' ) | |
134 #end if | |
135 | |
136 pstc.comppval = formals(comppvalue) | |
137 pstc.comppval\$pthr = as.numeric( '$comppval.pthr' ) | |
138 pstc.comppval\$sensitive = as.logical( '$comppval.sensitive' ) | |
139 | |
140 pstc.plotgraph = formals(plotgraph) | |
141 pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' ) | |
142 pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' ) | |
143 #if str($plotgraph.use.def) == "no": | |
144 pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' ) | |
145 pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' ) | |
146 #end if | |
147 | |
148 pstc.compscore = formals(compscore) | |
149 pstc.compscore\$nn = as.integer( '$compscore.nn' ) | |
150 pstc.compscore\$scthr = as.numeric( '$compscore.scthr' ) | |
151 | |
152 out.pdf='${outpdf}' | |
153 out.rdat='${outrdat}' | |
154 ]]> | |
155 </token> | |
156 </macros> |