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
date Thu, 22 Nov 2018 04:45:41 -0500
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-1:000000000000 0:9fec5dd8fbb9
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>