Mercurial > repos > iuc > raceid_inspecttrajectory

comparison macros_inspecttrajectories.xml @ 0:e0e9b24d76aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
author iuc
date Thu, 22 Nov 2018 04:42:18 -0500
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-1:000000000000 0:e0e9b24d76aa
1 <macros>
2 <macro name="inspecttrajectories_inputs" >
3 <param name="inputrds" type="data" format="rdata" label="Input RDS" help="Requires the RDS output from the trajectory analysis" />
4 <section name="trjsid" title="StemID Branch Link Examine" expanded="true" help="StemID derives cell lineage trees and predicts multipotent cell identities">
5 <conditional name="basic" >
6 <param name="doit" type="select" label="Perform StemID?" >
7 <expand macro="yesno_checkedno" />
8 </param>
9 <when value="no" />
10 <when value="yes" >
11 <param name="i" type="integer" min="1" value="1" label="Cluster Number" />
12 <param name="br" type="text" label="Trajectory Path i, j, k" help="A path of three clusters starting at i, passing through j, and ending at k." >
13 <expand macro="sanitize_numeric_vector" />
14 </param>
15 <expand macro="use_defaults_no">
16 <param name="zscore" type="boolean" checked="false" label="Plot Z-score Transformed Projections" />
17 <param name="ndiffgenes" type="integer" min="1" value="10" label="Number of DE Genes" help="Number of differentially expressed genes to output per cluster" />
18 </expand>
19 </when>
20 </conditional>
21 </section>
22 <section name="trjfid" title="FateID Branch Link Examine" expanded="true" help="FateID infers cell fate bias in multipotent progenitor cells" >
23 <conditional name="basic" >
24 <param name="doit" type="select" label="Perform FateID?" >
25 <expand macro="yesno_checkedno" />
26 </param>
27 <when value="no" />
28 <when value="yes" >
29 <param name="cellsfromz" type="text" value="" label="Cells from Clusters" help="Vector of valid cluster numbers ordered along the trajectory" >
30 <expand macro="sanitize_numeric_vector" />
31 </param>
32 <expand macro="use_defaults_no">
33 <param name="filterset_minexpr" type="integer" min="0" value="2" label="Min Expression" help="Minimum expression required for at least minnumber cells" />
34 <param name="filterset_minnumber" type="integer" min="0" value="1" label="Min Number of Cells" help="Minimum number of cells in which a gene needs to be expressed at least a level of minexpr."/>
35 <param name="getsom_nb" type="integer" min="1" value="1000" label="SOM Nodes" help="Number of nodes of the self-organizing map." />
36 <param name="getsom_alpha" type="float" min="0" value="0.5" label="Smoothing parameter" help="Pseudo-temporal expression profiles are derived by a local regression of expression values across the ordered cells using the function 'loess' from the package 'stats'. This is the parameter, which controls the degree of smoothing. Larger values return smoother profiles." />
37 <param name="procsom_corthr" type="float" min="0" max="1" value="0.85" label="Correlation threshold" help="The z-score of the average normalized pseudo-temporal expression profiles within each node of the self-organizing map is computed, and the correlation of these z-scores between neighbouring nodes is computed. If the correlation is greater than 'corthr', neighbouring nodes are merged" />
38 <param name="procsom_minsom" type="integer" min="0" value="3" label="Min SOM" help="Nodes of the self-organizing map with less than this number of transcripts are discarded" />
39 <param name="plotheat_xgrid" type="boolean" checked="false" label="Partitioning along the x-axis" />
40 <param name="plotheat_ygrid" type="boolean" checked="false" label="Partitioning along the y-axis" />
41 <param name="plotheat_xlab" type="boolean" checked="false" label="Average position is given for each partition along the x-axis" />
42 </expand>
43 <conditional name="som" >
44 <param name="doit" type="select" label="Perform Additional FateID Analysis with Self-Organised Map?" >
45 <expand macro="yesno_checkedno" />
46 </param>
47 <when value="no" />
48 <when value="yes" >
49 <conditional name="use_genes" >
50 <param name="typer" type="select" label="Genes to Inspect" >
51 <option value="genelist">List of Genes</option>
52 <option value="cln">Cluster</option>
53 </param>
54 <when value="genelist">
55 <param name="use_genes" type="text" value="" label="Gene List" >
56 <expand macro="sanitize_string_vector" />
57 </param>
58 </when>
59 <when value="cln" >
60 <param name="use_genes" type="integer" min="1" value="1" label="Cluster Number" />
61 </when>
62 </conditional>
63 <param name="use_types" type="text" value="\\_\\d+" label="Types Regex (select)" help="Regex to select types across cell names" >
64 <expand macro="sanitize_regex" />
65 </param>
66 <param name="title" type="text" value="Title" label="Plot title" />
67 <expand macro="use_defaults_no">
68 <param name="cluster" type="boolean" checked="false" label="Partitioning along the x-axis" />
69 <param name="alpha" type="float" min="0" max="1" value="0.5" label="Smoothing parameter" />
70 </expand>
71 </when>
72 </conditional>
73 </when>
74 </conditional>
75 </section>
76 </macro>
77 <macro name="inspecttrajectories_tests" >
78 <test>
79 <!-- default, generates a blank report -->
80 <param name="inputrds" value="out_traject_default.ltree.rdat" />
81 <output name="outpdf" value="out_traject_inspect_default.ltree.blank.pdf" compare="sim_size" delta="15" />
82 </test>
83 <test>
84 <!-- stemID branch inspection: vignette search "getproj" -->
85 <param name="inputrds" value="out_traject_default.ltree.rdat" />
86 <section name="trjsid" >
87 <conditional name="basic" >
88 <param name="doit" value="yes" />
89 <param name="i" value="3" />
90 <param name="br" value="1,3,8" />
91 </conditional>
92 </section>
93 <output name="outpdf" value="out_traject_inspect_stemid.pdf" compare="sim_size" delta="15" />
94 <output name="outdiffgenes" value="out_traject_inspect_stemid.tabular" />
95 </test>
96 <test>
97 <!-- fateID trajectory inspection: vignette search "cellsfromtree" -->
98 <param name="inputrds" value="out_traject_default.ltree.rdat" />
99 <section name="trjfid" >
100 <conditional name="basic" >
101 <param name="doit" value="yes" />
102 <param name="cellsfromz" value="2,1,4" />
103 <expand macro="test_nondef" >
104 <param name="filterset_minexpr" value="2" />
105 <param name="getsom_nb" value="1000" />
106 <param name="getsom_alpha" value="0.5" />
107 <param name="plotheat_xlab" value="true" />
108 </expand>
109 </conditional>
110 </section>
111 <output name="outpdf" value="out_traject_inspect_fateid.pdf" compare="sim_size" delta="15" />
112 </test>
113 <test>
114 <!-- fateID trajectory inspection with som: vignette search "SOM" -->
115 <param name="inputrds" value="out_traject_default.ltree.rdat" />
116 <section name="trjfid" >
117 <conditional name="basic" >
118 <param name="doit" value="yes" />
119 <param name="cellsfromz" value="2,1,4" />
120 <conditional name="som" >
121 <param name="doit" value="yes" />
122 <expand macro="test_nondef" >
123 <param name="typer" value="cln" />
124 <param name="use_genes" value="12" />
125 </expand>
126 </conditional>
127 </conditional>
128 </section>
129 <output name="outpdf" value="out_traject_inspect_fateid_som.pdf" compare="sim_size" delta="15" />
130 </test>
131 <test>
132 <!-- uses all 3 sections with additional non-default params -->
133 <param name="inputrds" value="out_traject_default.ltree.rdat" />
134 <section name="trjsid" >
135 <conditional name="basic" >
136 <param name="doit" value="yes" />
137 <param name="i" value="5" />
138 <param name="br" value="6,5,3" />
139 <expand macro="test_nondef" >
140 <param name="zscore" value="true" />
141 <param name="ndiffgenes" value="14" />
142 </expand>
143 </conditional>
144 </section>
145 <section name="trjfid" >
146 <conditional name="basic" >
147 <param name="doit" value="yes" />
148 <param name="cellsfromz" value="3,9,2" />
149 <expand macro="test_nondef" >
150 <param name="filterset_minexpr" value="1" />
151 <param name="filterset_minnumber" value="2" />
152 <param name="procsom_minsom" value="5" />
153 <param name="procsom_corthr" value="0.5" />
154 <param name="plotheat_ygrid" value="true" />
155 </expand>
156 <conditional name="som" >
157 <param name="doit" value="yes" />
158 <conditional name="use_genes" >
159 <param name="typer" value="genelist" />
160 <param name="use_genes" value="Clca4,Mki67,Defa24,Ybx1,Vasp,Apoa1" />
161 <expand macro="test_nondef" >
162 <param name="cluster" value="true" />
163 <param name="alpha" value="0.1" />
164 </expand>
165 </conditional>
166 </conditional>
167 </conditional>
168 </section>
169 <output name="outdiffgenes" value="out_traject_inspect_allthree.tabular" />
170 <output name="outpdf" value="out_traject_inspect_allthree.pdf" compare="sim_size" delta="15" />
171 </test>
172 </macro>
173 <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[
174 in.rdat = readRDS('${inputrds}')
175
176 perform.stemID = FALSE
177 perform.fateID = FALSE
178 perform.fateID.sominspect = FALSE
179
180 #if str($trjsid.basic.doit) == "yes"
181 perform.stemID = TRUE
182 trjsid.getproj = formals(getproj)
183
184 trjsid.numdiffgenes = 10
185 trjsid.getproj\$i = as.integer( '$trjsid.basic.i' )
186 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' )
187
188 #if str($trjsid.basic.use.def) == "no":
189
190 trjsid.getproj\$zscore = as.logical( '$trjsid.basic.use.zscore' )
191 trjsid.numdiffgenes = as.integer( '$trjsid.basic.use.ndiffgenes' )
192
193 #end if
194 #end if
195
196 #if str($trjfid.basic.doit) == "yes":
197 perform.fateID = TRUE
198 trjfid.cellsfrom = formals(cellsfromtree)
199 trjfid.filterset = formals(filterset)
200 trjfid.getsom = formals(getsom)
201 trjfid.procsom = formals(procsom)
202 trjfid.plotheat = list()
203
204 trjfid.cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' )
205 #if str($trjfid.basic.use.def) == "no":
206
207 trjfid.filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' )
208 trjfid.filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' )
209 trjfid.getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' )
210 trjfid.getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' )
211 trjfid.procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' )
212 trjfid.procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' )
213 trjfid.plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' )
214 trjfid.plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' )
215 trjfid.plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' )
216 #end if
217
218 #if str($trjfid.basic.som.doit) == "yes":
219 perform.fateID.sominspect = TRUE
220
221 trjfidsomi = list()
222 #if str($trjfid.basic.som.use_genes.typer) == "genelist":
223 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' )
224 #else if str($trjfid.basic.som.use_genes.typer) == "cln":
225 trjfidsomi.use.genes = as.integer( '$trjfid.basic.som.use_genes.use_genes' )
226 #end if
227
228 trjfidsomi.use.types = '$trjfid.basic.som.use_types'
229 trjfidsomi\$name = '$trjfid.basic.som.title'
230
231 #if str($trjfid.basic.som.use.def) == "no":
232 trjfidsomi\$cluster = as.logical( '$trjfid.basic.som.use.cluster' )
233 trjfidsomi\$alpha = as.numeric( '$trjfid.basic.som.use.alpha' )
234 #end if
235 #end if
236 #end if
237
238 out.pdf = '${outpdf}'
239 out.diffgenes = '${outdiffgenes}'
240
241 ]]>
242 </token>
243 </macros>