Mercurial > repos > iuc > raceid_inspectclusters
comparison raceid_inspectclusters.xml @ 4:20f522154663 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author | iuc |
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date | Mon, 12 Aug 2019 13:01:12 -0400 |
parents | 9fec5dd8fbb9 |
children | 41f34e925bd5 |
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3:0fa80752a314 | 4:20f522154663 |
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1 <tool id="raceid_inspectclusters" name="Cluster Inspection using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" > | 1 <tool id="raceid_inspectclusters" name="Cluster Inspection using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" > |
2 <description>examines gene expression within clusters</description> | 2 <description>examines gene expression within clusters</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 <import>macros_inspectclusters.xml</import> | 5 <import>macros_cheetah.xml</import> |
6 <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" > | |
7 <section name="@SECTIONNAME@" title="@SECTIONTITLE@" expanded="true" > | |
8 <param name="name_set" type="text" optional="true" label="Name of Set" > | |
9 <!-- Aname, Bname --> | |
10 <expand macro="sanitize_title" /> | |
11 </param> | |
12 <conditional name="meth" > | |
13 <param name="type" type="select" label="Selection method" > | |
14 <option value="cln" selected="true">Cluster Numbers</option> | |
15 <option value="regex" >Regular Expression</option> | |
16 <option value="manual" >Manual Selection</option> | |
17 </param> | |
18 <when value="cln" > | |
19 <param name="selector" type="text" value="" label="List of clusters" help="Clusters should be listed delimited by commas (e.g. 3,4,5)" > | |
20 <expand macro="sanitize_numeric_vector" /> | |
21 </param> | |
22 </when> | |
23 <when value="regex" > | |
24 <param name="selector" type="text" value="" label="Regular Expression to select gene names" > | |
25 <expand macro="sanitize_regex" /> | |
26 </param> | |
27 </when> | |
28 <when value="manual" > | |
29 <param name="selector" type="text" value="" label="List of genes" > | |
30 <expand macro="sanitize_string_vector" /> | |
31 </param> | |
32 </when> | |
33 </conditional> | |
34 </section> | |
35 </macro> | |
6 </macros> | 36 </macros> |
7 <expand macro="requirements" /> | 37 <expand macro="requirements" /> |
8 <version_command><![CDATA[ | 38 <expand macro="version_command_config" prog="clusterinspect.R" cheetah="INSPECTCLUSTERS_CHEETAH" out="&> '$outlog'" /> |
9 Rscript '$__tool_directory__/scripts/clusterinspect.R' @GET_VERSION@ | |
10 ]]></version_command> | |
11 | |
12 <command detect_errors="exit_code"><![CDATA[ | |
13 #set bin = 'clusterinspect.R' | |
14 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog' | |
15 ]]></command> | |
16 | |
17 <configfiles> | |
18 <configfile name="userconf" ><![CDATA[ | |
19 @STRING2VECTOR@ | |
20 | |
21 @INSPECTCLUSTERS_CHEETAH@ | |
22 ]]> | |
23 </configfile> | |
24 </configfiles> | |
25 <inputs> | 39 <inputs> |
26 <expand macro="inspectclusters_inputs" /> | 40 <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the cluster analysis" /> |
41 <conditional name="plotgen"> | |
42 <param name="do_opt" type="select" label="Plot Clusters?" help="Generates tSNE and F-R plots" > | |
43 <option value="yes" selected="true" >Yes</option> | |
44 <option value="no" >No</option> | |
45 </param> | |
46 <when value="no" /> | |
47 <when value="yes" > | |
48 <param name="clusts_plot" type="text" label="Cluster Numbers to plot" value="" help="Leave blank to plot all clusters" optional="true" > | |
49 <expand macro="sanitize_numeric_vector" /> | |
50 </param> | |
51 </when> | |
52 </conditional> | |
53 <conditional name="plotsym" > | |
54 <param name="do_opt" type="select" label="Perform Subset Analysis?" > | |
55 <expand macro="yesno_checkedno" /> | |
56 </param> | |
57 <when value="no" /> | |
58 <when value="yes"> | |
59 <param name="types_regex" type="text" optional="true" label="Types Regex (removal)" help="Regular expression to be used to remove portions of the cell names, in order to indicate cell type. e.g. if your cells are labelled as 'cdk5_1, cdk5_2, glow_1, glow_2', then a regex of '_\\d$' would trim off the ends and set the cell types to 'cdk5, cdk5, glow, glow'. " > | |
60 <expand macro="sanitize_regex" /> | |
61 </param> | |
62 <expand macro="use_defaults_no" > | |
63 <param name="subset_regex" type="text" optional="true" label="Subset of Types: Regex (select)" help="Regular expression to be used to select for cell types of interest. e.g. if we are only interested in 'cdk5' positive cells, then we would simply put 'cdk5' here. "> | |
64 <expand macro="sanitize_regex" /> | |
65 </param> | |
66 <param name="fr" type="boolean" checked="false" label="Output FR map instead of tSNE" help="Performs a Fruchterman-Rheingold projection instead of tSNE" /> | |
67 </expand> | |
68 </when> | |
69 </conditional> | |
70 <conditional name="gois" > | |
71 <param name="do_opt" type="select" label="Examine Genes of Interest" > | |
72 <expand macro="yesno_checkedno" /> | |
73 </param> | |
74 <when value="no" /> | |
75 <when value="yes"> | |
76 <param name="inspect_goi_genes" type="text" value="" label="Genes to Examine" > | |
77 <expand macro="sanitize_string_vector" /> | |
78 </param> | |
79 <param name="inspect_goi_cells" type="text" optional="true" label="Cells to Examine" help="Leave blank to examine all" ><!-- "":NULL --> | |
80 <expand macro="sanitize_string_vector" /> | |
81 </param> | |
82 <expand macro="use_defaults_no" > | |
83 <!-- Yes, examine genes of interest, but no do not use defaults... --> | |
84 <param name="inspect_goi_imputed" type="boolean" checked="false" label="Impute Genes" help="Only works if k-nearest neighbours was used in the clustering" /> | |
85 <param name="plotexp_n" type="text" optional="true" label="Title of plot" help="If blank, the list of genes are used" > | |
86 <expand macro="sanitize_title" /> | |
87 </param> | |
88 <param name="plotmarkg_cthr" type="integer" min="0" value="0" label="Cluster Threshold" help="Include only clusters with cells greater than this" /> | |
89 <param name="plotmarkg_cl" type="text" optional="true" label="Cluster List" help="List of cluster numbers to include. Leave blank to include all" > | |
90 <expand macro="sanitize_numeric_vector" /> | |
91 </param><!-- "":NULL --> | |
92 <param name="plotmarkg_order_cells" type="boolean" checked="false" label="Order Cells" help="Order heatmap by cell names, not by cluster" /> | |
93 <param name="plotmarkg_aggr" type="boolean" checked="false" label="Average Expression" help="Show only average expression for each cluster" /> | |
94 <param name="plotmarkg_norm" type="boolean" checked="false" label="Normalise Gene Expression " help="Normalise gene expression to 1 to depict genes on the same scale" /> | |
95 <param name="plotmarkg_flo" type="integer" max="-5" optional="true" label="Lower-bound for Gene Expression" /><!-- negative or null vals only for this seem to work--> | |
96 <param name="plotmarkg_cap" type="integer" min="1" optional="true" label="Upper-bound for Gene Expression" /> | |
97 <param name="plotmarkg_samples" type="text" optional="true" label="Regex to Select Sample Names For Each cell" > | |
98 <expand macro="sanitize_regex" /> | |
99 </param> | |
100 <param name="plotmarkg_cluster_cols" type="boolean" checked="false" label="Cluster columns" /> | |
101 <param name="plotmarkg_cluster_rows" type="boolean" checked="true" label="Cluster rows" /> | |
102 <param name="plotmarkg_cluster_set" type="boolean" checked="false" label="Order Clusters by Heirarchal Clustering of Cluster Medoids." /> | |
103 </expand> | |
104 </when> | |
105 </conditional> | |
106 <conditional name="diffgtest" > | |
107 <param name="do_opt" type="select" label="Differential Gene Testing" > | |
108 <expand macro="yesno_checkedno" /> | |
109 </param> | |
110 <when value="no" /> | |
111 <when value="yes" > | |
112 <expand macro="select_cells" sectionname="set_a" sectiontitle="Cells in Set A" /> | |
113 <expand macro="select_cells" sectionname="set_b" sectiontitle="Cells in Set B" /> | |
114 <expand macro="use_defaults_no" > | |
115 <param name="plotdiffg_pthr" type="float" min="0" max="1" value="0.05" label="P-value cutoff" help="Cutoff for displaying differentially expressed genes" /> | |
116 <param name="plotdiffg_padj" type="boolean" checked="true" label="Apply B-H Correction" help="Display genes with a Benjamini-Hochberg corrected false discovery rate lower than the above P-value threshold" /> | |
117 <param name="plotdiffg_lthr" type="float" min="0" value="0" label="Log2-Fold Threshold" help="Differentially expressed genes are displayed only for log2 fold-changes higher than this" /> | |
118 <param name="plotdiffg_mthr" type="float" optional="true" label="Log2 Mean Threshold" help="Differentially expressed genes are displayed only for log2 mean expression greater than this" /><!-- opt:-Inf --> | |
119 <param name="plotdiffg_show_names" type="boolean" checked="false" label="Display Gene Names" /> | |
120 </expand> | |
121 </when> | |
122 </conditional> | |
27 </inputs> | 123 </inputs> |
28 | |
29 <outputs> | 124 <outputs> |
30 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> | 125 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> |
31 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > | 126 <data name="outlog" format="txt" hidden="true" /><!-- useful for debugging, but hide from user --> |
32 <filter>use_log</filter> | |
33 </data> | |
34 </outputs> | 127 </outputs> |
35 <tests> | 128 <tests> |
36 <expand macro="inspectclusters_tests" /> | 129 <test><!-- general plots, plotgen --> |
130 <param name="inputrds" value="out_cluster_default.rdat" /> | |
131 <conditional name="plotgen" > | |
132 <param name="do_opt" value="yes" /> | |
133 </conditional> | |
134 <output name="outpdf" value="out_cluster_general_default.pdf" lines_diff="30" /> | |
135 </test> | |
136 <test><!-- general plots, plotgen with cluster 1,8,5 only --> | |
137 <param name="inputrds" value="out_cluster_default.rdat" /> | |
138 <conditional name="plotgen" > | |
139 <param name="do_opt" value="yes" /> | |
140 <param name="clusts_plot" value="1,8,5" /> | |
141 </conditional> | |
142 <output name="outpdf" value="out_cluster_general_default.pdf" lines_diff="30" /> | |
143 </test> | |
144 <test><!-- default test, plotsym --> | |
145 <param name="inputrds" value="out_cluster_default.rdat" /> | |
146 <conditional name="plotsym" > | |
147 <param name="do_opt" value="yes" /> | |
148 <param name="types_regex" value="\\_\\d+" /> | |
149 <expand macro="test_nondef" > | |
150 <param name="subset_regex" value="IV|V" /> | |
151 </expand> | |
152 </conditional> | |
153 <conditional name="gois" > | |
154 <param name="do_opt" value="yes" /> | |
155 <param name="inspect_goi_genes" value="Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5" /> | |
156 </conditional> | |
157 <output name="outpdf" value="out_cluster_inspect_default.pdf" lines_diff="30" /> | |
158 </test> | |
159 <test><!-- Advanced 1 --> | |
160 <param name="inputrds" value="out_cluster_default.rdat" /> | |
161 <conditional name="plotsym" > | |
162 <param name="do_opt" value="yes" /> | |
163 <param name="types_regex" value="\\_\\d+" /> | |
164 <expand macro="test_nondef" > | |
165 <param name="subset_regex" value="IV|V" /> | |
166 <param name="fr" value="true" /> | |
167 </expand> | |
168 </conditional> | |
169 <conditional name="gois" > | |
170 <param name="do_opt" value="yes" /> | |
171 <param name="inspect_goi_genes" value="Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5" /> | |
172 <expand macro="test_nondef" > | |
173 <param name="inspect_goi_imputed" value="false" /> | |
174 <param name="plotexp_n" value="Test Title" /> | |
175 <param name="plotmarkg_order_cells" value="true" /> | |
176 <param name="plotmarkg_aggr" value="true" /> | |
177 <param name="plotmarkg_norm" value="true" /> | |
178 <param name="plotmarkg_flo" value="-10" /> | |
179 <param name="plotmarkg_cap" value="100" /> | |
180 <param name="plotmarkg_samples" value="(\\_\\d+)$" /> | |
181 <param name="plotmarkg_cluster_cols" value="true" /> | |
182 <param name="plotmarkg_cluster_rows" value="false" /> | |
183 <param name="plotmarkg_cluster_set" value="true" /> | |
184 </expand> | |
185 </conditional> | |
186 <conditional name="diffgtest" > | |
187 <param name="do_opt" value="yes" /> | |
188 <section name="set_a" > | |
189 <param name="name_set" value="Test set A" /> | |
190 <conditional name="meth" > | |
191 <param name="type" value="regex" /> | |
192 <param name="selector" value="^V5.*" /> | |
193 </conditional> | |
194 </section> | |
195 <section name="set_b" > | |
196 <param name="name_set" value="Test set B" /> | |
197 <conditional name="meth" > | |
198 <param name="type" value="manual" /> | |
199 <param name="selector" value="I5d_3,I5d_4,I5d_6,I5d_8,I5d_9,I5d_10,I5d_11,I5d_12,I5d_13,I5d_14" /> | |
200 </conditional> | |
201 </section> | |
202 <expand macro="test_nondef" > | |
203 <param name="plotdiffg_pthr" value="0.1" /> | |
204 <param name="plotdiffg_padj" value="false" /> | |
205 <param name="plotdiffg_lthr" value="0.2" /> | |
206 <param name="plotdiffg_mthr" value="0.2" /> | |
207 <param name="plotdiffg_show_names" value="true" /> | |
208 </expand> | |
209 </conditional> | |
210 <output name="outpdf" value="out_cluster_inspect_advanced1.pdf" lines_diff="30"/> | |
211 </test> | |
212 <test><!-- Advanced 2 --> | |
213 <param name="inputrds" value="out_cluster_default.rdat" /> | |
214 <conditional name="plotsym" > | |
215 <param name="do_opt" value="yes" /> | |
216 <expand macro="test_nondef" > | |
217 <param name="fr" value="false" /> | |
218 </expand> | |
219 </conditional> | |
220 <conditional name="gois" > | |
221 <param name="do_opt" value="yes" /> | |
222 <param name="inspect_goi_genes" value="Sp1,Spc24,Spcs1,Spcs2,Spcs3" /> | |
223 <expand macro="test_nondef" > | |
224 <param name="plotexp_n" value="Test Title 2" /> | |
225 <param name="plotmarkg_order_cells" value="true" /> | |
226 <param name="plotmarkg_aggr" value="true" /> | |
227 <param name="plotmarkg_norm" value="false" /> | |
228 <param name="plotmarkg_flo" value="-10" /> | |
229 <param name="plotmarkg_cap" value="10" /> | |
230 <param name="plotmarkg_cluster_cols" value="true" /> | |
231 <param name="plotmarkg_cluster_rows" value="true" /> | |
232 <param name="plotmarkg_cluster_set" value="true" /> | |
233 </expand> | |
234 </conditional> | |
235 <conditional name="diffgtest" > | |
236 <param name="do_opt" value="yes" /> | |
237 <section name="set_a" > | |
238 <param name="name_set" value="Test set A" /> | |
239 <conditional name="meth" > | |
240 <param name="type" value="regex" /> | |
241 <param name="selector" value="^IV.*" /> | |
242 </conditional> | |
243 </section> | |
244 <section name="set_b" > | |
245 <param name="name_set" value="Test set B" /> | |
246 <conditional name="meth" > | |
247 <param name="type" value="cln" /> | |
248 <param name="selector" value="3" /> | |
249 </conditional> | |
250 </section> | |
251 <expand macro="test_nondef" > | |
252 <param name="plotdiffg_pthr" value="0.8" /> | |
253 <param name="plotdiffg_padj" value="true" /> | |
254 <param name="plotdiffg_lthr" value="0.8" /> | |
255 <param name="plotdiffg_mthr" value="0.8" /> | |
256 <param name="plotdiffg_show_names" value="false" /> | |
257 </expand> | |
258 </conditional> | |
259 <output name="outpdf" value="out_cluster_inspect_advanced2.pdf" lines_diff="30"/> | |
260 </test> | |
261 <test><!-- Advanced 3 --> | |
262 <param name="inputrds" value="out_cluster_default.rdat" /> | |
263 <conditional name="plotsym" > | |
264 <param name="do_opt" value="no" /> | |
265 </conditional> | |
266 <conditional name="gois" > | |
267 <param name="do_opt" value="no" /> | |
268 </conditional> | |
269 <conditional name="diffgtest" > | |
270 <param name="do_opt" value="yes" /> | |
271 <section name="set_a" > | |
272 <param name="name_set" value="Test set A" /> | |
273 <conditional name="meth" > | |
274 <param name="type" value="cln" /> | |
275 <param name="selector" value="1,2" /> | |
276 </conditional> | |
277 </section> | |
278 <section name="set_b" > | |
279 <param name="name_set" value="Test set B" /> | |
280 <conditional name="meth" > | |
281 <param name="type" value="cln" /> | |
282 <param name="selector" value="3,4,6" /> | |
283 </conditional> | |
284 </section> | |
285 </conditional> | |
286 <output name="outpdf" value="out_diffgene_multiple.pdf" lines_diff="30"/> | |
287 </test> | |
37 </tests> | 288 </tests> |
38 <help><![CDATA[ | 289 <help><![CDATA[ |
39 | 290 |
40 RaceID3 | 291 RaceID3 |
41 ========= | 292 ========= |
48 | 299 |
49 * Plot All Clusters: | 300 * Plot All Clusters: |
50 * Produces a tSNE of all clusters, as well as a force-directed Fruchterman-Reingold (F-R) layout which may have tidier plots. | 301 * Produces a tSNE of all clusters, as well as a force-directed Fruchterman-Reingold (F-R) layout which may have tidier plots. |
51 * Perform Subset Analysis: | 302 * Perform Subset Analysis: |
52 * tSNE and F-R plots with cells whose name match the specified regex highlighted | 303 * tSNE and F-R plots with cells whose name match the specified regex highlighted |
53 | 304 |
54 * Examine Genes of Interest: | 305 * Examine Genes of Interest: |
55 * Expression plots highlighting a gene or genes of interest across all clusters | 306 * Expression plots highlighting a gene or genes of interest across all clusters |
56 | 307 |
57 * Differential Gene Testing: | 308 * Differential Gene Testing: |
58 * Examining the expression between | 309 * Examining the expression between |
59 | 310 |
60 * A list of the most differentially expressed genes in each cluster | 311 * A list of the most differentially expressed genes in each cluster |
61 * An output PDF that provides heatmaps for: | 312 * An output PDF that provides heatmaps for: |
62 * The initial and final clustering (as determined using random forest) | 313 * The initial and final clustering (as determined using random forest) |
63 * Heatmaps for each of the most differentially expressed genes in each cluster | 314 * Heatmaps for each of the most differentially expressed genes in each cluster |