Mercurial > repos > iuc > raceid_inspecttrajectory

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
author iuc
date Tue, 05 Nov 2024 16:33:56 +0000
parents df8e4e54d367
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1 <tool id="raceid_inspecttrajectory" name="Lineage Branch Analysis using StemID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>inspects branches of a lineage tree</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>macros_cheetah.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements" />
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9 <expand macro="version_command_config" prog="trajectoryinspect.R" cheetah="INSPECTTRAJECTORIES_CHEETAH" />
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10 <inputs>
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11 <param name="inputrds" type="data" format="rds" label="Input RDS" help="Requires the RDS output from the trajectory analysis" />
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12 <section name="trjsid" title="StemID Branch Link Examine" expanded="true" help="StemID derives cell lineage trees and predicts multipotent cell identities">
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13 <conditional name="basic" >
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14 <param name="doit" type="select" label="Perform StemID?" >
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15 <expand macro="yesno_checkedno" />
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16 </param>
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17 <when value="no" />
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18 <when value="yes" >
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19 <param name="i" type="integer" min="1" value="1" label="Cluster Number" />
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20 <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." >
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21 <expand macro="sanitize_numeric_vector" />
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22 </param>
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23 <expand macro="use_defaults_no">
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24 <param name="zscore" type="boolean" checked="false" label="Plot Z-score Transformed Projections" />
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25 <param name="ndiffgenes" type="integer" min="1" value="10" label="Number of DE Genes" help="Number of differentially expressed genes to output per cluster" />
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26 </expand>
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27 </when>
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28 </conditional>
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29 </section>
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30 <section name="trjfid" title="FateID Branch Link Examine" expanded="true" help="FateID infers cell fate bias in multipotent progenitor cells" >
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31 <conditional name="basic" >
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32 <param name="doit" type="select" label="Perform FateID?" >
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33 <expand macro="yesno_checkedno" />
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34 </param>
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35 <when value="no" />
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36 <when value="yes" >
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37 <param name="cellsfromz" type="text" value="" label="Cells from Clusters" help="Vector of valid cluster numbers ordered along the trajectory" >
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38 <expand macro="sanitize_numeric_vector" />
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39 </param>
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40 <expand macro="use_defaults_no">
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41 <param name="filterset_minexpr" type="integer" min="0" value="2" label="Min Expression" help="Minimum expression required for at least minnumber cells" />
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42 <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."/>
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43 <param name="getsom_nb" type="integer" min="1" value="1000" label="SOM Nodes" help="Number of nodes of the self-organizing map." />
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44 <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." />
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45 <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" />
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46 <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" />
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47 <param name="plotheat_xgrid" type="boolean" checked="false" label="Partitioning along the x-axis" />
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48 <param name="plotheat_ygrid" type="boolean" checked="false" label="Partitioning along the y-axis" />
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49 <param name="plotheat_xlab" type="boolean" checked="false" label="Average position is given for each partition along the x-axis" />
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50 </expand>
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51 <conditional name="som" >
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52 <param name="doit" type="select" label="Perform Additional FateID Analysis with Self-Organised Map?" >
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53 <expand macro="yesno_checkedno" />
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54 </param>
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55 <when value="no" />
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56 <when value="yes" >
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57 <conditional name="use_genes" >
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58 <param name="typer" type="select" label="Genes to Inspect" >
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59 <option value="genelist">List of Genes</option>
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60 <option value="cln">Cluster</option>
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61 </param>
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62 <when value="genelist">
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63 <param name="use_genes" type="text" value="" label="Gene List" >
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64 <expand macro="sanitize_string_vector" />
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65 </param>
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66 </when>
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67 <when value="cln" >
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68 <param name="use_genes" type="integer" min="1" value="1" label="Cluster Number" />
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69 </when>
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70 </conditional>
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71 <param name="use_types" type="text" value="\\_\\d+" label="Types Regex (select)" help="Regex to select types across cell names" >
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72 <expand macro="sanitize_regex" />
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73 </param>
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74 <param name="title" type="text" value="Title" label="Plot title" />
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75 <expand macro="use_defaults_no">
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76 <param name="cluster" type="boolean" checked="false" label="Partitioning along the x-axis" />
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77 <param name="alpha" type="float" min="0" max="1" value="0.5" label="Smoothing parameter" />
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78 </expand>
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79 </when>
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80 </conditional>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
81 </when>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
82 </conditional>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
83 </section>
0
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
84 </inputs>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
85
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
86 <outputs>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
87 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
88 <data name="outdiffgenes" format="tabular" label="${tool.name} on ${on_string}: TrajectoryInspect - Differential Genes" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
89 <filter>trjsid['basic']['doit'] == "yes"</filter>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
90 </data>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
91 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
92 <filter>use_log</filter>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
93 </data>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
94 </outputs>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
95 <tests>
4
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
96 <test>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
97 <!-- default, generates a blank report -->
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
98 <param name="inputrds" value="out_traject_default.ltree.rdat" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
99 <output name="outpdf" value="out_traject_inspect_default.ltree.blank.pdf" compare="sim_size" delta="15" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
100 </test>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
101 <test>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
102 <!-- stemID branch inspection: vignette search "getproj" -->
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
103 <param name="inputrds" value="out_traject_default.ltree.rdat" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
104 <section name="trjsid" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
105 <conditional name="basic" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
106 <param name="doit" value="yes" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
107 <param name="i" value="3" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
108 <param name="br" value="1,3,8" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
109 </conditional>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
110 </section>
6
c8434a623268 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents: 4
diff changeset
111 <output name="outpdf" value="out_traject_inspect_stemid.pdf" compare="sim_size" delta="500" />
4
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
112 <output name="outdiffgenes" value="out_traject_inspect_stemid.tabular" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
113 </test>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
114 <test>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
115 <!-- fateID trajectory inspection: vignette search "cellsfromtree" -->
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
116 <param name="inputrds" value="out_traject_default.ltree.rdat" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
117 <section name="trjfid" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
118 <conditional name="basic" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
119 <param name="doit" value="yes" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
120 <param name="cellsfromz" value="2,1,4" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
121 <expand macro="test_nondef" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
122 <param name="filterset_minexpr" value="2" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
123 <param name="getsom_nb" value="1000" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
124 <param name="getsom_alpha" value="0.5" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
125 <param name="plotheat_xlab" value="true" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
126 </expand>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
127 </conditional>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
128 </section>
6
c8434a623268 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents: 4
diff changeset
129 <output name="outpdf" value="out_traject_inspect_fateid.pdf" compare="sim_size" delta="500" />
4
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
130 </test>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
131 <test>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
132 <!-- fateID trajectory inspection with som: vignette search "SOM" -->
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
133 <param name="inputrds" value="out_traject_default.ltree.rdat" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
134 <section name="trjfid" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
135 <conditional name="basic" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
136 <param name="doit" value="yes" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
137 <param name="cellsfromz" value="2,1,4" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
138 <conditional name="som" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
139 <param name="doit" value="yes" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
140 <expand macro="test_nondef" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
141 <param name="typer" value="cln" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
142 <param name="use_genes" value="12" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
143 </expand>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
144 </conditional>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
145 </conditional>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
146 </section>
6
c8434a623268 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents: 4
diff changeset
147 <output name="outpdf" value="out_traject_inspect_fateid_som.pdf" compare="sim_size" delta="500" />
4
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
148 </test>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
149 <test>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
150 <!-- uses all 3 sections with additional non-default params -->
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
151 <param name="inputrds" value="out_traject_default.ltree.rdat" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
152 <section name="trjsid" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
153 <conditional name="basic" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
154 <param name="doit" value="yes" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
155 <param name="i" value="5" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
156 <param name="br" value="6,5,3" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
157 <expand macro="test_nondef" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
158 <param name="zscore" value="true" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
159 <param name="ndiffgenes" value="14" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
160 </expand>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
161 </conditional>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
162 </section>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
163 <section name="trjfid" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
164 <conditional name="basic" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
165 <param name="doit" value="yes" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
166 <param name="cellsfromz" value="3,9,2" />
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
167 <expand macro="test_nondef" >
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
168 <param name="filterset_minexpr" value="1" />
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169 <param name="filterset_minnumber" value="2" />
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170 <param name="procsom_minsom" value="5" />
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171 <param name="procsom_corthr" value="0.5" />
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172 <param name="plotheat_ygrid" value="true" />
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173 </expand>
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174 <conditional name="som" >
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175 <param name="doit" value="yes" />
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176 <conditional name="use_genes" >
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177 <param name="typer" value="genelist" />
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178 <param name="use_genes" value="Clca4,Mki67,Defa24,Ybx1,Vasp,Apoa1" />
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179 <expand macro="test_nondef" >
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180 <param name="cluster" value="true" />
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181 <param name="alpha" value="0.1" />
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182 </expand>
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183 </conditional>
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184 </conditional>
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185 </conditional>
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186 </section>
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187 <output name="outdiffgenes" value="out_traject_inspect_allthree.tabular" />
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188 <output name="outpdf" value="out_traject_inspect_allthree.pdf" compare="sim_size" delta="500" />
4
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189 </test>
0
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190 </tests>
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191 <help><![CDATA[
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192 StemID2 and FateID
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193 =====================
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194
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195 Given a previous lineage tree generated an RDS file generated from the previous Trajectory step, we can explore the variation of gene expression for all cells that lie on a given branch or trajectory.
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196
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197 This will generate a PDF containing a heatmap of expression for all neighboring clusters that share links with cluster 5, as well as a plot of all cells along the branches between 1 to 3 and 3 to 10. A table of the most differentially expressed genes across these projection will also be output, which will provide a more qualitative assessment of how signficant our Apoa-expressing genes are along this projection.
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198
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199 For more information on the different types cluster and trajectory inspection that can be performed, please consult the RaceID vignette_.
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200
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201 .. _vignette: https://github.com/dgrun/RaceID3_StemID2_package/blob/master/vignettes/RaceID.Rmd
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202
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203 ]]></help>
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204 <expand macro="citations" />
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205 </tool>