Mercurial > repos > iuc > raceid_inspecttrajectory

comparison raceid_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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children 86e2358cf273
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-1:000000000000 0:e0e9b24d76aa
1 <tool id="raceid_inspecttrajectory" name="Lineage Branch Analysis using StemID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
2 <description>inspects branches of a lineage tree</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>macros_inspecttrajectories.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <version_command><![CDATA[
9 Rscript '$__tool_directory__/scripts/trajectoryinspect.R' @GET_VERSION@
10 ]]></version_command>
11
12 <command detect_errors="exit_code"><![CDATA[
13 #set bin = 'trajectoryinspect.R'
14 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
15 ]]></command>
16
17 <configfiles>
18 <configfile name="userconf" ><![CDATA[
19 @STRING2VECTOR@
20
21 @INSPECTTRAJECTORIES_CHEETAH@
22 ]]>
23 </configfile>
24 </configfiles>
25
26 <inputs>
27 <expand macro="inspecttrajectories_inputs" />
28 </inputs>
29
30 <outputs>
31 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
32 <data name="outdiffgenes" format="tabular" label="${tool.name} on ${on_string}: TrajectoryInspect - Differential Genes" >
33 <filter>trjsid['basic']['doit'] == "yes"</filter>
34 </data>
35 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
36 <filter>use_log</filter>
37 </data>
38
39 </outputs>
40 <tests>
41 <expand macro="inspecttrajectories_tests" />
42 </tests>
43 <help><![CDATA[
44 StemID2 and FateID
45 =====================
46
47 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.
48
49 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.
50
51 For more information on the different types cluster and trajectory inspection that can be performed, please consult the RaceID vignette_.
52
53 .. _vignette: https://github.com/dgrun/RaceID3_StemID2_package/blob/master/vignettes/RaceID.Rmd
54
55 ]]></help>
56 <expand macro="citations" />
57 </tool>