Mercurial > repos > iuc > raceid_inspecttrajectory

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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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e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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1 <tool id="raceid_inspecttrajectory" name="Lineage Branch Analysis using StemID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
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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_inspecttrajectories.xml</import>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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6 </macros>
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7 <expand macro="requirements" />
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8 <version_command><![CDATA[
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9 Rscript '$__tool_directory__/scripts/trajectoryinspect.R' @GET_VERSION@
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10 ]]></version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 #set bin = 'trajectoryinspect.R'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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14 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
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15 ]]></command>
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17 <configfiles>
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18 <configfile name="userconf" ><![CDATA[
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19 @STRING2VECTOR@
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21 @INSPECTTRAJECTORIES_CHEETAH@
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22 ]]>
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23 </configfile>
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24 </configfiles>
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26 <inputs>
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27 <expand macro="inspecttrajectories_inputs" />
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28 </inputs>
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30 <outputs>
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31 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
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32 <data name="outdiffgenes" format="tabular" label="${tool.name} on ${on_string}: TrajectoryInspect - Differential Genes" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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33 <filter>trjsid['basic']['doit'] == "yes"</filter>
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34 </data>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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35 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
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36 <filter>use_log</filter>
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37 </data>
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39 </outputs>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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40 <tests>
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41 <expand macro="inspecttrajectories_tests" />
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42 </tests>
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43 <help><![CDATA[
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44 StemID2 and FateID
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45 =====================
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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.
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48
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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.
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51 For more information on the different types cluster and trajectory inspection that can be performed, please consult the RaceID vignette_.
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53 .. _vignette: https://github.com/dgrun/RaceID3_StemID2_package/blob/master/vignettes/RaceID.Rmd
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54
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55 ]]></help>
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56 <expand macro="citations" />
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57 </tool>