annotate raceid_trajectory.xml @ 1:30d9118a650a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 71e6b205841c83391ea8fc69e10eac03f212f4d6
author iuc
date Thu, 28 Feb 2019 12:59:30 -0500
parents ff7cd3c7c1df
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ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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1 <tool id="raceid_trajectory" name="Lineage computation using StemID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
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2 <description>generates lineage from prior clustering</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>macros_trajectory.xml</import>
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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 '$__tool_directory__/scripts/pseudotemporal.R' @GET_VERSION@
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10 ]]></version_command>
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11
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12 <command detect_errors="exit_code"><![CDATA[
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13 #set bin = 'pseudotemporal.R'
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14 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
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15 ]]></command>
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16
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17 <configfiles>
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18 <configfile name="userconf" ><![CDATA[
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19 @STRING2VECTOR@
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20
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21 @TRAJECTORY_CHEETAH@
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22 ]]>
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23 </configfile>
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24 </configfiles>
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25 <inputs>
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26 <expand macro="trajectory_inputs" />
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27 <param name="use_log" type="boolean" checked="false" label="Output Log?" />
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28 </inputs>
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29 <outputs>
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30 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
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31 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
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32 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
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33 <filter>use_log</filter>
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34 </data>
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35 </outputs>
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36 <tests>
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37 <expand macro="trajectory_tests" />
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38 </tests>
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39 <help><![CDATA[
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40 StemID2
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41 =========
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43 StemID is an algorithm for the inference of lineage trees and differentiation trajectories based on pseudo-temporal ordering of single-cell transcriptomes. It utilizies the clusters predicted by RaceID clustering tool.
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45 In a nutshell, StemID infers links between clusters which are more populated with intermediate single-cell transcriptomes than expected by chance.
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47 This will generate an RDS object, and a PDF showing a minimal spanning tree between the clusters, with the strength between clusters given by the colour and thickness of the branches.
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49
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50 ]]></help>
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51 <expand macro="citations" />
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52 </tool>
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53