Mercurial > repos > iuc > raceid_trajectory
comparison raceid_trajectory.xml @ 0:ff7cd3c7c1df draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
author | iuc |
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date | Thu, 22 Nov 2018 04:43:00 -0500 |
parents | |
children | 3e5bb16abb55 |
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-1:000000000000 | 0:ff7cd3c7c1df |
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1 <tool id="raceid_trajectory" name="Lineage computation using StemID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" > | |
2 <description>generates lineage from prior clustering</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 <import>macros_trajectory.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <version_command><![CDATA[ | |
9 Rscript '$__tool_directory__/scripts/pseudotemporal.R' @GET_VERSION@ | |
10 ]]></version_command> | |
11 | |
12 <command detect_errors="exit_code"><![CDATA[ | |
13 #set bin = 'pseudotemporal.R' | |
14 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog' | |
15 ]]></command> | |
16 | |
17 <configfiles> | |
18 <configfile name="userconf" ><![CDATA[ | |
19 @STRING2VECTOR@ | |
20 | |
21 @TRAJECTORY_CHEETAH@ | |
22 ]]> | |
23 </configfile> | |
24 </configfiles> | |
25 <inputs> | |
26 <expand macro="trajectory_inputs" /> | |
27 <param name="use_log" type="boolean" checked="false" label="Output Log?" /> | |
28 </inputs> | |
29 <outputs> | |
30 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> | |
31 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" /> | |
32 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > | |
33 <filter>use_log</filter> | |
34 </data> | |
35 </outputs> | |
36 <tests> | |
37 <expand macro="trajectory_tests" /> | |
38 </tests> | |
39 <help><![CDATA[ | |
40 StemID2 | |
41 ========= | |
42 | |
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. | |
44 | |
45 In a nutshell, StemID infers links between clusters which are more populated with intermediate single-cell transcriptomes than expected by chance. | |
46 | |
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. | |
48 | |
49 | |
50 ]]></help> | |
51 <expand macro="citations" /> | |
52 </tool> | |
53 |