Mercurial > repos > iuc > raceid_trajectory
comparison raceid_trajectory.xml @ 8:c92d0f9338c5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 455bad7eca54164f95755174904842907846bb42"
author | iuc |
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date | Mon, 20 Dec 2021 10:13:20 +0000 |
parents | e93b008c637a |
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7:e93b008c637a | 8:c92d0f9338c5 |
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1 <tool id="raceid_trajectory" name="Lineage computation using StemID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > | 1 <tool id="raceid_trajectory" name="Lineage computation using StemID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
2 <description>generates lineage from prior clustering</description> | 2 <description>generates lineage from prior clustering</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 <import>macros_cheetah.xml</import> | 5 <import>macros_cheetah.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
8 <expand macro="version_command_config" prog="pseudotemporal.R" cheetah="TRAJECTORY_CHEETAH" /> | 8 <expand macro="version_command_config" prog="pseudotemporal.R" cheetah="TRAJECTORY_CHEETAH" /> |
9 | 9 |
10 <inputs> | 10 <inputs> |
11 <param name="inputrds" type="data" format="rdata" label="Input RDS" help="This is the output RData file given by the Cluster stage" /> | 11 <param name="inputrds" type="data" format="rds" label="Input RDS" help="This is the output RDS file given by the Cluster stage" /> |
12 <section name="projcell" title="Compute transcriptome entropy of each cell" expanded="true" > | 12 <section name="projcell" title="Compute transcriptome entropy of each cell" expanded="true" > |
13 <param name="knn" type="integer" min="0" value="3" label="KNN" help="Number of nearest neighbours to consider." /> | 13 <param name="knn" type="integer" min="0" value="3" label="KNN" help="Number of nearest neighbours to consider." /> |
14 <param name="cthr" type="integer" min="0" value="5" label="Cluster Threshold" help="Clusters to be included in the StemID analysis must have more than this number of cells" /> | 14 <param name="cthr" type="integer" min="0" value="5" label="Cluster Threshold" help="Clusters to be included in the StemID analysis must have more than this number of cells" /> |
15 <expand macro="use_defaults_no" > | 15 <expand macro="use_defaults_no" > |
16 <param name="nmode" type="boolean" checked="true" label="Neighbour Mode" help="Assign a cell of a given cluster to the cluster with the smallest average distance of the knn nearest neighbours within this cluster." /> | 16 <param name="nmode" type="boolean" checked="true" label="Neighbour Mode" help="Assign a cell of a given cluster to the cluster with the smallest average distance of the knn nearest neighbours within this cluster." /> |
42 </section> | 42 </section> |
43 <param name="use_log" type="boolean" checked="false" label="Output Log?" /> | 43 <param name="use_log" type="boolean" checked="false" label="Output Log?" /> |
44 </inputs> | 44 </inputs> |
45 <outputs> | 45 <outputs> |
46 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> | 46 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> |
47 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" /> | 47 <data name="outrdat" format="rds" label="${tool.name} on ${on_string}: RDS" /> |
48 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > | 48 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > |
49 <filter>use_log</filter> | 49 <filter>use_log</filter> |
50 </data> | 50 </data> |
51 </outputs> | 51 </outputs> |
52 <tests> | 52 <tests> |