Mercurial > repos > iuc > raceid_trajectory
view raceid_trajectory.xml @ 6:72979cac22b2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
author | iuc |
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date | Thu, 15 Apr 2021 19:00:04 +0000 |
parents | 3e5bb16abb55 |
children | e93b008c637a |
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<tool id="raceid_trajectory" name="Lineage computation using StemID" version="@VERSION_RACEID@+galaxy@VERSION_WRAPPER@" > <description>generates lineage from prior clustering</description> <macros> <import>macros.xml</import> <import>macros_cheetah.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command_config" prog="pseudotemporal.R" cheetah="TRAJECTORY_CHEETAH" /> <inputs> <param name="inputrds" type="data" format="rdata" label="Input RDS" help="This is the output RData file given by the Cluster stage" /> <section name="projcell" title="Compute transcriptome entropy of each cell" expanded="true" > <param name="knn" type="integer" min="0" value="3" label="KNN" help="Number of nearest neighbours to consider." /> <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" /> <expand macro="use_defaults_no" > <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." /> <param name="fr" type="boolean" checked="false" label="F-R layout?" help="Use Fruchterman-Rheigold layout instead of t-SNE" /> </expand> </section> <section name="projback" title="Compute Cell Projections for Randomized Background Distribution" expanded="true" > <param name="pdishuf" type="integer" min="100" value="2000" label="Shuffle Projections" help="Number of randomizations of cell positions for which to compute projections of cells on inter-cluster links" /> <expand macro="use_defaults_no" > <param name="fast" type="boolean" checked="false" label="Use a fast approximate background model to infer links" /> <param name="rseed" type="integer" value="17000" label="Random seed" /> </expand> </section> <section name="comppval" title="Computing P-values for Link Significance" expanded="true" > <param name="pthr" type="float" value="0.01" label="P-value cutoff" help="Cutoff for link significance. This threshold is applied for the calculation of link scores reflecting how uniformly a link is occupied by cells." /> <param name="sensitive" type="boolean" checked="false" label="Sensitivity" help="All cells on the most highly significant link are and the link itself are disregard to test significance of the remaining links with a binomial p-value" /> </section> <section name="plotgraph" title="StemID2 Lineage Graph" expanded="true" > <param name="showcells" type="boolean" checked="false" label="Show Cells" help="Projections of cells are shown in the plot" /> <param name="scthr" type="float" min="0" max="1" value="0" label="Score Threshold" help="Score threshold for links to be shown in the graph" /> <expand macro="use_defaults_no"> <!-- <param name="showtsne" type="boolean" checked="true" label="Show tSNE" help="Show transparent t-SNE map of cells in the background" /> --> <param name="tp" type="float" min="0" max="1" value="0.5" label="Transparency" help="Level of transparency of t-SNE map" /> </expand> </section> <section name="compscore" title="Compute StemID2 score" expanded="true" > <param name="nn" type="integer" min="0" value="1" label="Number of Neighbours" help="Number of higher order neighbours to be included for the determination of links" /> <param name="scthr" type="float" min="0" max="1" value="0" label="Score Threshold" help="Score threshold for links to be included in the calculation" /> </section> <param name="use_log" type="boolean" checked="false" label="Output Log?" /> </inputs> <outputs> <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" /> <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > <filter>use_log</filter> </data> </outputs> <tests> <test> <!-- All defaults --> <param name="inputrds" value="out_cluster_default.rdat" /> <output name="outpdf" value="out_traject_default.pdf" compare="sim_size" delta="15" /> <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="500" /> </test> <test> <!-- Manually specify the defaults: should ideally give same output as above test --> <param name="inputrds" value="out_cluster_default.rdat" /> <section name="projcell" > <param name="knn" value="3" /> <param name="cthr" value="5" /> <expand macro="test_nondef" > <param name="nmode" value="true" /> <param name="fr" value="false" /> </expand> </section> <section name="projback" > <param name="pdishuf" value="2000" /> <expand macro="test_nondef" > <param name="fast" value="false" /> <param name="rseed" value="17000" /> </expand> </section> <section name="comppval" > <param name="pthr" value="0.01" /> <param name="sensitive" value="false" /> </section> <section name="plotgraph" > <param name="showcells" value="false" /> <param name="scthr" value="0" /> <expand macro="test_nondef" > <!-- <param name="showtsne" value="true" /> --> <param name="tp" value="0.5" /> </expand> </section> <section name="compscore" > <param name="nn" value="1" /> <param name="scthr" value="0" /> </section> <output name="outpdf" value="out_traject_default.pdf" compare="sim_size" delta="500" /> <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="500" /> </test> <test> <!-- Non-defaults --> <param name="inputrds" value="out_cluster_default.rdat" /> <section name="projcell"> <param name="knn" value="4" /> <param name="cthr" value="4" /> <expand macro="test_nondef" > <param name="nmode" value="false" /> <param name="fr" value="true" /> </expand> </section> <section name="projback"> <param name="pdishuf" value="1500" /> <expand macro="test_nondef" > <param name="fast" value="true" /> <param name="rseed" value="1500" /> </expand> </section> <section name="comppval"> <param name="pthr" value="0.05" /> <param name="sensitive" value="true" /> </section> <section name="plotgraph"> <param name="showcells" value="true" /> <param name="scthr" value="0.5" /> <expand macro="test_nondef" > <!-- <param name="showtsne" value="false" /> --> <param name="tp" value="0.25" /> </expand> </section> <section name="compscore"> <param name="nn" value="2" /> <param name="scthr" value="0.5" /> </section> <output name="outpdf" value="out_traject_adv_nondef.pdf" compare="sim_size" delta="500" /> </test> </tests> <help><![CDATA[ StemID2 ========= 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. In a nutshell, StemID infers links between clusters which are more populated with intermediate single-cell transcriptomes than expected by chance. 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. ]]></help> <expand macro="citations" /> </tool>