Mercurial > repos > iuc > raceid_clustering
diff macros_trajectory.xml @ 0:4ea021bd7513 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 04:43:57 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_trajectory.xml Thu Nov 22 04:43:57 2018 -0500 @@ -0,0 +1,156 @@ +<macros> + <macro name="trajectory_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> + </macro> + <macro name="trajectory_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="15" /> + </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="15" /> + <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="15" /> + </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="15" /> + </test> + </macro> + <token name="@TRAJECTORY_CHEETAH@"><![CDATA[ + +in.rdat = readRDS('${inputrds}') + +pstc.projc = formals(projcells) +pstc.projc\$knn = as.integer( '$projcell.knn' ) +pstc.projc\$cthr = as.integer( '$projcell.cthr' ) +#if str($projcell.use.def) == "no": +pstc.projc\$nmode = as.logical( '$projcell.use.nmode' ) +pstc.projc\$fr = as.logical( '$projcell.use.fr' ) +#end if + +pstc.projb = formals(projback) +pstc.projb\$pdishuf = as.integer( '$projback.pdishuf' ) +#if str($projback.use.def) == "no": +pstc.projb\$fast = as.logical( '$projback.use.fast' ) +pstc.projb\$rseed = as.integer( '$projback.use.rseed' ) +#end if + +pstc.comppval = formals(comppvalue) +pstc.comppval\$pthr = as.numeric( '$comppval.pthr' ) +pstc.comppval\$sensitive = as.logical( '$comppval.sensitive' ) + +pstc.plotgraph = formals(plotgraph) +pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' ) +pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' ) +#if str($plotgraph.use.def) == "no": +pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' ) +pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' ) +#end if + +pstc.compscore = formals(compscore) +pstc.compscore\$nn = as.integer( '$compscore.nn' ) +pstc.compscore\$scthr = as.numeric( '$compscore.scthr' ) + +out.pdf='${outpdf}' +out.rdat='${outrdat}' + ]]> + </token> +</macros>