--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_cluster.xml	Thu Nov 22 04:42:18 2018 -0500
@@ -0,0 +1,403 @@
+<macros>
+    <macro name="cluster_inputs" >
+        <param name="intable" type="data" format="tabular" label="Count Matrix" />
+        <section name="filt" title="Filtering" expanded="true" >
+            <param name="mintotal" type="integer" min="1" value="3000" label="Min Transcripts" help="The minimum total transcripts required. Cells with less than mintotal transcripts are filtered out." />
+            <param name="minexpr" type="integer" min="1" value="5" label="Min Expression" help="The minimum required transcript counts of a gene in the minimum number of cells (below)" />
+            <param name="minnumber" type="integer" min="1" value="5" label="Min Cells" help="The minumum number of cells for gene expression to be counted"  />
+            <expand macro="use_defaults_no" >
+                <param name="knn" type="integer" min="0" value="10" label="K-nearest-neighbours" help="Number of nearest neighbors used to infer corresponding cell types in different batches" />
+                <param name="CGenes" type="text" optional="true" label="CGenes" help="Filter out genes with correlated expression for cell type inference" >
+                    <expand macro="sanitize_string_vector" />
+                </param>
+                <param name="FGenes" type="text" optional="true" label="FGenes" help="Explicitly filter out genes for cell type inference" >
+                    <expand macro="sanitize_string_vector" />
+                </param>
+                <param name="LBatch_regexes" type="text" optional="true" label="Batch Regex" help="List of regexes to capture experimental batches for batch effect correction" >
+                    <expand macro="sanitize_string_vector" />
+                </param>
+                <param name="ccor" type="float" value="0.4" label="CCor" help="Correlation coefficient used as a threshold for determining correlated genes" />
+                <param name="bmode" type="select" label="Batch Mode" help="Method to regress out batch effects" >
+                    <option value="RaceID" selected="true" >RaceID</option>
+                    <option value="scran">SCRAN</option>
+                </param>
+                <conditional name="ccc" >
+                    <param name="use" type="select" label="Perform Cell-cycle correction?" >
+                        <option value="yes" >Yes</option>
+                        <option value="no" selected="true" >No</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes" >
+                        <param name="vset" type="text" optional="true" label="List of Gene Sets" >
+                            <expand macro="sanitize_string_vector" />
+                        </param>
+                        <param name="pvalue" type="float" value="0.01" min="0" max="1" label="P-value Cutoff" help="P-value cutoff for determining enriched components" />
+                        <param name="quant" type="float" value="0.01" min="0" max="1" label="Quantification Fraction" help="Upper and lower fraction of gene loadings use for determining enriched components"  />
+                        <param name="ncomp" type="integer" min="0" optional="true" label="Number of components to use" help="If left blank, the maximum number of components are used" /><!-- 0 = NULL -->
+                        <param name="dimr" type="boolean" value="true" label="Derive Components from saturation criterion"  />
+                        <param name="mode" type="select" label="Type of Component Analysis" help="If ICA is selected, ensure that the number of components value above is sufficiently high" >
+                            <option value="pca" selected="true">PCA</option>
+                            <option value="ica">ICA</option>
+                        </param>
+                        <param name="logscale" type="boolean" value="false" label="Log-transform data prior to PCA or ICA" help="" />
+                    </when>
+                </conditional>
+            </expand>
+        </section>
+        <section name="clust" title="Clustering" expanded="true" >
+            <!-- CompDist -->
+            <param name="metric" type="select" label="Distance Metric" >
+                <option value="pearson" selected="true" >Pearson</option>
+                <option value="spearman">Spearman</option>
+                <option value="logpearson">Log Pearson</option>
+                <option value="euclidean">Euclidean</option>
+            </param>
+            <!-- ClustExp -->
+            <param name="funcluster" type="select" label="Clustering method" >
+                <option value="kmedoids" selected="true" >K-medoids</option>
+                <option value="kmeans">K-means</option>
+                <option value="hclust">H-Clust</option>
+            </param>
+            <expand macro="use_defaults_no" >
+                <!-- CompDist -->
+                <param name="fselect" type="boolean" value="true" label="Perform feature selection" />
+                <param name="knn" type="integer" min="0" optional="true" label="KNN" help="Number of nearest neighbours for imputing gene expression" /><!-- 0: NULL -->
+                <!-- ClustExp -->
+                <param name="sat" type="boolean" checked="true" label="Saturation-based clustering?" help="Determine number of clusters on saturation point of the mean within-cluster dispersion as a function of the cluster number." />
+                <param name="clustnr" type="integer" min="0" value="30" label="Max number of clusters using Saturation-by-mean" help="Max number of clusters for the derivation of the cluster number by the saturation of mean within-cluster-dispersion." />
+                <param name="samp" type="integer" min="0" optional="true" label="Sample random number of cells" help="Number of random sample of cells used for the inference of cluster number and Jaccard similarity" /><!-- 0:NULL -->
+                <param name="cln" type="integer" min="0" optional="true" label="Number of clusters" /><!-- 0:Null -->
+                <param name="bootnr" type="integer" min="0" value="50" label="Number of booststrapping runs" />
+                <param name="rseed" type="integer" value="17000" label="Random seed" />
+            </expand>
+        </section>
+        <section name="outlier" title="Outliers" expanded="true" >
+            <!-- Find Outliers -->
+            <param name="outminc" type="integer" min="0" value="5" label="Minimum Transcripts" help="minimal transcript count of a gene in a clusters to be tested for being an outlier gene" />
+            <param name="outlg" type="integer" min="1" value="2" label="Minimum Genes" help="Minimum number of outlier genes required for being an outlier cell" />
+            <!-- RFCorrect -->
+            <param name="final" type="boolean" value="true" label="Plot Final Clusters?" help="Reclassification of cell types using out-of-bag analysis is performed based on the final clusters after outlier identification. If 'FALSE', then the cluster partition prior to outlier identification is used for reclassification." />
+            <expand macro="use_defaults_no" >
+                <!-- Find Outliers -->
+                <param name="probthr" type="float" min="0" value="0.001" label="Outlier Probability Threshold" help="Probability threshold for the above specified minimum number of genes to be an outlier cell. This probability is computed from a negative binomial background model of expression in a cluster" />
+                <param name="outdistquant" type="float" min="0" max="1" value="0.95" label="Outlier Distance Quantile" help="Outlier cells are merged to outlier clusters if their distance smaller than the outdistquant-quantile of the distance distribution of pairs of cells in the orginal clusters after outlier removal" />
+                <!-- RFCorrect -->
+                <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null -->
+                <param name="nbfactor" type="integer" min="0" value="5" label="Tree Factor" help="Number of trees based on the number of cells multiplied by this factor. Effective only if the number of trees parameter is set to 0" />
+                <param name="rfseed" type="integer" value="12345" label="Random Seed" />
+            </expand>
+        </section>
+        <section name="tsne" title="tSNE and FR" expanded="true" >
+            <!-- CompTSNE -->
+            <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" />
+            <!-- CompFR -->
+            <param name="knn" type="integer" min="0" value="10" label="KNN" help="Number of nearest neighbours used for the inference of the Fruchterman-Rheingold layout" />
+            <expand macro="use_defaults_no" >
+                <!-- CompTSNE -->
+                <param name="initial_cmd" type="boolean" checked="true" label="tSNE map initialised by classical multidimensional scaling" />
+                <param name="rseed_tsne" type="integer" value="15555" label="Random Seed (tSNE)" />
+                <!-- CompFR -->
+                <param name="rseed_fr" type="integer" min="0" value="15555" label="Random Seed (FR)" />
+            </expand>
+        </section>
+        <section name="extra" title="Extra Parameters" expanded="false" >
+            <param name="tablelim" type="integer" min="1" value="25" label="Table Limit" help="Top N genes to print per cluster" />
+            <param name="plotlim" type="integer" min="1" value="10" label="Plot Limit" help="Top N genes to plot. Must be less than or equal to the Table Limit" />
+            <param name="foldchange" type="float" min="0" value="1" label="Fold change" />
+            <param name="pvalue" type="float" min="0" max="1" value="0.01" label="P-value Cutoff" help="P-value cutoff for the inference of differential gene expression" />
+        </section>
+    </macro>
+    <macro name="cluster_tests" >
+        <test>
+            <!-- default test -->
+            <conditional name="tool" >
+                <param name="mode" value="cluster" />
+                <!-- This is a file with a single word 'test', which prompts the scripts to use the test intestinalData in the library -->
+                <param name="intable" value="use.intestinal" />
+            </conditional>
+            <output name="outgenelist" value="intestinal.genelist" />
+            <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" />
+        </test>
+        <test>
+            <!-- defaults, feeding in a matrix with reduced filtering -->
+            <conditional name="tool" >
+                <param name="mode" value="cluster" />
+                <param name="intable" value="matrix.tabular" />
+                <section name="filt" >
+                    <param name="mintotal" value="1000" />
+                    <param name="minexpr" value="1" />
+                    <param name="minnumber" value="3" />
+                </section>
+                <param name="use_log" value="true" />
+                <output name="outgenelist" value="matrix.genelist" />
+                <output name="outrdat" value="matrix.rdat" compare="sim_size" delta="15" />
+                <output name="outpdf" value="matrix.pdf" compare="sim_size" delta="10" />
+                <output name="outlog" value="matrix.log" />
+            </conditional>
+        </test>
+        <test>
+            <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
+            <conditional name="tool" >
+                <param name="mode" value="cluster" />
+                <param name="intable" value="use.intestinal" />
+                <section name="filt" >
+                    <param name="mintotal" value="3000" />
+                    <param name="minexpr" value="5" />
+                    <param name="minnumber" value="5" />
+                    <expand macro="test_nondef" >
+                        <param name="knn" value="10" />
+                        <param name="ccor" value="0.4" />
+                        <param name="bmode" value="RaceID" />
+                    </expand>
+                </section>
+                <section name="clust" >
+                    <param name="metric" value="pearson" />
+                    <param name="funcluster" value="kmedoids" />
+                    <expand macro="test_nondef" >
+                        <param name="fselect" value="true" />
+                        <param name="sat" value="true" />
+                        <param name="clustnr" value="30" />
+                        <param name="bootnr" value="50" />
+                        <param name="rseed" value="17000" />
+                    </expand>
+                </section>
+                <section name="outlier" >
+                    <param name="outminc" value="5" />
+                    <param name="outlg" value="2" />
+                    <param name="final" value="false" />
+                    <expand macro="test_nondef" section_name="outlier" >
+                        <param name="probthr" value="0.001" />
+                        <param name="outdistquant" value="0.95" />
+                        <param name="rfseed" value="12345" />
+                        <param name="nbfactor" value="5" />
+                    </expand>
+                </section>
+                <section name="tsne" >
+                    <param name="perplexity" value="30" />
+                    <param name="knn" value="10" />
+                    <expand macro="test_nondef" section_name="tsne" >
+                        <param name="initial_cmd" value="true" />
+                        <param name="rseed_tsne" value="15555" />
+                        <param name="rfseed_fr" value="15555" />
+                    </expand>
+                </section>
+            </conditional>
+            <output name="outgenelist" value="intestinal.genelist" />
+            <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" />
+        </test>
+        <test>
+            <!-- Advanced. Opts, CC used  -->
+            <conditional name="tool" >
+                <param name="mode" value="cluster" />
+                <param name="intable" value="use.intestinal" />
+                <section name="filt" >
+                    <param name="mintotal" value="2000" />
+                    <param name="minexpr" value="3" />
+                    <param name="minnumber" value="2" />
+                    <expand macro="test_nondef" >
+                        <param name="knn" value="5" />
+                        <param name="ccor" value="0.5" />
+                        <param name="CGenes" value="Gga3,Ggact,Ggct" />
+                        <param name="FGenes" value="Zxdc,Zyg11a,Zyg11b,Zyx" />
+                        <param name="LBatch_regexes" value="^I5,^II5,^III5,^IV5d,^V5d" />
+                        <param name="bmode" value="scran" />
+                        <conditional name="ccc" >
+                            <param name="use" value="yes" />
+                            <param name="pvalue" value="0.05" />
+                            <param name="quant" value="0.05" />
+                            <param name="ncomp" value="3" />
+                            <param name="dimr" value="true" />
+                            <param name="mode" value="pca" />
+                            <param name="logscale" value="true" />
+                        </conditional>
+                    </expand>
+                </section>
+                <section name="clust" >
+                    <param name="metric" value="euclidean" />
+                    <param name="funcluster" value="hclust" />
+                    <expand macro="test_nondef" >
+                        <param name="fselect" value="false" />
+                        <param name="knn" value="5" />
+                        <param name="sat" value="false" />
+                        <param name="samp" value="10" />
+                        <param name="cln" value="10" />
+                        <param name="clustnr" value="10" />
+                        <param name="bootnr" value="30" />
+                        <param name="rseed" value="17000" />
+                    </expand>
+                </section>
+                <section name="outlier" >
+                    <param name="outminc" value="3" />
+                    <param name="outlg" value="5" />
+                    <param name="final" value="true" />
+                    <expand macro="test_nondef" >
+                        <param name="probthr" value="0.01" />
+                        <param name="outdistquant" value="0.5" />
+                        <param name="rfseed" value="12345" />
+                        <param name="nbfactor" value="5" />
+                        <param name="nbtree" value="10" />
+                    </expand>
+                </section>
+                <section name="tsne" >
+                    <param name="perplexity" value="20" />
+                    <param name="knn" value="6" />
+                    <expand macro="test_nondef" >
+                        <param name="initial_cmd" value="false" />
+                        <param name="rseed_tsne" value="15555" />
+                        <param name="rfseed_fr" value="15555" />
+                    </expand>
+                </section>
+            </conditional>
+            <output name="outgenelist" value="intestinal_advanced.genelist" />
+            <output name="outpdf" value="intestinal_advanced.pdf" compare="sim_size" delta="150" />
+        </test>
+    </macro>
+    <token name="@FILTNORM_CHEETAH@"><![CDATA[
+## Perform do.filter
+use.filtnormconf = TRUE
+
+## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
+use.cluster = FALSE
+
+in.table = read.table(
+    '${intable}',
+    stringsAsFactors = F,
+    na.strings=c("NA", "-", "?", "."),
+    sep='\t',
+    header=TRUE,
+    row.names=1
+)
+
+## Hidden flag to use test data instead
+## see: test-data/use.intestinal
+
+use.test.data = (names(in.table)[1] == "test")
+
+sc = NULL
+if (use.test.data) {
+  sc = SCseq(intestinalData)
+  message("Loading test data from library")
+} else {
+  sc = SCseq(in.table)
+}
+
+
+filt = formals(filterdata)
+filt.ccc = formals(CCcorrect)
+filt.use.ccorrect = FALSE
+filt.lbatch.regexes = NULL
+
+filt\$mintotal = as.integer( '$filt.mintotal' )
+filt\$minexpr = as.integer( '$filt.minexpr' )
+filt\$minnumber = as.integer( '$filt.minnumber' )
+#if str($filt.use.def) == "no":
+filt\$knn = as.integer( '$filt.use.knn' )
+filt\$ccor = as.numeric( '$filt.use.ccor' )
+filt\$bmode = as.character( '$filt.use.bmode' )
+    #if $filt.use.LBatch_regexes:
+filt.lbatch.regexes = string2textvector( '$filt.use.LBatch_regexes' )
+    #end if
+    #if $filt.use.CGenes:
+filt\$CGenes = string2textvector( '$filt.use.CGenes' )
+    #end if
+    #if $filt.use.FGenes:
+filt\$FGenes = string2textvector( '$filt.use.FGenes' )
+    #end if
+    #if str($filt.use.ccc.use) == "yes"
+filt.use.ccorrect = TRUE
+        #if $filt.use.ccc.vset:
+filt.ccc\$vset = string2textvector( '$filt.use.ccc.vset' )
+        #end if
+        #if $filt.use.ccc.ncomp:
+filt.ccc\$nComp = as.integer( '$filt.use.ccc.ncomp' )
+        #end if
+filt.ccc\$pvalue = as.numeric( '$filt.use.ccc.pvalue' )
+filt.ccc\$quant = as.numeric( '$filt.use.ccc.quant' )
+filt.ccc\$dimR = as.logical( '$filt.use.ccc.dimr' )
+filt.ccc\$mode = as.character( '$filt.use.ccc.mode.value' )
+filt.ccc\$logscale = as.logical( '$filt.use.ccc.logscale' )
+    #end if
+#end if
+
+out.pdf = '${outpdf}'
+out.rdat = '${outrdat}'
+
+]]></token>
+    <token name="@CLUSTER_CHEETAH@"><![CDATA[
+
+in.rdat = readRDS('${inputrds}')
+
+sc = in.rdat
+
+## Perform do.filter
+use.filtnormconf = FALSE
+
+## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
+use.cluster = TRUE
+
+
+clust.compdist = formals(compdist)
+clust.clustexp = formals(clustexp)
+clust.compdist\$metric = as.character( '$clust.metric' )
+clust.clustexp\$FUNcluster = as.character( '$clust.funcluster' )
+
+#if str($clust.use.def) == "no":
+
+clust.compdist\$FSelect = as.logical( '$clust.use.fselect' )
+    #if $clust.use.knn:
+clust.compdist\$knn = as.integer( '$clust.use.knn' )
+    #end if
+clust.clustexp\$sat = as.logical( '$clust.use.sat' )
+    #if $clust.use.samp:
+clust.clustexp\$samp = as.integer( '$clust.use.samp' )
+    #end if
+    #if $clust.use.cln:
+clust.clustexp\$cln = as.integer( '$clust.use.cln' )
+clust.clustexp\$clustnr = as.integer( '$clust.use.clustnr' )
+clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' )
+##clust.clustexp\$rseed = as.integer( '$clust.use.rseed' )
+    #end if
+#end if
+
+outlier.use.randomforest = FALSE
+outlier.findoutliers = formals(findoutliers)
+outlier.clustheatmap = formals(clustheatmap)
+outlier.rfcorrect = formals(rfcorrect)
+
+outlier.findoutliers\$outminc = as.integer( '$outlier.outminc' )
+outlier.findoutliers\$outlg = as.integer( '$outlier.outlg' )
+outlier.rfcorrect\$final = as.logical( '$outlier.final' )
+
+#if str($outlier.use.def) == "no":
+    #if $outlier.use.nbtree:
+outlier.rfcorrect\$nbtree = as.integer( '$outlier.use.nbtree' )
+    #end if
+outlier.findoutliers\$probthr = as.numeric( '$outlier.use.probthr' )
+outlier.findoutliers\$outdistquant = as.numeric( '$outlier.use.outdistquant' )
+##outlier.rfcorrect\$rfseed = as.integer( '$outlier.use.rfseed' )
+outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' )
+#end if
+
+cluster.comptsne = formals(comptsne)
+cluster.compfr = formals(compfr)
+
+cluster.comptsne\$perplexity = as.integer( '$tsne.perplexity' )
+cluster.compfr\$knn = as.integer( '$tsne.knn' )
+#if str($tsne.use.def) == "no":
+cluster.comptsne\$initial_cmd = as.logical( '$tsne.use.initial_cmd' )
+cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' )
+cluster.compfr\$rseed = as.integer( '$tsne.use.rseed_fr' )
+#end if
+
+genelist.tablelim = as.integer( '$extra.tablelim' )
+genelist.plotlim = as.integer( '$extra.plotlim' )
+genelist.foldchange = as.integer( '$extra.foldchange' )
+genelist.pvalue = as.numeric( '$extra.pvalue' )
+
+out.pdf = '${outpdf}'
+out.rdat = '${outrdat}'
+out.genelist = '${outgenelist}'
+
+]]>
+    </token>
+</macros>