Boolean variables

tools/tertiary-analysis/pyscenic/pyscenic_ctx.xml

@@ -15,20 +15,14 @@
     pyscenic ctx tf2targets.tsv \${PySCENIC_DB} 
         --expression_mtx_fname expr_mat.loom
     --output regulons.tsv
-#if $no_pruning
-    --no_pruning
-#end if
+$no_pruning
 #if $chunk_size
     --chunk_size '${chunk_size}'
 #end if
     --mode custom_multiprocessing
     --num_workers \${GALAXY_SLOTS:-1}
-#if $all_modules
-    --all_modules
-#end if
-#if $transpose
-    --transpose
-#end if
+$all_modules
+$transpose
 #if $rank_threshold
     --rank_threshold '${rank_threshold}'
 #end if
@@ -59,9 +53,7 @@
 #if $min_genes
     --min_genes '${min_genes}'
 #end if
-#if $mask_dropouts
-    --mask_dropouts
-#end if
+$mask_dropouts
 #if $cell_id_attribute
     --cell_id_attribute '${cell_id_attribute}'
 #end if
@@ -79,10 +71,10 @@ mv regulons.tsv '${output}'
         <param type="data" name="database_fname" label="Database File" help="Regulatory feature databases. Supported formats: feather"/>
         <param type="data" name="annotations_fname" format="tabular" label="Annotations File" help="File that contains the motif annotations to use."/>
         <param type="data" name="expression_mtx" format="loom" label="Expression Matrix" help="The expression matrix for the single cell experiment."/>
-        <param type="boolean" name="no_pruning" label="No Pruning" optional="true" help="Do not perform pruning, i.e. find enriched motifs."/>
+        <param type="boolean" name="no_pruning" label="No Pruning" truevalue="--no_pruning" falsevalue="" help="Do not perform pruning, i.e. find enriched motifs."/>
         <param type="integer" name="chunk_size" label="Chunk Size" optional="true" help="The size of the module chunks assigned to a node in the dask graph (default: 100)."/>
-        <param type="boolean" name="all_modules" label="All Modules" optional="true" help="Include positive and negative regulons in the analysis (default: no, i.e. only positive)."/>
-        <param type="boolean" name="transpose" label="Transpose" optional="true" help="Transpose the expression matrix (rows=genes x columns=cells)."/>
+        <param type="boolean" name="all_modules" label="All Modules" truevalue="--all_modules" falsevalue="" help="Include positive and negative regulons in the analysis (default: no, i.e. only positive)."/>
+        <param type="boolean" name="transpose" label="Transpose Expression Matrix" truevalue="-t" falsevalue="" help="Use this if the matrix is cell x genes instead of genes x cells as expected"/>
         <param type="float" name="rank_threshold" label="Rank Threshold" optional="true" help="The rank threshold used for deriving the target genes of an enriched motif."/>
         <param type="float" name="auc_threshold" label="AUC Threshold" optional="true" help="The threshold used for calculating the AUC of a feature as fraction of ranked genes."/>
         <param type="float" name="nes_threshold" label="NES Threshold" optional="true" help="The Normalized Enrichment Score (NES) threshold for finding enriched features."/>
@@ -92,7 +84,7 @@ mv regulons.tsv '${output}'
         <param type="integer" name="top_n_targets" label="Top N Targets" optional="true" help="The number of top targets to retain for each feature."/>
         <param type="integer" name="top_n_regulators" label="Top N Regulators" optional="true" help="The number of top regulators to retain for each feature."/>
         <param type="integer" name="min_genes" label="Minimum Genes" optional="true" help="The minimum number of genes a module needs to have to be considered for regulatory network analysis."/>
-        <param type="boolean" name="mask_dropouts" label="Mask Dropouts" optional="true" help="Mask dropouts in the expression matrix."/>
+        <param type="boolean" name="mask_dropouts" label="Mask Dropouts" truevalue="--mask_dropouts" falsevalue="" help="Mask dropouts in the expression matrix."/>
         <param type="text" name="cell_id_attribute" label="Cell ID Attribute" optional="true" help="The name of the attribute in the loom expression matrix that contains cell IDs."/>
         <param type="text" name="gene_attribute" label="Gene Attribute" optional="true" help="The name of the attribute in the loom expression matrix that contains gene names."/>
         <param name="sparse" type="boolean" label="Sparse Matrix" truevalue="--sparse" falsevalue="" help="If set, load the expression data as a sparse matrix. Currently applies to the grn inference step only."/>

tools/tertiary-analysis/pyscenic/pyscenic_grn.xml

@@ -14,9 +14,7 @@
                 pyscenic grn 
             #end if
             -o tf2targets.tsv
-            #if $transpose
-            -t
-            #end if
+            $transpose
             #if $method
             -m '${method}'
             #end if
@@ -40,7 +38,7 @@
         <param name="expression_mtx" type="data" format="loom" label="Expression Matrix Loom File" help="In format rows=genes x columns=cells"/>
         <param name="tfs_fname" type="data" format="txt" label="Transcription Factors File" help="Simple text file, one transcription factor symbol per line"/>
         <param name="use_arboretum" type="boolean" label="Use arboretum" checked="false" help="Uses the arboretum approach instead of pyscenic grn call, which can be better for multi processing"/>
-        <param name="transpose" type="boolean" default_value="false" label="Transpose Expression Matrix" help="Use this if the matrix is cell x genes instead of genes x cells as expected"/>
+        <param name="transpose" type="boolean" truevalue="-t" falsevalue="" label="Transpose Expression Matrix" help="Use this if the matrix is cell x genes instead of genes x cells as expected"/>
         <param name="method" type="select" label="Method">
             <option value="genie3">GENIE3</option>
             <option value="grnboost2" selected="true">GRNBoost2</option>