From 528b03ed3c31a6de433f0bb0614f6ac0eccf7292 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Thu, 15 Aug 2024 17:30:32 +0100
Subject: [PATCH] Apply suggestions from bgruening's code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml b/tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml
index 8ea7992a..48e00c9c 100644
--- a/tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml
+++ b/tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml
@@ -17,11 +17,11 @@
         #if $weights
            -w
         #end if
-           --num_workers \${GALAXY_SLOTS:-1}
+       --num_workers \${GALAXY_SLOTS:-1}
         #if $seed
            --seed "${seed}"
         #end if
-        #if $rank_threshold
+        #if str($rank_threshold):
            --rank_threshold "${rank_threshold}"
         #end if
         #if $auc_threshold
@@ -36,9 +36,7 @@
         #if $gene_attribute
            --gene_attribute "${gene_attribute}"
         #end if
-        #if $sparse
-           --sparse
-        #end if
+        $sparse
 
         && mv aucell.tsv "${output}"
     ]]></command>
@@ -54,7 +52,7 @@
       <param name="nes_threshold" type="float" label="NES Threshold" help="The Normalized Enrichment Score (NES) threshold for finding enriched features (default: 3.0)." optional="true" />
       <param name="cell_id_attribute" type="text" label="Cell ID Attribute" help="The name of the column attribute that specifies the identifiers of the cells in the loom file." optional="true" />
       <param name="gene_attribute" type="text" label="Gene Attribute" help="The name of the row attribute that specifies the gene symbols in the loom file." optional="true" />
-      <param name="sparse" type="boolean" label="Sparse Matrix" help="If set, load the expression data as a sparse matrix. Currently applies to the grn inference step only." optional="true" />
+      <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." optional="true" />
     </inputs>
   
     <outputs>