diff alevin.xml @ 14:b3458e0f1931 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1

--- a/alevin.xml	Wed Oct 29 10:45:57 2025 +0000
+++ b/alevin.xml	Fri Oct 31 19:17:21 2025 +0000
@@ -62,24 +62,17 @@
         #if $whitelist:
             --whitelist '${optional.whitelist}'
         #end if
-        #if $optional.numCellBootstraps:
-            --numCellBootstraps '${optional.numCellBootstraps}'
-        #end if
-        #if $optional.forceCells:
-            --forceCells '${optional.forceCells}'
-        #end if
-        #if $optional.expectCells:
-            --expectCells '${optional.expectCells}'
-        #end if
+        --numCellBootstraps '${optional.numCellBootstraps}'
+        --forceCells '${optional.forceCells}'
+        --expectCells '${optional.expectCells}'
         #if $optional.mrna:
             --mrna '${optional.mrna}'
         #end if
         #if $optional.rrna:
             --rrna '${optional.rrna}'
         #end if
-        #if $optional.keepCBFraction:
-            --keepCBFraction '${optional.keepCBFraction}'
-        #end if
+        --minScoreFraction '${optional.minScoreFraction}'
+        --keepCBFraction '${optional.keepCBFraction}'
         ${optional.noDedup}
         #if 'dumpBfh' in $output_files:
             --dumpBfh
@@ -91,12 +84,8 @@
             --dumpUmiGraph
         #end if
         ${optional.dumpMtx}
-        #if $optional.maxNumBarcodes:
-            --maxNumBarcodes '${optional.maxNumBarcodes}'
-        #end if
-        #if $optional.freqThreshold:
-            --freqThreshold '${optional.freqThreshold}'
-        #end if
+        --maxNumBarcodes '${optional.maxNumBarcodes}'
+        --freqThreshold '${optional.freqThreshold}'
         ## && gunzip output/alevin/quants_tier_mat.gz -> the output is binary file
         #if $optional.dumpMtx != "--dumpMtx":
             && python '$__tool_directory__/vpolo_convert.py' -m
@@ -180,14 +169,17 @@
             <param argument="--mrna" type="data" format="tsv" optional="true" label="Mito-RNA genes file" help="Single column tsv of mitochondrial genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
             <param argument="--rrna" type="data" format="tsv" optional="true" label="Ribosomal RNA file" help="Single column tsv of ribosomal genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
             <param argument="--dumpMtx" type="boolean" truevalue="--dumpMtx" falsevalue="" checked="false" label=" Dump cell v transcripts count matrix in MTX format" help="Converts the default binary format of alevin for gene-count matrix into a human readable mtx (matrix market exchange) sparse format."/>
-            <param argument="--forceCells" type="integer" min="0" optional="true" label="Number of cells" help="Explicitly specify the number of cells."/>
-            <param argument="--expectCells" type="integer" min="0" optional="true" label="Upper bound on expected number of cells" help="define a close upper bound on expected number of cells."/>
+            <param argument="--forceCells" type="integer" min="0" value="0" label="Number of cells" help="Explicitly specify the number of cells."/>
+            <param argument="--expectCells" type="integer" min="0" value="0" label="Upper bound on expected number of cells" help="define a close upper bound on expected number of cells."/>
             <param argument="--numCellBootstraps" type="integer" min="0" value="0" optional="true" label="Generate mean and variance for cell x gene matrix by boostrap" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>
-            <param argument="--minScoreFraction" type="float" optional="true" label="Minimum allowed score for a mapping" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads).
-                The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/>
-            <param argument="--keepCBFraction" type="float" min="0" max="1" optional="true" label="Fraction of cellular barcodes to keep" help="Use 1 to quantify all"/>
+            <param argument="--minScoreFraction" type="float" value="0.87" label="Minimum allowed score for a mapping" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads). The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded.">
+                <validator type="in_range" min="0" exclude_max="1"/>
+            </param>
+            <param argument="--keepCBFraction" type="float" min="0" max="1" value="0.0" label="Fraction of cellular barcodes to keep" help="Use 1 to quantify all">
+                <validator type="in_range" min="0" exclude_max="1"/>
+            </param>
             <param argument="--maxNumBarcodes" type="integer" min="0" value="100000" label="Maximum allowable limit to process the cell barcodes" help="Default: 100000"/>
-            <param argument="--freqThreshold" type="integer" min="0" value="10" optional="true" label="Minimum frequency for a barcode to be considered" help="Default: 10"/>
+            <param argument="--freqThreshold" type="integer" min="0" value="10" label="Minimum frequency for a barcode to be considered" help="Default: 10"/>
         </section>
     </inputs>
     <outputs>
@@ -271,7 +263,7 @@
                 <assert_contents>
                     <has_text text="MatrixMarket" />
                     <has_n_columns n="5" />
-                    <has_n_lines n="101" />
+                    <has_n_lines n="100" />
                 </assert_contents>
             </output>
         </test>
@@ -310,7 +302,7 @@
                 <assert_contents>
                     <has_text text="MatrixMarket" />
                     <has_n_columns n="5" />
-                    <has_n_lines n="101" />
+                    <has_n_lines n="100" />
                 </assert_contents>
             </output>
         </test>