diff macros.xml @ 10:a6fba3d92531 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"

--- a/macros.xml	Fri Jan 15 17:39:11 2021 +0000
+++ b/macros.xml	Mon Mar 15 13:46:45 2021 +0000
@@ -5,7 +5,7 @@
     the index versions in sync, but you should manually adjust the +galaxy
     version number. -->
     <!-- STAR version to be used -->
-    <token name="@VERSION@">2.7.7a</token>
+    <token name="@VERSION@">2.7.8a</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
     by the current version.
@@ -163,10 +163,7 @@
     ]]></token>
     <xml name="ref_selection">
         <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
-        <!-- Currently, this parameter is not exposed in the wrapper,
-             but used only in the tests to avoid excessive index sizes for
-             the tiny test genomes. -->
-        <param name="genomeSAindexNbases" type="hidden" value="" />
+          <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
     </xml>
     <xml name="stdio" >
         <stdio>
@@ -209,8 +206,9 @@
         </conditional>
     </xml>
     <xml name="umidedup_options">
-        <option value="1MM_All" selected="true">All</option>
-        <option value="1MM_Directional" >Directional</option>
+        <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other</option>
+        <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
+        <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
     </xml>
     <xml name="anchor_types">
         <option value="0">Read start</option>
@@ -225,5 +223,26 @@
     <xml name="cb_match_wl_cellranger">
         <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
         <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
+        <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3)</option>
+    </xml>
+    <xml name="solo_adapter_params">
+        <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
+            <sanitizer>
+                <valid initial="string.digits">
+                    <add value="-"/>
+                    <add value="A"/>
+                    <add value="T"/>
+                    <add value="C"/>
+                    <add value="G"/>
+                    <add value="N"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence" />
+        <param argument="--clipAdapterType" type="select" >
+            <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option>
+            <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
+            <option value="None" >No adapter clipping</option>
+        </param>
     </xml>
 </macros>