# HG changeset patch
# User iuc
# Date 1615815967 0
# Node ID c772497b2c322498c79566635cb9621fcd5ec4f2
# Parent  7ed2edc1337f91851e55af4da347af48b2d6a90b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"

diff -r 7ed2edc1337f -r c772497b2c32 macros.xml
--- a/macros.xml	Fri Jan 15 17:38:35 2021 +0000
+++ b/macros.xml	Mon Mar 15 13:46:07 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>
diff -r 7ed2edc1337f -r c772497b2c32 rg_rnaStar.xml
--- a/rg_rnaStar.xml	Fri Jan 15 17:38:35 2021 +0000
+++ b/rg_rnaStar.xml	Mon Mar 15 13:46:07 2021 +0000
@@ -867,7 +867,54 @@
             <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
             <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
         </test>
-    </tests>
+        <!-- test "genomeSAindexNbases" parameter -->
+        <test expect_num_outputs="3">
+            <conditional name="singlePaired">
+                <param name="sPaired" value="single" />
+                <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
+            </conditional>
+            <conditional name="refGenomeSource">
+                <param name="geneSource" value="history" />
+                <param name="genomeFastaFiles" value="tophat_test.fa" />
+                <param name="genomeSAindexNbases" value="14" />
+            </conditional>
+            <section name="oformat">
+                <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
+                <param name="outSAMmapqUnique" value="255" />
+            </section>
+            <section name="algo">
+                <conditional name="params">
+                    <param name="settingsType" value="default" />
+                </conditional>
+            </section>
+            <output name="output_log" file="rnastar_test_genomeSAindexNbases.log" compare="re_match_multiline" />
+            <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases.bed"/>
+            <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases.bam" compare="sim_size" delta="634" />
+        </test>
+        <test expect_num_outputs="3">
+            <conditional name="singlePaired">
+                <param name="sPaired" value="single" />
+                <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
+            </conditional>
+            <conditional name="refGenomeSource">
+                <param name="geneSource" value="history" />
+                <param name="genomeFastaFiles" value="tophat_test.fa" />
+                <param name="genomeSAindexNbases" value="10" />
+            </conditional>
+            <section name="oformat">
+                <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
+                <param name="outSAMmapqUnique" value="255" />
+            </section>
+            <section name="algo">
+                <conditional name="params">
+                    <param name="settingsType" value="default" />
+                </conditional>
+            </section>
+            <output name="output_log" file="rnastar_test_genomeSAindexNbases_02.log" compare="re_match_multiline" />
+            <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases_02.bed"/>
+            <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases_02.bam" compare="sim_size" delta="634" />
+        </test>
+      </tests>
     <help><![CDATA[
 **What it does**
 
diff -r 7ed2edc1337f -r c772497b2c32 test-data/rnastar_test_genomeSAindexNbases.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_genomeSAindexNbases.bed	Mon Mar 15 13:46:07 2021 +0000
@@ -0,0 +1,2 @@
+test_chromosome	251	350	1	1	0	27	0	37
+test_chromosome	401	500	1	1	0	25	0	36
diff -r 7ed2edc1337f -r c772497b2c32 test-data/rnastar_test_genomeSAindexNbases.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_genomeSAindexNbases.log	Mon Mar 15 13:46:07 2021 +0000
@@ -0,0 +1,37 @@
+                                 Started job on |	Mar 08 19:43:44
+                             Started mapping on |	Mar 08 19:43:45
+                                    Finished on |	Mar 08 19:43:45
+       Mapping speed, Million of reads per hour |	inf
+
+                          Number of input reads |	100
+                      Average input read length |	75
+                                    UNIQUE READS:
+                   Uniquely mapped reads number |	99
+                        Uniquely mapped reads % |	99.00%
+                          Average mapped length |	74.65
+                       Number of splices: Total |	52
+            Number of splices: Annotated (sjdb) |	0
+                       Number of splices: GT/AG |	52
+                       Number of splices: GC/AG |	0
+                       Number of splices: AT/AC |	0
+               Number of splices: Non-canonical |	0
+                      Mismatch rate per base, % |	2.00%
+                         Deletion rate per base |	0.00%
+                        Deletion average length |	0.00
+                        Insertion rate per base |	0.00%
+                       Insertion average length |	0.00
+                             MULTI-MAPPING READS:
+        Number of reads mapped to multiple loci |	1
+             % of reads mapped to multiple loci |	1.00%
+        Number of reads mapped to too many loci |	0
+             % of reads mapped to too many loci |	0.00%
+                                  UNMAPPED READS:
+  Number of reads unmapped: too many mismatches |	0
+       % of reads unmapped: too many mismatches |	0.00%
+            Number of reads unmapped: too short |	0
+                 % of reads unmapped: too short |	0.00%
+                Number of reads unmapped: other |	0
+                     % of reads unmapped: other |	0.00%
+                                  CHIMERIC READS:
+                       Number of chimeric reads |	0
+                            % of chimeric reads |	0.00%
diff -r 7ed2edc1337f -r c772497b2c32 test-data/rnastar_test_genomeSAindexNbases_02.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_genomeSAindexNbases_02.bed	Mon Mar 15 13:46:07 2021 +0000
@@ -0,0 +1,2 @@
+test_chromosome	251	350	1	1	0	27	0	37
+test_chromosome	401	500	1	1	0	25	0	36
diff -r 7ed2edc1337f -r c772497b2c32 test-data/rnastar_test_genomeSAindexNbases_02.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_genomeSAindexNbases_02.log	Mon Mar 15 13:46:07 2021 +0000
@@ -0,0 +1,37 @@
+                                 Started job on |	Mar 08 19:43:59
+                             Started mapping on |	Mar 08 19:43:59
+                                    Finished on |	Mar 08 19:43:59
+       Mapping speed, Million of reads per hour |	inf
+
+                          Number of input reads |	100
+                      Average input read length |	75
+                                    UNIQUE READS:
+                   Uniquely mapped reads number |	99
+                        Uniquely mapped reads % |	99.00%
+                          Average mapped length |	74.65
+                       Number of splices: Total |	52
+            Number of splices: Annotated (sjdb) |	0
+                       Number of splices: GT/AG |	52
+                       Number of splices: GC/AG |	0
+                       Number of splices: AT/AC |	0
+               Number of splices: Non-canonical |	0
+                      Mismatch rate per base, % |	2.00%
+                         Deletion rate per base |	0.00%
+                        Deletion average length |	0.00
+                        Insertion rate per base |	0.00%
+                       Insertion average length |	0.00
+                             MULTI-MAPPING READS:
+        Number of reads mapped to multiple loci |	1
+             % of reads mapped to multiple loci |	1.00%
+        Number of reads mapped to too many loci |	0
+             % of reads mapped to too many loci |	0.00%
+                                  UNMAPPED READS:
+  Number of reads unmapped: too many mismatches |	0
+       % of reads unmapped: too many mismatches |	0.00%
+            Number of reads unmapped: too short |	0
+                 % of reads unmapped: too short |	0.00%
+                Number of reads unmapped: other |	0
+                     % of reads unmapped: other |	0.00%
+                                  CHIMERIC READS:
+                       Number of chimeric reads |	0
+                            % of chimeric reads |	0.00%
diff -r 7ed2edc1337f -r c772497b2c32 test-data/rnastar_test_mapped_reads_genomeSAindexNbases.bam
Binary file test-data/rnastar_test_mapped_reads_genomeSAindexNbases.bam has changed
diff -r 7ed2edc1337f -r c772497b2c32 test-data/rnastar_test_mapped_reads_genomeSAindexNbases_02.bam
Binary file test-data/rnastar_test_mapped_reads_genomeSAindexNbases_02.bam has changed