# HG changeset patch
# User iuc
# Date 1748721103 0
# Node ID 4746de55986ef0aa3ba19b7c3892601b4d8764a3
# Parent  9b7a86a83fce87bad8e76ee8f0fc51d49d7c9083
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256

diff -r 9b7a86a83fce -r 4746de55986e macros.xml
--- a/macros.xml	Thu Dec 05 06:48:08 2024 +0000
+++ b/macros.xml	Sat May 31 19:51:43 2025 +0000
@@ -4,8 +4,8 @@
     The data manager uses a symlink to this macro file to keep the STAR and
     the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
     <!-- STAR version to be used -->
-    <token name="@TOOL_VERSION@">2.7.11a</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">2.7.11b</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
@@ -121,7 +121,7 @@
                 #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
                     --genomeTransformVCF '${refGenomeSource.diploidconditional.genomeTransformVCF}'
                     --genomeTransformType Diploid
-                #end if   
+                #end if
             #end if
             --runThreadN \${GALAXY_SLOTS:-4}
             ## in bytes
@@ -371,6 +371,13 @@
             </change_format>
         </data>
     </xml>
+    <xml name="quantTranscriptomeSAMoutput_param">
+        <param argument="--quantTranscriptomeSAMoutput" type="select" label="Alignment filtering for TranscriptomeSAM output">
+            <option value="BanSingleEnd_BanIndels_ExtendSoftclip" selected="true">prohibit indels and single-end alignments, extend softclips - compatible with RSEM</option>
+            <option value="BanSingleEnd">prohibit single-end alignments, allow indels and softclips</option>
+            <option value="BanSingleEnd_ExtendSoftclip">prohibit single-end alignments, extend softclips, allow indels</option>
+        </param>
+    </xml>
     <xml name="quantMode">
         <conditional name="quantmode_output">
             <param argument="--quantMode" type="select" label="Per gene/transcript output" help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
@@ -382,10 +389,10 @@
             <when value="-"/>
             <when value="GeneCounts"/>
             <when value="TranscriptomeSAM">
-                <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled."/>
+                <expand macro="quantTranscriptomeSAMoutput_param"/>
             </when>
             <when value="TranscriptomeSAM GeneCounts">
-                <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled."/>
+                <expand macro="quantTranscriptomeSAMoutput_param"/>
             </when>
         </conditional>
     </xml>
@@ -432,4 +439,149 @@
             <when value=""/>
         </conditional>
     </xml>
+    <xml name="full_algo_params">
+        <section name="seed" title="Seed parameters" expanded="false">
+            <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
+            <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/>
+            <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/>
+            <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
+            <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
+            <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
+            <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
+        </section>
+        <section name="align" title="Alignment parameters" expanded="false">
+            <param argument="--alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
+            <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
+            <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
+            <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
+            <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true">
+                <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/>
+                <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax2" type="integer" min="-1" value="-1" label="GT/AG and CT/AC motif"/>
+                <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax3" type="integer" min="-1" value="0" label="GC/AG and CT/GC motif"/>
+                <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax4" type="integer" min="-1" value="0" label="AT/AC and GT/AT motif"/>
+            </section>
+            <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
+            <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
+            <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/>
+            <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
+            <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
+            <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
+            <param argument="--alignEndsType" type="select" label="type of read ends alignment">
+                <option value="Local">standard local alignment with soft-clipping allowed</option>
+                <option value="EndToEnd">force end-to-end read alignment, do not soft-clip</option>
+                <option value="Extend5pOfRead1">fully extend only the 5p of the read1, all other ends: local alignment</option>
+                <option value="Extend5pOfReads12">fully extend only the 5p of the both read1 and read2, all other ends: local alignment</option>
+            </param>
+            <param argument="--peOverlapNbasesMin" type="integer" min="0" value="0"
+            label="minimum number of overlap bases to trigger mates merging and realignment" />
+            <param argument="--peOverlapMMp" type="float" min="0" max="1" value="0.01"
+            label="maximum proportion of mismatched bases in the overlap area" />
+        </section>
+        <section name="chim_settings" title="Chimeric alignment parameters" expanded="false">
+            <param argument="--chimSegmentMin" type="integer" min="1" value="12"
+            label="Minimum length of chimeric segment"
+            help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used." />
+            <param argument="--chimScoreMin" type="integer" min="0" value="0"
+            label="Minimum total (summed) score of chimeric segments"/>
+            <param argument="--chimScoreDropMax" type="integer" min="0" value="20"
+            label="Maximum difference of chimeric score from read length"/>
+            <param argument="--chimScoreSeparation" type="integer" min="0" value="10"
+            label="Minimum difference between the best chimeric score and the next one"/>
+            <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1"
+            label="Penalty for a non-GT/AG chimeric junction"/>
+            <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20"
+            label="Minimum overhang for a chimeric junction"/>
+            <param argument="--chimSegmentReadGapMax" type="integer" min="0" value="0"
+            label="Maximum gap in the read sequence between chimeric segments" />
+            <param argument="--chimFilter" type="boolean" truevalue="banGenomicN" falsevalue="None" checked="true"
+            label="Discard chimeric alignments with Ns in the genome sequence around the chimeric junction" />
+            <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10"
+            label="Maximum number of multi-alignments for the main chimeric segment."
+            help="A value of 1 prohibits multimapping main segments"/>
+            <param argument="--chimMultimapNmax" type="integer" min="1" value="1"
+            label="Maximum number of chimeric multi-alignments"
+            help="The default value of 1 only considers unique alignments. If you chose to report chimeric alignments alongside regular ones in the BAM output, this setting is ignored and only uniquely mapping chimeric reads get reported. " />
+            <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1"
+            label="Score range for multi-mapping chimeras"
+            help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" />
+        </section>
+        <expand macro="limits" />
+    </xml>
+    <xml name="chim_params">
+        <param argument="--chimOutType" type="select"
+        label="Report chimeric alignments?"
+        help="Choose if and how chimeric alignments should be reported. STAR-Fusion users should select the 'Junctions' option and use the resulting tabular dataset as input to STAR-Fusion. Everyone else: note that selecting 'WithinBAM' or 'WithinBAM Junctions' disables the --chimMultimapNmax setting in the algorithmic parameters section below (the tool will only consider uniquely mapped reads in the search for chimeric alignments). If you disable the reporting of chimeric alignments here, then all chimeric alignment settings in the algorithmic parameters section below will be ignored.">
+            <option value="">Don't report chimeric alignments</option>
+            <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option>
+            <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>
+            <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option>
+            <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option>
+        </param>
+    </xml>
+    <token name="@ALGO_FULL@"><![CDATA[
+            ## Extended parameter options
+
+            ## Seed parameter options
+            --seedSearchStartLmax ${algo.params.seed.seedSearchStartLmax}
+            --seedSearchStartLmaxOverLread ${algo.params.seed.seedSearchStartLmaxOverLread}
+            --seedSearchLmax ${algo.params.seed.seedSearchLmax}
+            --seedMultimapNmax ${algo.params.seed.seedMultimapNmax}
+            --seedPerReadNmax ${algo.params.seed.seedPerReadNmax}
+            --seedPerWindowNmax ${algo.params.seed.seedPerWindowNmax}
+            --seedNoneLociPerWindow ${algo.params.seed.seedNoneLociPerWindow}
+
+            ## Alignment parameter options
+            --alignIntronMin ${algo.params.align.alignIntronMin}
+            --alignIntronMax ${algo.params.align.alignIntronMax}
+            --alignMatesGapMax ${algo.params.align.alignMatesGapMax}
+            --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}
+            --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4}
+            --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin}
+            --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin}
+            --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate}
+            --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax}
+            --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax}
+            --alignTranscriptsPerReadNmax ${algo.params.align.alignTranscriptsPerReadNmax}
+            --alignEndsType ${algo.params.align.alignEndsType}
+            --peOverlapNbasesMin ${algo.params.align.peOverlapNbasesMin}
+            --peOverlapMMp ${algo.params.align.peOverlapMMp}
+            ## Chimeric alignment parameter options
+            #if str($chimOutType):
+                --chimSegmentMin ${algo.params.chim_settings.chimSegmentMin}
+                --chimScoreMin ${algo.params.chim_settings.chimScoreMin}
+                --chimScoreDropMax $algo.params.chim_settings.chimScoreDropMax
+                --chimScoreSeparation $algo.params.chim_settings.chimScoreSeparation
+                --chimScoreJunctionNonGTAG $algo.params.chim_settings.chimScoreJunctionNonGTAG
+                --chimSegmentReadGapMax $algo.params.chim_settings.chimSegmentReadGapMax
+                --chimFilter $algo.params.chim_settings.chimFilter
+                --chimJunctionOverhangMin $algo.params.chim_settings.chimJunctionOverhangMin
+                --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax
+                #if str($chimOutType) == 'Junctions':
+                    --chimMultimapNmax $algo.params.chim_settings.chimMultimapNmax
+                #else:
+                    --chimMultimapNmax 0
+                #end if
+                --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange
+            #end if
+
+            ## Limits
+            @LIMITS@
+    ]]></token>
+    <token name="@ALGO_DEFAULT@"><![CDATA[
+            ## Go with STAR's default algorithmic settings,
+            ## but we need to provide a reasonable default
+            ## (taken from STAR-Fusion)
+            ## for --chimSegmentMin in case the user enabled chimeric
+            ## alignments (the STAR default is 0, which disables chimeric
+            ## alignments). For consistency, also set
+            ## --chimMultimapNmax to 1 when chimeric alignments are reported
+            ## in Junctions format only.
+            #if str($chimOutType):
+                --chimSegmentMin 12
+                #if str($chimOutType) == 'Junctions':
+                    --chimMultimapNmax 1
+                #end if
+            #end if
+    ]]></token>
+
 </macros>
diff -r 9b7a86a83fce -r 4746de55986e rg_rnaStar.xml
--- a/rg_rnaStar.xml	Thu Dec 05 06:48:08 2024 +0000
+++ b/rg_rnaStar.xml	Sat May 31 19:51:43 2025 +0000
@@ -69,7 +69,7 @@
 
         --quantMode ${refGenomeSource.GTFconditional.quantmode_output.quantMode}
         #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
-            --quantTranscriptomeBan ${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeBan}
+            --quantTranscriptomeSAMoutput '${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeSAMoutput}'
         #end if
 
         ## Output format parameters
@@ -98,7 +98,7 @@
             #if 'diploidconditional' in $refGenomeSource:
                 #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
                     '${refGenomeSource.diploidconditional.genomeTransformOutput}'
-                #end if   
+                #end if
             #end if
         #end if
 
@@ -156,7 +156,7 @@
             --chimMultimapScoreRange 10
             --chimMultimapNmax 10
             --chimNonchimScoreDropMin 10
-        
+
         #elif str( $algo.params.settingsType ) == 'arriba':
             ## Preset parameters for Arriba
             --peOverlapNbasesMin 10
@@ -171,68 +171,9 @@
             --chimMultimapNmax 50
 
         #elif str( $algo.params.settingsType ) == 'full':
-            ## Extended parameter options
-
-            ## Seed parameter options
-            --seedSearchStartLmax ${algo.params.seed.seedSearchStartLmax}
-            --seedSearchStartLmaxOverLread ${algo.params.seed.seedSearchStartLmaxOverLread}
-            --seedSearchLmax ${algo.params.seed.seedSearchLmax}
-            --seedMultimapNmax ${algo.params.seed.seedMultimapNmax}
-            --seedPerReadNmax ${algo.params.seed.seedPerReadNmax}
-            --seedPerWindowNmax ${algo.params.seed.seedPerWindowNmax}
-            --seedNoneLociPerWindow ${algo.params.seed.seedNoneLociPerWindow}
-
-            ## Alignment parameter options
-            --alignIntronMin ${algo.params.align.alignIntronMin}
-            --alignIntronMax ${algo.params.align.alignIntronMax}
-            --alignMatesGapMax ${algo.params.align.alignMatesGapMax}
-            --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}
-            --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4}
-            --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin}
-            --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin}
-            --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate}
-            --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax}
-            --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax}
-            --alignTranscriptsPerReadNmax ${algo.params.align.alignTranscriptsPerReadNmax}
-            --alignEndsType ${algo.params.align.alignEndsType}
-            --peOverlapNbasesMin ${algo.params.align.peOverlapNbasesMin}
-            --peOverlapMMp ${algo.params.align.peOverlapMMp}
-            ## Chimeric alignment parameter options
-            #if str($chimOutType):
-                --chimSegmentMin ${algo.params.chim_settings.chimSegmentMin}
-                --chimScoreMin ${algo.params.chim_settings.chimScoreMin}
-                --chimScoreDropMax $algo.params.chim_settings.chimScoreDropMax
-                --chimScoreSeparation $algo.params.chim_settings.chimScoreSeparation
-                --chimScoreJunctionNonGTAG $algo.params.chim_settings.chimScoreJunctionNonGTAG
-                --chimSegmentReadGapMax $algo.params.chim_settings.chimSegmentReadGapMax
-                --chimFilter $algo.params.chim_settings.chimFilter
-                --chimJunctionOverhangMin $algo.params.chim_settings.chimJunctionOverhangMin
-                --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax
-                #if str($chimOutType) == 'Junctions':
-                    --chimMultimapNmax $algo.params.chim_settings.chimMultimapNmax
-                #else:
-                    --chimMultimapNmax 0
-                #end if
-                --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange
-            #end if
-
-            ## Limits
-            @LIMITS@
+        @ALGO_FULL@
         #else:
-            ## Go with STAR's default algorithmic settings,
-            ## but we need to provide a reasonable default
-            ## (taken from STAR-Fusion)
-            ## for --chimSegmentMin in case the user enabled chimeric
-            ## alignments (the STAR default is 0, which disables chimeric
-            ## alignments). For consistency, also set
-            ## --chimMultimapNmax to 1 when chimeric alignments are reported
-            ## in Junctions format only.
-            #if str($chimOutType):
-                --chimSegmentMin 12
-                #if str($chimOutType) == 'Junctions':
-                    --chimMultimapNmax 1
-                #end if
-            #end if
+        @ALGO_DEFAULT@
         #end if
         --outBAMsortingThreadN \${GALAXY_SLOTS:-4}
         --outBAMsortingBinsN $perf.outBAMsortingBinsN
@@ -375,16 +316,7 @@
                 label="Pregenerated splice junctions datasets of your samples" />
             </when>
         </conditional>
-        <param argument="--chimOutType" type="select"
-        label="Report chimeric alignments?"
-        help="Choose if and how chimeric alignments should be reported. STAR-Fusion users should select the 'Junctions' option and use the resulting tabular dataset as input to STAR-Fusion. Everyone else: note that selecting 'WithinBAM' or 'WithinBAM Junctions' disables the --chimMultimapNmax setting in the algorithmic parameters section below (the tool will only consider uniquely mapped reads in the search for chimeric alignments). If you disable the reporting of chimeric alignments here, then all chimeric alignment settings in the algorithmic parameters section below will be ignored.">
-            <option value="">Don't report chimeric alignments</option>
-            <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option>
-            <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>
-            <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option>
-            <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option>
-        </param>
-
+        <expand macro="chim_params"/>
         <section name="oformat" title="BAM output format specification" expanded="true">
             <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true"
             label="Read alignment tags to include in the BAM output"
@@ -466,73 +398,7 @@
                 <when value="arriba"/>
 
                 <when value="full">
-                    <section name="seed" title="Seed parameters" expanded="false">
-                        <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
-                        <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/>
-                        <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/>
-                        <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
-                        <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
-                        <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
-                        <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
-                    </section>
-
-                    <section name="align" title="Alignment parameters" expanded="false">
-                        <param argument="--alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
-                        <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
-                        <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
-                        <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
-                        <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true">
-                            <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/>
-                            <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax2" type="integer" min="-1" value="-1" label="GT/AG and CT/AC motif"/>
-                            <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax3" type="integer" min="-1" value="0" label="GC/AG and CT/GC motif"/>
-                            <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax4" type="integer" min="-1" value="0" label="AT/AC and GT/AT motif"/>
-                        </section>
-                        <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
-                        <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
-                        <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/>
-                        <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
-                        <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
-                        <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
-                        <param argument="--alignEndsType" type="select" label="type of read ends alignment">
-                            <option value="Local">standard local alignment with soft-clipping allowed</option>
-                            <option value="EndToEnd">force end-to-end read alignment, do not soft-clip</option>
-                            <option value="Extend5pOfRead1">fully extend only the 5p of the read1, all other ends: local alignment</option>
-                            <option value="Extend5pOfReads12">fully extend only the 5p of the both read1 and read2, all other ends: local alignment</option>
-                        </param>
-                        <param argument="--peOverlapNbasesMin" type="integer" min="0" value="0"
-                        label="minimum number of overlap bases to trigger mates merging and realignment" />
-                        <param argument="--peOverlapMMp" type="float" min="0" max="1" value="0.01"
-                        label="maximum proportion of mismatched bases in the overlap area" />
-                    </section>
-                    <section name="chim_settings" title="Chimeric alignment parameters" expanded="false">
-                        <param argument="--chimSegmentMin" type="integer" min="1" value="12"
-                        label="Minimum length of chimeric segment"
-                        help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used." />
-                        <param argument="--chimScoreMin" type="integer" min="0" value="0"
-                        label="Minimum total (summed) score of chimeric segments"/>
-                        <param argument="--chimScoreDropMax" type="integer" min="0" value="20"
-                        label="Maximum difference of chimeric score from read length"/>
-                        <param argument="--chimScoreSeparation" type="integer" min="0" value="10"
-                        label="Minimum difference between the best chimeric score and the next one"/>
-                        <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1"
-                        label="Penalty for a non-GT/AG chimeric junction"/>
-                        <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20"
-                        label="Minimum overhang for a chimeric junction"/>
-                        <param argument="--chimSegmentReadGapMax" type="integer" min="0" value="0"
-                        label="Maximum gap in the read sequence between chimeric segments" />
-                        <param argument="--chimFilter" type="boolean" truevalue="banGenomicN" falsevalue="None" checked="true"
-                        label="Discard chimeric alignments with Ns in the genome sequence around the chimeric junction" />
-                        <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10"
-                        label="Maximum number of multi-alignments for the main chimeric segment."
-                        help="A value of 1 prohibits multimapping main segments"/>
-                        <param argument="--chimMultimapNmax" type="integer" min="1" value="1"
-                        label="Maximum number of chimeric multi-alignments"
-                        help="The default value of 1 only considers unique alignments. If you chose to report chimeric alignments alongside regular ones in the BAM output, this setting is ignored and only uniquely mapping chimeric reads get reported. " />
-                        <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1"
-                        label="Score range for multi-mapping chimeras"
-                        help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" />
-                    </section>
-                    <expand macro="limits" />
+                    <expand macro="full_algo_params"/>
                 </when>
             </conditional>
         </section>
@@ -1215,8 +1081,8 @@
 In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity
 
 - under *Output filter criteria*,
-  **Would you like to set additional output filters?**: select `Yes` to set 
-  **Maximum number of alignments to output a read's alignment results, plus 1** to 50 
+  **Would you like to set additional output filters?**: select `Yes` to set
+  **Maximum number of alignments to output a read's alignment results, plus 1** to 50
 
 - under *Algorithmic settings*, **Configure seed, alignment and limits options**:
   `use parameters suggested for Arriba`.
@@ -1253,7 +1119,7 @@
 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
 .. _Arriba: https://github.com/suhrig/arriba
 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
-.. _parameters: https://arriba.readthedocs.io/en/latest/workflow/
+.. _parameters: https://github.com/suhrig/arriba/wiki/03-Workflow
     ]]></help>
     <expand macro="citations"/>
 </tool>
diff -r 9b7a86a83fce -r 4746de55986e test-data/filtered4_algo_full.bam
Binary file test-data/filtered4_algo_full.bam has changed