# HG changeset patch
# User iuc
# Date 1511527428 18000
# Node ID e0ca9500999b03222e49b9f4f3f4056f6d0070e9
# Parent  69f044db244586fc9388b5133f21ca18f5ff33e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9

diff -r 69f044db2445 -r e0ca9500999b bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Tue Nov 14 15:02:02 2017 -0500
+++ b/bowtie2_wrapper.xml	Fri Nov 24 07:43:48 2017 -0500
@@ -1,324 +1,327 @@
-<tool id="bowtie2" name="Bowtie2" version="2.3.2.2" profile="17.01">
+<tool id="bowtie2" name="Bowtie2" version="2.3.3.1" profile="17.01">
     <description>- map reads against reference genome</description>
     <macros>
         <import>bowtie2_macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="2.3.2">bowtie2</requirement>
-        <requirement type="package" version="1.3.1">samtools</requirement>
+        <requirement type="package" version="2.3.3.1">bowtie2</requirement>
+        <requirement type="package" version="1.6">samtools</requirement>
     </requirements>
     <version_command>bowtie2 --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        ## prepare bowtie2 index
-        #set index_path = ''
-        #if str($reference_genome.source) == "history":
-            bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
-            ln -s -f '$reference_genome.own_file' genome.fa &&
-            #set index_path = 'genome'
-        #else:
-            #set index_path = $reference_genome.index.fields.path
-        #end if
+## prepare bowtie2 index
+#set index_path = ''
+#if str($reference_genome.source) == "history":
+    bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
+    ln -s -f '$reference_genome.own_file' genome.fa &&
+    #set index_path = 'genome'
+#else:
+    #set index_path = $reference_genome.index.fields.path
+#end if
 
-        ## Link in the input files, so bowtie2 can tell their type
+## Link in the input files, so bowtie2 can tell their type
 
-        #set compressed="False"
-        #set reads_are_fastq = True
-        #if str($library.type) == 'paired':
-            #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read1 = "input_f.fastq.gz"
-                #set compressed = "GZ"
-            #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read1 = "input_f.fastq.bz2"
-                #set compressed = "BZ2"
-            #else if $library.input_1.is_of_type('fasta'):
-                #set reads_are_fastq = False
-                #set read1 = "input_f.fasta"
-            #else:
-                #set read1 = "input_f.fastq"
-            #end if
-            ln -f -s '${library.input_1}' ${read1} &&
+#set compressed="False"
+#set reads_are_fastq = True
+#if str($library.type) == 'paired':
+    #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read1 = "input_f.fastq.gz"
+        #set compressed = "GZ"
+    #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read1 = "input_f.fastq.bz2"
+        #set compressed = "BZ2"
+    #else if $library.input_1.is_of_type('fasta'):
+        #set reads_are_fastq = False
+        #set read1 = "input_f.fasta"
+    #else:
+        #set read1 = "input_f.fastq"
+    #end if
+    ln -f -s '${library.input_1}' ${read1} &&
 
-            #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read2 = "input_r.fastq.gz"
-                #set compressed = "GZ"
-            #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read2 = "input_r.fastq.bz2"
-                #set compressed = "BZ2"
-            #else if $library.input_2.is_of_type('fasta'):
-                #set read2 = "input_r.fasta"
-            #else:
-                #set read2 = "input_r.fastq"
-            #end if
-            ln -f -s '${library.input_2}' ${read2} &&
-        #else if str($library.type) == 'paired_collection':
-            #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read1 = "input_f.fastq.gz"
-                #set compressed = "GZ"
-            #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read1 = "input_f.fastq.bz2"
-                #set compressed = "BZ2"
-            #else if $library.input_1.forward.is_of_type('fasta'):
-                #set reads_are_fastq = False
-                #set read1 = "input_f.fasta"
-            #else:
-                #set read1 = "input_f.fastq"
-            #end if
-            ln -s '${library.input_1.forward}' ${read1} &&
+    #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read2 = "input_r.fastq.gz"
+        #set compressed = "GZ"
+    #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read2 = "input_r.fastq.bz2"
+        #set compressed = "BZ2"
+    #else if $library.input_2.is_of_type('fasta'):
+        #set read2 = "input_r.fasta"
+    #else:
+        #set read2 = "input_r.fastq"
+    #end if
+    ln -f -s '${library.input_2}' ${read2} &&
+#else if str($library.type) == 'paired_collection':
+    #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read1 = "input_f.fastq.gz"
+        #set compressed = "GZ"
+    #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read1 = "input_f.fastq.bz2"
+        #set compressed = "BZ2"
+    #else if $library.input_1.forward.is_of_type('fasta'):
+        #set reads_are_fastq = False
+        #set read1 = "input_f.fasta"
+    #else:
+        #set read1 = "input_f.fastq"
+    #end if
+    ln -s '${library.input_1.forward}' ${read1} &&
 
-            #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read2 = "input_r.fastq.gz"
-                #set compressed = "GZ"
-            #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read2 = "input_r.fastq.bz2"
-                #set compressed = "BZ2"
-            #else if $library.input_1.reverse.is_of_type("fasta"):
-                #set read2 = "input_r.fasta"
-            #else:
-                #set read2 = "input_r.fastq"
-            #end if
-            ln -s '${library.input_1.reverse}' ${read2} &&
+    #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read2 = "input_r.fastq.gz"
+        #set compressed = "GZ"
+    #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read2 = "input_r.fastq.bz2"
+        #set compressed = "BZ2"
+    #else if $library.input_1.reverse.is_of_type("fasta"):
+        #set read2 = "input_r.fasta"
+    #else:
+        #set read2 = "input_r.fastq"
+    #end if
+    ln -s '${library.input_1.reverse}' ${read2} &&
 
-        #else if str($library.type) == 'paired_interleaved':
-            #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read1 = "input_il.fastq.gz"
-                #set compressed = "GZ"
-            #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read1 = "input_il.fastq.bz2"
-                #set compressed = "BZ2"
-            #else if $library.input_1.is_of_type("fasta"):
-                #set reads_are_fastq = False
-                #set read1 = "input_il.fasta"
-            #else:
-                #set read1 = "input_il.fastq"
-            #end if
-            ln -s '${library.input_1}' ${read1} &&
+#else if str($library.type) == 'paired_interleaved':
+    #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read1 = "input_il.fastq.gz"
+        #set compressed = "GZ"
+    #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read1 = "input_il.fastq.bz2"
+        #set compressed = "BZ2"
+    #else if $library.input_1.is_of_type("fasta"):
+        #set reads_are_fastq = False
+        #set read1 = "input_il.fasta"
+    #else:
+        #set read1 = "input_il.fastq"
+    #end if
+    ln -s '${library.input_1}' ${read1} &&
+#else:
+    #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set read1 = "input_f.fastq.gz"
+        #set compressed = "GZ"
+    #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+        #set read1 = "input_f.fastq.bz2"
+        #set compressed = "BZ2"
+    #else if $library.input_1.is_of_type("fasta"):
+        #set reads_are_fastq = False
+        #set read1 = "input_f.fasta"
+    #else:
+        #set read1 = "input_f.fastq"
+    #end if
+    ln -s '${library.input_1}' ${read1} &&
+#end if
+
+## execute bowtie2
+
+bowtie2
+
+## number of threads
+-p \${GALAXY_SLOTS:-4}
+
+## index file path
+-x '$index_path'
+
+## Input reads are fasta?
+#if not reads_are_fastq:
+    -f
+#end if
+
+## Input reads
+#if str( $library.type ) == "single":
+    -U '${read1}'
+    #if str( $library.unaligned_file ) == "true":
+        #if $compressed == "GZ":
+            --un-gz '${output_unaligned_reads_l}'
+        #else if $compressed == "BZ2":
+            --un-bz2 '${output_unaligned_reads_l}'
         #else:
-            #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read1 = "input_f.fastq.gz"
-                #set compressed = "GZ"
-            #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read1 = "input_f.fastq.bz2"
-                #set compressed = "BZ2"
-            #else if $library.input_1.is_of_type("fasta"):
-                #set reads_are_fastq = False
-                #set read1 = "input_f.fasta"
-            #else:
-                #set read1 = "input_f.fastq"
-            #end if
-            ln -s '${library.input_1}' ${read1} &&
+            --un '${output_unaligned_reads_l}'
         #end if
-
-        ## execute bowtie2
-
-        bowtie2
-
-        ## number of threads
-        -p \${GALAXY_SLOTS:-4}
-
-        ## index file path
-        -x '$index_path'
-
-        ## Input reads are fasta?
-        #if not reads_are_fastq:
-            -f
+    #end if
+    #if str( $library.aligned_file ) == "true":
+        #if $compressed == "GZ":
+            --al-gz '${output_aligned_reads_l}'
+        #else if $compressed == "BZ2":
+            --al-bz2 '${output_aligned_reads_l}'
+        #else:
+            --al '${output_aligned_reads_l}'
         #end if
-
-        ## Input reads
-        #if str( $library.type ) == "single":
-            -U '${read1}'
-            #if str( $library.unaligned_file ) == "true":
-                #if $compressed == "GZ":
-                    --un-gz '${output_unaligned_reads_l}'
-                #else if $compressed == "BZ2":
-                    --un-bz2 '${output_unaligned_reads_l}'
-                #else:
-                    --un '${output_unaligned_reads_l}'
-                #end if
-            #end if
-            #if str( $library.aligned_file ) == "true":
-                #if $compressed == "GZ":
-                    --al-gz '${output_aligned_reads_l}'
-                #else if $compressed == "BZ2":
-                    --al-bz2 '${output_aligned_reads_l}'
-                #else:
-                    --al '${output_aligned_reads_l}'
-                #end if
-            #end if
+    #end if
 
-        #elif str( $library.type ) == "paired_interleaved":
-            --interleaved '${read1}'
-            #if str( $library.unaligned_file ) == "true":
-                #if $compressed == "GZ":
-                    --un-gz '${output_unaligned_reads_l}'
-                #else if $compressed == "BZ2":
-                    --un-bz2 '${output_unaligned_reads_l}'
-                #else:
-                    --un '${output_unaligned_reads_l}'
-                #end if
-            #end if
-            #if str( $library.aligned_file ) == "true":
-                #if $compressed == "GZ":
-                    --al-gz '${output_aligned_reads_l}'
-                #else if $compressed == "BZ2":
-                    --al-bz2 '${output_aligned_reads_l}'
-                #else:
-                    --al '${output_aligned_reads_l}'
-                #end if
-            #end if
+#elif str( $library.type ) == "paired_interleaved":
+    --interleaved '${read1}'
+    #if str( $library.unaligned_file ) == "true":
+        #if $compressed == "GZ":
+            --un-gz '${output_unaligned_reads_l}'
+        #else if $compressed == "BZ2":
+            --un-bz2 '${output_unaligned_reads_l}'
+        #else:
+            --un '${output_unaligned_reads_l}'
+        #end if
+    #end if
+    #if str( $library.aligned_file ) == "true":
+        #if $compressed == "GZ":
+            --al-gz '${output_aligned_reads_l}'
+        #else if $compressed == "BZ2":
+            --al-bz2 '${output_aligned_reads_l}'
+        #else:
+            --al '${output_aligned_reads_l}'
+        #end if
+    #end if
+#else:
+    -1 '${read1}'
+    -2 '${read2}'
+    #if str( $library.unaligned_file ) == "true":
+        #if $compressed == "GZ":
+            --un-conc-gz '${output_unaligned_reads_l}'
+        #else if $compressed == "BZ2":
+            --un-conc-bz2 '${output_unaligned_reads_l}'
+        #else:
+            --un-conc '${output_unaligned_reads_l}'
+        #end if
+    #end if
+    #if str( $library.aligned_file ) == "true":
+        #if $compressed == "GZ":
+            --al-conc-gz '${output_aligned_reads_l}'
+        #else if $compressed == "BZ2":
+            --al-conc-bz2 '${output_aligned_reads_l}'
         #else:
-            -1 '${read1}'
-            -2 '${read2}'
-            #if str( $library.unaligned_file ) == "true":
-                #if $compressed == "GZ":
-                    --un-conc-gz '${output_unaligned_reads_l}'
-                #else if $compressed == "BZ2":
-                    --un-conc-bz2 '${output_unaligned_reads_l}'
-                #else:
-                    --un-conc '${output_unaligned_reads_l}'
-                #end if
-            #end if
-            #if str( $library.aligned_file ) == "true":
-                #if $compressed == "GZ":
-                    --al-conc-gz '${output_aligned_reads_l}'
-                #else if $compressed == "BZ2":
-                    --al-conc-bz2 '${output_aligned_reads_l}'
-                #else:
-                    --al-conc '${output_aligned_reads_l}'
-                #end if
-            #end if
-            #if str( $library.paired_options.paired_options_selector ) == "yes":
-                -I "${library.paired_options.I}"
-                -X "${library.paired_options.X}"
-                ${library.paired_options.fr_rf_ff}
-                ${library.paired_options.no_mixed}
-                ${library.paired_options.no_discordant}
-                ${library.paired_options.dovetail}
-                ${library.paired_options.no_contain}
-                ${library.paired_options.no_overlap}
-            #end if
+            --al-conc '${output_aligned_reads_l}'
         #end if
+    #end if
+    #if str( $library.paired_options.paired_options_selector ) == "yes":
+        -I ${library.paired_options.I}
+        -X ${library.paired_options.X}
+        ${library.paired_options.fr_rf_ff}
+        ${library.paired_options.no_mixed}
+        ${library.paired_options.no_discordant}
+        ${library.paired_options.dovetail}
+        ${library.paired_options.no_contain}
+        ${library.paired_options.no_overlap}
+    #end if
+#end if
 
-        ## Read group information.
-        @define_read_group_helpers@
-        #if str( $library.type ) == "single":
-            #set $rg_auto_name = $read_group_name_default($library.input_1)
-        #elif str( $library.type ) == "paired":
-            #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
-        #else
-            #set $rg_auto_name = $read_group_name_default($library.input_1)
-        #end if
-        @set_use_rg_var@
-        @set_read_group_vars@
-        #if $use_rg
-          $format_read_group("", $rg_id, '"', arg='--rg-id ')
-          $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
-          $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
-          $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
-          $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
-          $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
-          $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
-          $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
-          $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
-          $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
-          $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
-          $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
-        #end if
+## Read group information.
+@define_read_group_helpers@
+#if str( $library.type ) == "single":
+    #set $rg_auto_name = $read_group_name_default($library.input_1)
+#elif str( $library.type ) == "paired":
+    #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
+#else
+    #set $rg_auto_name = $read_group_name_default($library.input_1)
+#end if
+@set_use_rg_var@
+@set_read_group_vars@
+#if $use_rg
+  $format_read_group("", $rg_id, '"', arg='--rg-id ')
+  $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
+  $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
+  $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
+  $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
+  $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
+  $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
+  $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
+  $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
+  $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
+  $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
+  $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
+#end if
 
-        ## Analysis type
-        #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
-            $analysis_type.presets
-        #elif str( $analysis_type.analysis_type_selector ) == "full":
-            #if str( $analysis_type.input_options.input_options_selector ) == "yes":
-                --skip "${analysis_type.input_options.skip}"
-                --qupto "${analysis_type.input_options.qupto}"
-                --trim5 "${analysis_type.input_options.trim5}"
-                --trim3 "${analysis_type.input_options.trim3}"
-                ${analysis_type.input_options.qv_encoding}
-                ${analysis_type.input_options.solexa_quals}
-                ${analysis_type.input_options.int_quals}
-            #end if
+## Analysis type
+#if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
+    $analysis_type.presets
+#elif str( $analysis_type.analysis_type_selector ) == "full":
+    #if str( $analysis_type.input_options.input_options_selector ) == "yes":
+        --skip ${analysis_type.input_options.skip}
+        --qupto ${analysis_type.input_options.qupto}
+        --trim5 ${analysis_type.input_options.trim5}
+        --trim3 ${analysis_type.input_options.trim3}
+        ${analysis_type.input_options.qv_encoding}
+        ${analysis_type.input_options.solexa_quals}
+        ${analysis_type.input_options.int_quals}
+    #end if
 
-            #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
-                -N "${analysis_type.alignment_options.N}"
-                -L "${analysis_type.alignment_options.L}"
-                -i "${analysis_type.alignment_options.i}"
-                --n-ceil "${analysis_type.alignment_options.n_ceil}"
-                --dpad "${analysis_type.alignment_options.dpad}"
-                --gbar "${analysis_type.alignment_options.gbar}"
-                ${analysis_type.alignment_options.ignore_quals}
-                ${analysis_type.alignment_options.nofw}
-                ${analysis_type.alignment_options.norc}
-                ${analysis_type.alignment_options.no_1mm_upfront}
-                #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
-                    --end-to-end
-                    --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}"
-                #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
-                    --local
-                    --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"
-                #end if
-            #end if
+    #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
+        -N ${analysis_type.alignment_options.N}
+        -L ${analysis_type.alignment_options.L}
+        -i '${analysis_type.alignment_options.i}'
+        --n-ceil '${analysis_type.alignment_options.n_ceil}'
+        --dpad ${analysis_type.alignment_options.dpad}
+        --gbar ${analysis_type.alignment_options.gbar}
+        ${analysis_type.alignment_options.ignore_quals}
+        ${analysis_type.alignment_options.nofw}
+        ${analysis_type.alignment_options.norc}
+        ${analysis_type.alignment_options.no_1mm_upfront}
+        #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
+            --end-to-end
+            --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
+        #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
+            --local
+            --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
+        #end if
+    #end if
 
-            #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
-                #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
-                    --ma "${analysis_type.scoring_options.ma}"
-                #end if
-                --mp "${analysis_type.scoring_options.mp}"
-                --np "${analysis_type.scoring_options.np}"
-                --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"
-                --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}"
-            #end if
+    #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
+        #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
+            --ma ${analysis_type.scoring_options.ma}
+        #end if
+        --mp '${analysis_type.scoring_options.mp}'
+        --np ${analysis_type.scoring_options.np}
+        --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
+        --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
+    #end if
 
-            #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
-                -k "${analysis_type.reporting_options.k}"
-            #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
-                -a
-            #end if
+    #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
+        -k ${analysis_type.reporting_options.k}
+    #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
+        -a
+    #end if
 
-            #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
-                -D "${analysis_type.effort_options.D}"
-                -R "${analysis_type.effort_options.R}"
-            #end if
+    #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
+        -D ${analysis_type.effort_options.D}
+        -R ${analysis_type.effort_options.R}
+    #end if
 
-            #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
-                ${analysis_type.sam_options.no_unal}
-                ${analysis_type.sam_options.omit_sec_seq}
-            #end if
+    #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
+        ${analysis_type.sam_options.no_unal}
+        ${analysis_type.sam_options.omit_sec_seq}
+        ${analysis_type.sam_options.sam-no-qname-trunc}
+        ${analysis_type.sam_options.xeq}
+        ${analysis_type.sam_options.soft-clipped-unmapped-tlen}
+    #end if
 
-            #if str( $analysis_type.other_options.other_options_selector ) == "yes":
-                ${analysis_type.other_options.reorder}
-                ${analysis_type.other_options.non_deterministic}
-                --seed "${analysis_type.other_options.seed}"
-            #end if
-
-        #elif str( $analysis_type.analysis_type_selector ) == "cline":
-            ${analysis_type.cline}
-        #end if
+    #if str( $analysis_type.other_options.other_options_selector ) == "yes":
+        ${analysis_type.other_options.reorder}
+        ${analysis_type.other_options.non_deterministic}
+        --seed ${analysis_type.other_options.seed}
+    #end if
 
-        ## mapping stats (i.e. stderr from bowtie2)
-        #if $save_mapping_stats
-            2> '$mapping_stats'
-        #end if
+#elif str( $analysis_type.analysis_type_selector ) == "cline":
+    ${analysis_type.cline}
+#end if
 
-        ## output file
-        #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
-            | samtools sort -O bam -o '$output'
-        #else
-            > '$output_sam'
-        #end if
+## mapping stats (i.e. stderr from bowtie2)
+#if $save_mapping_stats
+    2> '$mapping_stats'
+#end if
 
-        ## rename unaligned sequence files
-        #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
-            #from os.path import splitext
-            #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
-            && mv "${ _unaligned_root }.1${_unaligned_ext}" '$output_unaligned_reads_l'
-            && mv "${ _unaligned_root }.2${_unaligned_ext}" '$output_unaligned_reads_r'
-        #end if
-        #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
-            #from os.path import splitext
-            #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
-            && mv "${ _aligned_root }.1${_aligned_ext}" '$output_aligned_reads_l'
-            && mv "${ _aligned_root }.2${_aligned_ext}" '$output_aligned_reads_r'
-        #end if
+## output file
+#if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
+    | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
+#else
+    > '$output_sam'
+#end if
+
+## rename unaligned sequence files
+#if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
+    #from os.path import splitext
+    #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
+    && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
+    && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
+#end if
+#if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
+    #from os.path import splitext
+    #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
+    && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
+    && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
+#end if
 
         ]]></command>
     <inputs>
@@ -333,34 +336,25 @@
 
             <when value="single">
                 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
-
                 <expand macro="align_unalign" />
-
             </when>
             <when value="paired">
                 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
                 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
-
                 <expand macro="align_unalign" />
                 <expand macro="paired_end_options" />
-
             </when>
             <when value="paired_collection">
                 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
-
                 <expand macro="align_unalign" />
                 <expand macro="paired_end_options" />
-
             </when>
             <when value="paired_interleaved">
                 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
-               
                 <expand macro="align_unalign" />
                 <expand macro="paired_end_options" />
-
             </when>
         </conditional>
-
         <!-- reference genome -->
         <conditional name="reference_genome">
           <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
@@ -379,7 +373,6 @@
             <param name="own_file" type="data" format="fasta" label="Select reference genome" />
           </when>
         </conditional>
-
         <!-- read group settings -->
         <expand macro="read_group_conditional" />
         <conditional name="analysis_type">
@@ -502,7 +495,6 @@
                         <!-- do nothing -->
                     </when>
                 </conditional>
-
                 <conditional name="sam_options">
                     <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
                         <option value="yes">Yes</option>
@@ -511,6 +503,9 @@
                     <when value="yes">
                         <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
                         <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
+                        <param argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
+                        <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
+                        <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
                     </when>
                     <when value="no">
                         <!-- do nothing -->
@@ -535,11 +530,8 @@
         </conditional>
         <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
     </inputs>
-
     <!-- define outputs -->
-
     <outputs>
-
         <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
             <filter>library['unaligned_file'] is True</filter>
             <actions>
@@ -618,7 +610,6 @@
                 </conditional>
             </actions>
         </data>
-
         <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
           <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
           <actions>
@@ -639,7 +630,6 @@
             </conditional>
           </actions>
         </data>
-
         <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
           <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
           <actions>
@@ -663,9 +653,7 @@
         <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
           <filter>save_mapping_stats is True</filter>
         </data>
-
     </outputs>
-
     <tests>
         <test>
             <!-- test on paired-end datasets -->
@@ -779,7 +767,6 @@
             <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
         </test>
     </tests>
-
     <help><![CDATA[
 **Bowtie2 Overview**