# HG changeset patch
# User iuc
# Date 1643922805 0
# Node ID 6d44c9f1a42b4200ec447097571fdd1441613745
# Parent  8157a81f511c4881e9eeb7a6b03e3b6c8d8e7051
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"

diff -r 8157a81f511c -r 6d44c9f1a42b bbmap.xml
--- a/bbmap.xml	Tue Feb 01 23:01:08 2022 +0000
+++ b/bbmap.xml	Thu Feb 03 21:13:25 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy3" profile="@PROFILE@">
     <description>short-read aligner</description>
     <macros>
         <import>macros.xml</import>
@@ -44,59 +44,274 @@
     ln -s '${read2}' '${read2_file}' &&
 #end if
 
-bbmap.sh t=\${GALAXY_SLOTS:-4} ref='${ref}'
+bbmap.sh
+
+#### Indexing Parameters
+nodisk=f
+ref='${ref}'
+k=13
+usemodulo=f
+rebuild=f
+
+#### Input Parameters
 #if str($input_type_cond.input_type) == 'single':
     in='${read1_file}'
 #else:
-    in1='${read1_file}' in2='${read2_file}'
+    in='${read1_file}' in2='${read2_file}'
 #end if
-#if str($output_sort) == 'coordinate':
-    out='mapped.bam'; samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output' 'mapped.bam'
-#elif str($output_sort) == 'name':
-    out='mapped.bam'; samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output' 'mapped.bam'
+fastareadlen=500
+unpigz=f
+touppercase=t
+
+#### Sampling Parameters
+reads=-1
+samplerate=1
+skipreads=0
+
+#### Mapping Parameters
+maxindel=$mapping_options.maxindel
+strictmaxindel='$mapping_options.strictmaxindel'
+tipsearch=$mapping_options.tipsearch
+minid=$mapping_options.minid
+minhits=$mapping_options.minhits
+local='$mapping_options.local'
+perfectmode='$mapping_options.perfectmode'
+semiperfectmode='$mapping_options.semiperfectmode'
+threads=\${GALAXY_SLOTS:-4}
+ambiguous='$mapping_options.ambiguous'
+samestrandpairs='$mapping_options.samestrandpairs'
+requirecorrectstrand='$mapping_options.requirecorrectstrand'
+killbadpairs='$mapping_options.killbadpairs'
+pairedonly='$mapping_options.pairedonly'
+rcomp='$mapping_options.rcomp'
+rcompmate='$mapping_options.rcompmate'
+pairlen=$mapping_options.pairlen
+rescuedist=$mapping_options.rescuedist
+rescuemismatches=$mapping_options.rescuemismatches
+averagepairdist=$mapping_options.averagepairdist
+deterministic='$mapping_options.deterministic'
+bandwidthratio='$mapping_options.bandwidthratio'
+bandwidth='$mapping_options.bandwidth'
+usejni='f'
+maxsites2=$mapping_options.maxsites2
+ignorefrequentkmers='$mapping_options.ignorefrequentkmers'
+excludefraction=$mapping_options.excludefraction
+greedy='$mapping_options.greedy'
+kfilter=$mapping_options.kfilter
+
+#### Quality and Trimming Parameters
+qin='auto'
+qout='auto'
+qtrim='$qt_options.qtrim'
+untrim='$qt_options.untrim'
+trimq=$qt_options.trimq
+mintrimlength=$qt_options.mintrimlength
+fakefastaquality=$qt_options.fakefastaquality
+ignorebadquality='$qt_options.ignorebadquality'
+usequality='$qt_options.usequality'
+minaveragequality=$qt_options.minaveragequality
+maqb=$qt_options.maqb
+
+#### Post-Filtering options
+idfilter=$pf_options.idfilter
+subfilter=$pf_options.subfilter
+insfilter=$pf_options.insfilter
+delfilter=$pf_options.delfilter
+indelfilter=$pf_options.indelfilter
+editfilter=$pf_options.editfilter
+inslenfilter=$pf_options.inslenfilter
+dellenfilter=$pf_options.dellenfilter
+nfilter=$pf_options.nfilter
+
+#### Output parameters
+secondary='$output_options.secondary'
+maxsites=$output_options.maxsites
+sssr=$output_options.sssr
+ssao='$output_options.ssao'
+quickmatch='$output_options.quickmatch'
+trimreaddescriptions='$output_options.trimreaddescriptions'
+machineout='$output_options.machineout'
+printunmappedcount='$output_options.printunmappedcount'
+renamebyinsert='$output_options.renamebyinsert'
+#if str($output_options.output_sort) == 'coordinate':
+    out='all_reads.bam'
+    outu='unmapped_reads.bam'
+    outm='mapped_reads.bam'
+    && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_all_reads' 'all_reads.bam'
+    && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
+    && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
+#elif str($output_options.output_sort) == 'name':
+    out='all_reads.bam'
+    outu='unmapped_reads.bam'
+    outm='mapped_reads.bam'
+    && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_all_reads' 'all_reads.bam'
+    && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
+    && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
 #else:
-    out='mapped.bam' && mv 'mapped.bam' '$output'
+    out='all_reads.bam'
+    outu='unmapped_reads.bam'
+    outm='mapped_reads.bam'
+    && mv 'all_reads.bam' '$output_all_reads'
+    && mv 'unmapped_reads.bam' '$output_unmapped_reads'
+    && mv 'mapped_reads.bam' '$output_mapped_reads'
 #end if
 ]]></command>
     <inputs>
         <expand macro="input_type_cond"/>
         <expand macro="reference_source_cond"/>
-        <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can significantly extend the run time of the tool (it runs using a single thread).">
-            <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
-            <option value="name">Sort by read names</option>
-            <option value="unsorted">Not sorted (sorted as input)</option>
-        </param>
+        <section name="mapping_options" title="Mapping options">
+            <param argument="maxindel" type="integer" value="16000" label="Maximum indel length" help="Don't look for indels longer than this (lower is faster)"/>
+            <param argument="strictmaxindel" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not allow indels longer than the specified maximum indel length?" help="By default these are not sought, but may be found anyway"/>
+            <param argument="tipsearch" type="integer" value="100" label="Look this far for read-end deletions with anchors shorter than K using brute force"/>
+            <param argument="minid" type="float" value="0.76" label="Approximate minimum alignment identity to look for" help="Higher is faster and less sensitive"/>
+            <param argument="minhits" type="integer" value="1" label="Minimum number of seed hits required for candidate sites" help="Higher is faster"/>
+            <param argument="local" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Use local (rather than global) alignments?"/>
+            <param argument="perfectmode" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Allow only perfect mappings?"/>
+            <param argument="semiperfectmode" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Allow only perfect and semiperfect (perfect except for N's in the reference) mappings?"/>
+            <param name="ambiguous" type="select" label="Specify behavior on ambiguously-mapped reads with multiple top-scoring mapping locations">
+                <option value="best" selected="true">Use the first best site</option>
+                <option value="toss">Consider unmapped</option>
+                <option value="random">Select one top-scoring site randomly</option>
+                <option value="all">Retain all top-scoring sites</option>
+            </param>
+            <param argument="samestrandpairs" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Map paired reads to the same strand?" help="No value will map to opposite strands"/>
+            <param argument="requirecorrectstrand" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Forbid pairing of reads without correct strand orientation?" help="Select No for long-mate-pair libraries"/>
+            <param argument="killbadpairs" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Mark the read with the lower mapping quality as unmapped if a read pair is mapped with an inappropriate insert size or orientation?"/>
+            <param argument="pairedonly" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Treat unpaired reads as unmapped?"/>
+            <param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Reverse complement both reads prior to mapping (for LMP outward-facing libraries)?"/>
+            <param argument="rcompmate" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Reverse complement read2 prior to mapping?"/>
+            <param argument="pairlen" type="integer" value="32000" label="Maximum allowed distance between paired reads"/>
+            <param argument="rescuedist" type="integer" value="1200" label="Maximum average insert size for trying to rescue paired reads" help="Lower is faster"/>
+            <param argument="rescuemismatches" type="integer" value="32" label="Maximum mismatches allowed in a rescued read" help="Lower is faster"/>
+            <param argument="averagepairdist" type="integer" value="100" label="Initial average distance between paired reads" help="Varies dynamically; does not need to be specified"/>
+            <param argument="deterministic" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Run in deterministic mode?" help="BBMap is deterministic without this flag if using single-ended reads?"/>
+            <param argument="bandwidthratio" type="integer" value="0" label="Restrict alignment band to this fraction of read length" help="Zero value ignores"/>
+            <param argument="bandwidth" type="integer" value="0" label="Set the bandwidth directly to this fraction of read length" help="Faster but less accurate"/>
+            <param argument="maxsites2" type="integer" value="800" label="Maximum number of alignments per read to output"/>
+            <param argument="ignorefrequentkmers" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Discard low-information kmers that occur often?"/>
+            <param argument="excludefraction" type="float" value="0.03" label="Fraction of kmers to ignore" help="For example, 0.03 will ignore the most common 3% of kmers"/>
+            <param argument="greedy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use a greedy algorithm to discard the least-useful kmers on a per-read basis?"/>
+            <param argument="kfilter" type="integer" value="0" label="Potential mapping sites must have at least this many consecutive exact matches" help="Zero value ignores"/>
+        </section>
+        <section name="qt_options" title="Quality and trimming options">
+            <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
+                <option value="f" selected="true">No trimming</option>
+                <option value="l">Trim left</option>
+                <option value="r">Trim right</option>
+                <option value="lr">Trim both</option>
+            </param>
+            <param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/>
+            <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
+            <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
+            <param argument="fakefastaquality" type="integer" value="-1" max="50" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/>
+            <param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/>
+            <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
+            <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/>
+            <param argument="maqb" type="integer" value="0" label="Calculate maq from this many initial bases" help="Zero value ignores"/>
+        </section>
+        <section name="output_options" title="Output options">
+            <param argument="secondary" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output secondary alignments?"/>
+            <param argument="maxsites" type="integer" value="5" label="Maximum number of total alignments to output per read" help="Relevant only when outputting secondary alignments"/>
+            <param argument="sssr" type="float" value="0.95" label="Output only secondary alignments with score of at least this fraction of primary"/>
+            <param argument="ssao" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Only output secondary alignments for ambiguously-mapped reads?"/>
+            <param argument="quickmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Generate cigar strings more quickly?"/>
+            <param argument="trimreaddescriptions" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Truncate read and ref names at the first whitespace, assuming that the remainder is a comment or description?"/>
+            <param argument="machineout" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output statistics in machine-friendly (key=value) format?"/>
+            <param argument="printunmappedcount" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output the total number of unmapped reads and bases?" help="If input is paired, the number will be of pairs for which both reads are unmapped"/>
+            <param argument="renamebyinsert" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Rename reads based on their mapped insert size?"/>
+            <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can significantly extend the run time of the tool (it runs using a single thread)">
+                <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
+                <option value="name">Sort by read names</option>
+                <option value="unsorted">Not sorted (sorted as input)</option>
+            </param>
+        </section>
+        <section name="pf_options" title="Post-filtering options">
+            <param argument="idfilter" type="integer" value="0" min="0" max="1" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/>
+            <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/>
+            <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/>
+            <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/>
+            <param argument="indelfilter" type="integer" value="-1" label="Ban alignments with more than this many indels" help="Negative value ignores"/>
+            <param argument="editfilter" type="integer" value="-1" label="Ban alignments with more than this many edits" help="Negative value ignores"/>
+            <param argument="inslenfilter" type="integer" value="-1" label="Ban alignments with an insertion longer than this" help="Negative value ignores"/>
+            <param argument="dellenfilter" type="integer" value="-1" label="Ban alignments with a deletion longer than this" help="Negative value ignores"/>
+            <param argument="nfilter" type="integer" value="-1" label="Ban alignments with more than this many ns (includes nocall, noref, and off scaffold ends)" help="Negative value ignores"/>
+        </section>
     </inputs>
     <outputs>
-        <data format="bam" name="output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
+        <data format="bam" name="output_all_reads" label="${tool.name} on ${on_string} (all reads)">
+            <expand macro="dbKeyActionsBBMap"/>
+            <change_format>
+                <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/>
+                <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/>
+            </change_format>
+        </data>
+        <data format="bam" name="output_unmapped_reads" label="${tool.name} on ${on_string} (unmapped reads)">
             <expand macro="dbKeyActionsBBMap"/>
             <change_format>
-                <when input="output_sort" value="name" format="qname_sorted.bam" />
-                <when input="output_sort" value="unsorted" format="qname_input_sorted.bam" />
+                <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/>
+                <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/>
+            </change_format>
+        </data>
+        <data format="bam" name="output_mapped_reads" label="${tool.name} on ${on_string} (mapped reads)">
+            <expand macro="dbKeyActionsBBMap"/>
+            <change_format>
+                <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/>
+                <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/>
             </change_format>
         </data>
     </outputs>
     <tests>
         <!-- Single file, cached reference, output coordinate sorted -->
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="3">
             <param name="input_type" value="single"/>
             <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
-            <output name="output" file="output1.bam" ftype="bam" lines_diff="4">
-                <metadata name="dbkey" value="89" />
+            <param name="output_sort" value="coordinate"/>
+            <output name="output_all_reads" ftype="bam">
+                <metadata name="dbkey" value="89"/>
+                <assert_contents>
+                    <has_size value="9433" delta="300"/>
+                </assert_contents>
+            </output>
+            <output name="output_unmapped_reads" ftype="bam">
+                <metadata name="dbkey" value="89"/>
+                <assert_contents>
+                    <has_size value="9432" delta="300"/>
+                </assert_contents>
+            </output>
+            <output name="output_mapped_reads" ftype="bam">
+                <metadata name="dbkey" value="89"/>
+                <assert_contents>
+                    <has_size value="938" delta="100"/>
+                </assert_contents>
             </output>
         </test>
         <!-- Paired reads in separate datasets, cached reference, output name sorted -->
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="3">
             <param name="input_type" value="pair"/>
             <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
             <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
             <param name="output_sort" value="name"/>
-            <output name="output" file="output2.bam" ftype="qname_sorted.bam" lines_diff="4">
-                <metadata name="dbkey" value="89" />
+            <output name="output_all_reads" ftype="qname_sorted.bam">
+                <metadata name="dbkey" value="89"/>
+                <assert_contents>
+                    <has_size value="17103" delta="600"/>
+                </assert_contents>
+            </output>
+            <output name="output_unmapped_reads" ftype="qname_sorted.bam">
+                <metadata name="dbkey" value="89"/>
+                <assert_contents>
+                    <has_size value="17105" delta="600"/>
+                </assert_contents>
+            </output>
+            <output name="output_mapped_reads" ftype="qname_sorted.bam">
+                <metadata name="dbkey" value="89"/>
+                <assert_contents>
+                    <has_size value="967" delta="100"/>
+                </assert_contents>
             </output>
         </test>
         <!-- Collection of Paired reads, history reference, output unsorted -->
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="3">
             <param name="input_type" value="paired"/>
             <param name="reads_collection">
                 <collection type="paired">
@@ -107,8 +322,23 @@
             <param name="ref_source" value="history"/>
             <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/>
             <param name="output_sort" value="unsorted"/>
-            <output name="output" file="output3.bam" ftype="qname_input_sorted.bam" lines_diff="4">
-                <metadata name="dbkey" value="89" />
+            <output name="output_all_reads" ftype="qname_input_sorted.bam">
+                <metadata name="dbkey" value="89"/>
+                <assert_contents>
+                    <has_size value="17059" delta="600"/>
+                </assert_contents>
+            </output>
+            <output name="output_unmapped_reads" ftype="qname_input_sorted.bam">
+                <metadata name="dbkey" value="89"/>
+                <assert_contents>
+                    <has_size value="17059" delta="600"/>
+                </assert_contents>
+            </output>
+            <output name="output_mapped_reads" ftype="qname_input_sorted.bam">
+                <metadata name="dbkey" value="89"/>
+                <assert_contents>
+                    <has_size value="906" delta="100"/>
+                </assert_contents>
             </output>
         </test>
     </tests>
diff -r 8157a81f511c -r 6d44c9f1a42b macros.xml
--- a/macros.xml	Tue Feb 01 23:01:08 2022 +0000
+++ b/macros.xml	Thu Feb 03 21:13:25 2022 +0000
@@ -1,10 +1,10 @@
 <macros>
     <token name="@WRAPPER_VERSION@">1.0.0</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">20.09</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="38.92">bbmap</requirement>
+            <requirement type="package" version="38.93">bbmap</requirement>
         </requirements>
     </xml>
     <macro name="dbKeyActionsBBMap">
diff -r 8157a81f511c -r 6d44c9f1a42b test-data/output1.bam
Binary file test-data/output1.bam has changed
diff -r 8157a81f511c -r 6d44c9f1a42b test-data/output2.bam
Binary file test-data/output2.bam has changed
diff -r 8157a81f511c -r 6d44c9f1a42b test-data/output3.bam
Binary file test-data/output3.bam has changed