bbtools_bbmap: bbmap.xml annotate

annotate bbmap.xml @ 12:3f94a2e3d513 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit e6a741fc2fe38e91a310e9c29467c814a2d34cac

author	iuc
date	Sat, 18 May 2024 19:14:17 +0000
parents	7f19559b8b55
children

rev	line source
7 9ed6579f52f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f iuc parents: 6 diff changeset	1 <tool id="bbtools_bbmap" name="BBTools: BBMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	2 <description>short-read aligner</description>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	3 <macros>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	4 <import>macros.xml</import>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	5 </macros>
7 9ed6579f52f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f iuc parents: 6 diff changeset	6 <expand macro="edam_ontology"/>
12 3f94a2e3d513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit e6a741fc2fe38e91a310e9c29467c814a2d34cac iuc parents: 11 diff changeset	7 <xrefs>
3f94a2e3d513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit e6a741fc2fe38e91a310e9c29467c814a2d34cac iuc parents: 11 diff changeset	8 <xref type="bio.tools">bbmap</xref>
3f94a2e3d513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit e6a741fc2fe38e91a310e9c29467c814a2d34cac iuc parents: 11 diff changeset	9 </xrefs>
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	10 <expand macro="requirements"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	11 <command detect_errors="exit_code"><![CDATA[
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	12 #if str($ref_source_cond.ref_source) == 'cached'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	13 #set ref = str($ref_source_cond.reference.fields.path)
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	14 #else:
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	15 #set ref = $ref_source_cond.reference
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	16 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	17
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	18 #if str($input_type_cond.input_type) in ['single', 'pair']:
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	19 #set read1 = $input_type_cond.read1
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	20 ## bbmap uses the file extension to determine the input format.
3 8157a81f511c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97" iuc parents: 2 diff changeset	21 #set ext = '.fastq'
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	22 #if $read1.ext.endswith('.gz'):
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	23 #set ext = $ext + '.gz'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	24 #end if
3 8157a81f511c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97" iuc parents: 2 diff changeset	25 #set read1_file = 'forward' + $ext
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	26 ln -s '${read1}' '${read1_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	27 #if str($input_type_cond.input_type) == 'pair':
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	28 #set read2 = $input_type_cond.read2
3 8157a81f511c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97" iuc parents: 2 diff changeset	29 #set read2_file = 'reverse' + $ext
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	30 ln -s '${read2}' '${read2_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	31 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	32 #else:
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	33 #set read1 = $input_type_cond.reads_collection['forward']
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	34 ## bbmap uses the file extension to determine the input format.
11 7f19559b8b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29 iuc parents: 7 diff changeset	35 #set ext = '.fastq'
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	36 #if $read1.ext.endswith('.gz'):
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	37 #set ext = $ext + '.gz'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	38 #end if
11 7f19559b8b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29 iuc parents: 7 diff changeset	39 #set read1_file = 'forward' + $ext
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	40 ln -s '${read1}' '${read1_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	41 #set read2 = $input_type_cond.reads_collection['reverse']
11 7f19559b8b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29 iuc parents: 7 diff changeset	42 #set read2_file = 'reverse' + $ext
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	43 ln -s '${read2}' '${read2_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	44 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	45
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	46 bbmap.sh
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	47
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	48 #### Indexing Parameters
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	49 nodisk=f
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	50 ref='${ref}'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	51 k=13
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	52 usemodulo=f
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	53 rebuild=f
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	54
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	55 #### Input Parameters
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	56 #if str($input_type_cond.input_type) == 'single':
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	57 in='${read1_file}'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	58 #else:
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	59 in='${read1_file}' in2='${read2_file}'
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	60 #end if
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	61 fastareadlen=500
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	62 unpigz=f
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	63 touppercase=t
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	64
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	65 #### Sampling Parameters
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	66 reads=-1
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	67 samplerate=1
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	68 skipreads=0
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	69
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	70 #### Mapping Parameters
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	71 maxindel=$mapping_options.maxindel
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	72 strictmaxindel='$mapping_options.strictmaxindel'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	73 tipsearch=$mapping_options.tipsearch
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	74 minid=$mapping_options.minid
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	75 minhits=$mapping_options.minhits
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	76 local='$mapping_options.local'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	77 perfectmode='$mapping_options.perfectmode'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	78 semiperfectmode='$mapping_options.semiperfectmode'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	79 threads=\${GALAXY_SLOTS:-4}
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	80 ambiguous='$mapping_options.ambiguous'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	81 samestrandpairs='$mapping_options.samestrandpairs'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	82 requirecorrectstrand='$mapping_options.requirecorrectstrand'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	83 killbadpairs='$mapping_options.killbadpairs'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	84 pairedonly='$mapping_options.pairedonly'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	85 rcomp='$mapping_options.rcomp'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	86 rcompmate='$mapping_options.rcompmate'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	87 pairlen=$mapping_options.pairlen
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	88 rescuedist=$mapping_options.rescuedist
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	89 rescuemismatches=$mapping_options.rescuemismatches
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	90 averagepairdist=$mapping_options.averagepairdist
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	91 deterministic='$mapping_options.deterministic'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	92 bandwidthratio='$mapping_options.bandwidthratio'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	93 bandwidth='$mapping_options.bandwidth'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	94 usejni='f'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	95 maxsites2=$mapping_options.maxsites2
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	96 ignorefrequentkmers='$mapping_options.ignorefrequentkmers'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	97 excludefraction=$mapping_options.excludefraction
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	98 greedy='$mapping_options.greedy'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	99 kfilter=$mapping_options.kfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	100
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	101 #### Quality and Trimming Parameters
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	102 qin='auto'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	103 qout='auto'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	104 qtrim='$qt_options.qtrim'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	105 untrim='$qt_options.untrim'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	106 trimq=$qt_options.trimq
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	107 mintrimlength=$qt_options.mintrimlength
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	108 fakefastaquality=$qt_options.fakefastaquality
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	109 ignorebadquality='$qt_options.ignorebadquality'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	110 usequality='$qt_options.usequality'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	111 minaveragequality=$qt_options.minaveragequality
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	112 maqb=$qt_options.maqb
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	113
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	114 #### Post-Filtering options
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	115 idfilter=$pf_options.idfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	116 subfilter=$pf_options.subfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	117 insfilter=$pf_options.insfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	118 delfilter=$pf_options.delfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	119 indelfilter=$pf_options.indelfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	120 editfilter=$pf_options.editfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	121 inslenfilter=$pf_options.inslenfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	122 dellenfilter=$pf_options.dellenfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	123 nfilter=$pf_options.nfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	124
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	125 #### Output parameters
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	126 secondary='$output_options.secondary'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	127 maxsites=$output_options.maxsites
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	128 sssr=$output_options.sssr
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	129 ssao='$output_options.ssao'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	130 quickmatch='$output_options.quickmatch'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	131 trimreaddescriptions='$output_options.trimreaddescriptions'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	132 machineout='$output_options.machineout'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	133 printunmappedcount='$output_options.printunmappedcount'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	134 renamebyinsert='$output_options.renamebyinsert'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	135 #if str($output_options.output_sort) == 'coordinate':
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	136 out='all_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	137 outu='unmapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	138 outm='mapped_reads.bam'
6 858a65b52cf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95 iuc parents: 5 diff changeset	139 && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_all_reads' 'all_reads.bam'
858a65b52cf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95 iuc parents: 5 diff changeset	140 && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
858a65b52cf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95 iuc parents: 5 diff changeset	141 && samtools sort --no-PG -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	142 #elif str($output_options.output_sort) == 'name':
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	143 out='all_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	144 outu='unmapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	145 outm='mapped_reads.bam'
6 858a65b52cf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95 iuc parents: 5 diff changeset	146 && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_all_reads' 'all_reads.bam'
858a65b52cf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95 iuc parents: 5 diff changeset	147 && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
858a65b52cf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95 iuc parents: 5 diff changeset	148 && samtools sort --no-PG -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	149 #else:
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	150 out='all_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	151 outu='unmapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	152 outm='mapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	153 && mv 'all_reads.bam' '$output_all_reads'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	154 && mv 'unmapped_reads.bam' '$output_unmapped_reads'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	155 && mv 'mapped_reads.bam' '$output_mapped_reads'
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	156 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	157 ]]></command>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	158 <inputs>
2 e0ca2ec4f5d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad" iuc parents: 0 diff changeset	159 <expand macro="input_type_cond"/>
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	160 <expand macro="reference_source_cond"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	161 <section name="mapping_options" title="Mapping options">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	162 <param argument="maxindel" type="integer" value="16000" label="Maximum indel length" help="Don't look for indels longer than this (lower is faster)"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	163 <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"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	164 <param argument="tipsearch" type="integer" value="100" label="Look this far for read-end deletions with anchors shorter than K using brute force"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	165 <param argument="minid" type="float" value="0.76" label="Approximate minimum alignment identity to look for" help="Higher is faster and less sensitive"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	166 <param argument="minhits" type="integer" value="1" label="Minimum number of seed hits required for candidate sites" help="Higher is faster"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	167 <param argument="local" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Use local (rather than global) alignments?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	168 <param argument="perfectmode" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Allow only perfect mappings?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	169 <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?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	170 <param name="ambiguous" type="select" label="Specify behavior on ambiguously-mapped reads with multiple top-scoring mapping locations">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	171 <option value="best" selected="true">Use the first best site</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	172 <option value="toss">Consider unmapped</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	173 <option value="random">Select one top-scoring site randomly</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	174 <option value="all">Retain all top-scoring sites</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	175 </param>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	176 <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"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	177 <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"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	178 <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?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	179 <param argument="pairedonly" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Treat unpaired reads as unmapped?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	180 <param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Reverse complement both reads prior to mapping (for LMP outward-facing libraries)?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	181 <param argument="rcompmate" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Reverse complement read2 prior to mapping?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	182 <param argument="pairlen" type="integer" value="32000" label="Maximum allowed distance between paired reads"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	183 <param argument="rescuedist" type="integer" value="1200" label="Maximum average insert size for trying to rescue paired reads" help="Lower is faster"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	184 <param argument="rescuemismatches" type="integer" value="32" label="Maximum mismatches allowed in a rescued read" help="Lower is faster"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	185 <param argument="averagepairdist" type="integer" value="100" label="Initial average distance between paired reads" help="Varies dynamically; does not need to be specified"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	186 <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?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	187 <param argument="bandwidthratio" type="integer" value="0" label="Restrict alignment band to this fraction of read length" help="Zero value ignores"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	188 <param argument="bandwidth" type="integer" value="0" label="Set the bandwidth directly to this fraction of read length" help="Faster but less accurate"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	189 <param argument="maxsites2" type="integer" value="800" label="Maximum number of alignments per read to output"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	190 <param argument="ignorefrequentkmers" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Discard low-information kmers that occur often?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	191 <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"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	192 <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?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	193 <param argument="kfilter" type="integer" value="0" label="Potential mapping sites must have at least this many consecutive exact matches" help="Zero value ignores"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	194 </section>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	195 <section name="qt_options" title="Quality and trimming options">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	196 <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	197 <option value="f" selected="true">No trimming</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	198 <option value="l">Trim left</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	199 <option value="r">Trim right</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	200 <option value="lr">Trim both</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	201 </param>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	202 <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"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	203 <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	204 <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	205 <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"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	206 <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?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	207 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	208 <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	209 <param argument="maqb" type="integer" value="0" label="Calculate maq from this many initial bases" help="Zero value ignores"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	210 </section>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	211 <section name="output_options" title="Output options">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	212 <param argument="secondary" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output secondary alignments?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	213 <param argument="maxsites" type="integer" value="5" label="Maximum number of total alignments to output per read" help="Relevant only when outputting secondary alignments"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	214 <param argument="sssr" type="float" value="0.95" label="Output only secondary alignments with score of at least this fraction of primary"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	215 <param argument="ssao" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Only output secondary alignments for ambiguously-mapped reads?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	216 <param argument="quickmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Generate cigar strings more quickly?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	217 <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?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	218 <param argument="machineout" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output statistics in machine-friendly (key=value) format?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	219 <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"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	220 <param argument="renamebyinsert" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Rename reads based on their mapped insert size?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	221 <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)">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	222 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	223 <option value="name">Sort by read names</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	224 <option value="unsorted">Not sorted (sorted as input)</option>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	225 </param>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	226 </section>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	227 <section name="pf_options" title="Post-filtering options">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	228 <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"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	229 <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	230 <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	231 <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	232 <param argument="indelfilter" type="integer" value="-1" label="Ban alignments with more than this many indels" help="Negative value ignores"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	233 <param argument="editfilter" type="integer" value="-1" label="Ban alignments with more than this many edits" help="Negative value ignores"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	234 <param argument="inslenfilter" type="integer" value="-1" label="Ban alignments with an insertion longer than this" help="Negative value ignores"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	235 <param argument="dellenfilter" type="integer" value="-1" label="Ban alignments with a deletion longer than this" help="Negative value ignores"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	236 <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"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	237 </section>
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	238 </inputs>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	239 <outputs>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	240 <data format="bam" name="output_all_reads" label="${tool.name} on ${on_string} (all reads)">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	241 <expand macro="dbKeyActionsBBMap"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	242 <change_format>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	243 <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	244 <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	245 </change_format>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	246 </data>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	247 <data format="bam" name="output_unmapped_reads" label="${tool.name} on ${on_string} (unmapped reads)">
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	248 <expand macro="dbKeyActionsBBMap"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	249 <change_format>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	250 <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	251 <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	252 </change_format>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	253 </data>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	254 <data format="bam" name="output_mapped_reads" label="${tool.name} on ${on_string} (mapped reads)">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	255 <expand macro="dbKeyActionsBBMap"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	256 <change_format>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	257 <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	258 <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/>
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	259 </change_format>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	260 </data>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	261 </outputs>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	262 <tests>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	263 <!-- Single file, cached reference, output coordinate sorted -->
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	264 <test expect_num_outputs="3">
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	265 <param name="input_type" value="single"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	266 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	267 <param name="output_sort" value="coordinate"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	268 <output name="output_all_reads" ftype="bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	269 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	270 <assert_contents>
7 9ed6579f52f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f iuc parents: 6 diff changeset	271 <has_size value="9310" delta="300"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	272 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	273 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	274 <output name="output_unmapped_reads" ftype="bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	275 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	276 <assert_contents>
7 9ed6579f52f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f iuc parents: 6 diff changeset	277 <has_size value="9310" delta="300"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	278 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	279 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	280 <output name="output_mapped_reads" ftype="bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	281 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	282 <assert_contents>
6 858a65b52cf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95 iuc parents: 5 diff changeset	283 <has_size value="851" delta="100"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	284 </assert_contents>
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	285 </output>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	286 </test>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	287 <!-- Paired reads in separate datasets, cached reference, output name sorted -->
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	288 <test expect_num_outputs="3">
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	289 <param name="input_type" value="pair"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	290 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	291 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	292 <param name="output_sort" value="name"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	293 <output name="output_all_reads" ftype="qname_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	294 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	295 <assert_contents>
7 9ed6579f52f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f iuc parents: 6 diff changeset	296 <has_size value="16893" delta="600"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	297 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	298 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	299 <output name="output_unmapped_reads" ftype="qname_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	300 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	301 <assert_contents>
7 9ed6579f52f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f iuc parents: 6 diff changeset	302 <has_size value="16893" delta="600"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	303 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	304 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	305 <output name="output_mapped_reads" ftype="qname_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	306 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	307 <assert_contents>
6 858a65b52cf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95 iuc parents: 5 diff changeset	308 <has_size value="860" delta="100"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	309 </assert_contents>
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	310 </output>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	311 </test>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	312 <!-- Collection of Paired reads, history reference, output unsorted -->
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	313 <test expect_num_outputs="3">
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	314 <param name="input_type" value="paired"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	315 <param name="reads_collection">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	316 <collection type="paired">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	317 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	318 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	319 </collection>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	320 </param>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	321 <param name="ref_source" value="history"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	322 <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	323 <param name="output_sort" value="unsorted"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	324 <output name="output_all_reads" ftype="qname_input_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	325 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	326 <assert_contents>
7 9ed6579f52f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f iuc parents: 6 diff changeset	327 <has_size value="16928" delta="600"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	328 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	329 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	330 <output name="output_unmapped_reads" ftype="qname_input_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	331 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	332 <assert_contents>
7 9ed6579f52f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f iuc parents: 6 diff changeset	333 <has_size value="16928" delta="600"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	334 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	335 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	336 <output name="output_mapped_reads" ftype="qname_input_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	337 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	338 <assert_contents>
6 858a65b52cf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ef7069328751b534fd4c90115e5afc59b82d8a95 iuc parents: 5 diff changeset	339 <has_size value="878" delta="100"/>
4 6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300" iuc parents: 3 diff changeset	340 </assert_contents>
0 07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	341 </output>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	342 </test>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	343 </tests>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	344 <help>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	345 What it does
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	346
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	347 BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. It is fast and extremely accurate, particularly
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	348 with highly mutated genomes or reads with long indels, even whole-gene deletions over 100kbp long. It has no upper limit
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	349 to genome size or number of contigs and has been successfully used for mapping to an 85 gigabase soil metagenome with over
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	350 200 million contigs. the indexing phase is very fast compared to other aligners.
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	351
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	352 BBMap can output many different statistics files; an empirical read quality histogram, insert-size distribution, and genome
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	353 coverage with or without generating a sam file. It is useful in quality control of libraries and sequencing runs or
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	354 evaluating new sequencing platforms.
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	355
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	356 Options
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	357
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	358 Bam sorting mode - the generated bam files can be sorted according to three criteria: coordinates, names and input order.
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	359
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	360 * Sort by chromosomal coordinates - the file is sorted by coordinates (i.e., the reads from the beginning of the first
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	361 chromosome are first in the file.
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	362 * Sort by read names - the file is sorted by the reference ID (i.e., the QNAME field).
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	363 * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file.
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	364
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	365 </help>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	366 <expand macro="citations"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	367 </tool>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" iuc parents: diff changeset	368

Mercurial > repos > iuc > bbtools_bbmap

annotate bbmap.xml @ 12:3f94a2e3d513 draft default tip