irma: irma.xml annotate

annotate irma.xml @ 2:69ce61289a2a draft

planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 90383425c43b2b8de5bb2d87ada1240c7014c1c8

author	iuc
date	Fri, 24 Jan 2025 21:46:59 +0000
parents	736090e99c59
children	205a59cb55f1

rev	line source
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	1 <tool id="irma" name="IRMA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	2 <description>Construct robust assemblies of highly variable RNA viruses</description>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	3 <macros>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	4 <token name="@TOOL_VERSION@">1.2.0</token>
2 69ce61289a2a planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 90383425c43b2b8de5bb2d87ada1240c7014c1c8 iuc parents: 1 diff changeset	5 <token name="@VERSION_SUFFIX@">2</token>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	6 </macros>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	7 <xrefs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	8 <xref type="bio.tools">irma-virus</xref>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	9 </xrefs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	10 <requirements>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">irma</requirement>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	12 <requirement type="package" version="3.12">python</requirement>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	13 </requirements>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	14 <command detect_errors="exit_code"><![CDATA[
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	15 ## handle gz inputs
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	16 #if $input_type == 'single'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	17 #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz')
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	18 ln -sf '${input_type_conditional.fastq_input1}' file1.fastq.gz &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	19 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	20 #elif $input_type == 'paired_collection'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	21 #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz')
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	22 ln -sf '${input_type_conditional.fastq_input.forward}' file1.fastq.gz &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	23 ln -sf '${input_type_conditional.fastq_input.reverse}' file2.fastq.gz &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	24 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	25 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	26
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	27 ## irma command
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	28 IRMA '${module}'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	29 #if $input_type_conditional.input_type == 'single'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	30 #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz')
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	31 file1.fastq.gz
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	32 #else
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	33 '${input_type_conditional.fastq_input1}'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	34 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	35 #elif $input_type_conditional.input_type == 'paired_collection'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	36 #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz')
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	37 file1.fastq.gz
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	38 file2.fastq.gz
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	39 #else
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	40 '${input_type_conditional.fastq_input.forward}'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	41 '${input_type_conditional.fastq_input.reverse}'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	42 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	43 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	44 resultDir &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	45 ## IRMA does not write empty output files
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	46 ## so the following script makes sure all expected outputs exist unconditionally
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	47 python3 '$__tool_directory__/createMissingFiles.py' &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	48 cat irma_config.sh
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	49 ]]></command>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	50 <configfiles>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	51 <configfile filename='irma_config.sh'><![CDATA[
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	52 SINGLE_LOCAL_PROC=\${GALAXY_SLOTS:-1}
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	53 DOUBLE_LOCAL_PROC=\$((SINGLE_LOCAL_PROC/2 + (SINGLE_LOCAL_PROC==1)))
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	54 TMP=\$TMPDIR
2 69ce61289a2a planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 90383425c43b2b8de5bb2d87ada1240c7014c1c8 iuc parents: 1 diff changeset	55 ASSEM_PROG="MINIMAP2"
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	56 #if $advanced_config.customize == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	57 #if $advanced_config.reference == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	58 SKIP_E=$advanced_config.reference.SKIP_E
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	59 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	60 #if $advanced_config.read_gathering == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	61 MAX_ROUNDS=$advanced_config.read_gathering.MAX_ROUNDS
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	62 USE_MEDIAN=$advanced_config.read_gathering.USE_MEDIAN
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	63 QUAL_THRESHOLD=$advanced_config.read_gathering.QUAL_THRESHOLD
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	64 MIN_LEN=$advanced_config.read_gathering.MIN_LEN
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	65 INCL_CHIM=$advanced_config.read_gathering.INCL_CHIM
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	66 ADAPTER=$advanced_config.read_gathering.ADAPTER
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	67 ENFORCE_CLIPPED_LENGTH=$advanced_config.read_gathering.ENFORCE_CLIPPED_LENGTH
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	68 MERGE_SECONDARY=$advanced_config.read_gathering.MERGE_SECONDARY
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	69 RESIDUAL_ASSEMBLY_FACTOR=$advanced_config.read_gathering.RESIDUAL_ASSEMBLY_FACTOR
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	70 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	71 #if $advanced_config.match_step == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	72 MIN_RP=$advanced_config.match_step.MIN_RP
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	73 MIN_RC=$advanced_config.match_step.MIN_RC
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	74 MIN_BLAT_MATCH=$advanced_config.match_step.MIN_BLAT_MATCH
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	75 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	76 #if $advanced_config.sort_step == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	77 SORT_PROG=$advanced_config.sort_step.SORT_PROG
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	78 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	79 #if $advanced_config.align_step == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	80 ALIGN_PROG=$advanced_config.align_step.ALIGN_PROG
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	81 DEL_TYPE=$advanced_config.align_step.DEL_TYPE
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	82 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	83 #if $advanced_config.assembly == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	84 MAX_ITER_ASSEM=$advanced_config.assembly.MAX_ITER_ASSEM
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	85 NO_MERGE=$advanced_config.assembly.NO_MERGE
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	86 INS_T=$advanced_config.assembly.INS_T
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	87 DEL_T=$advanced_config.assembly.DEL_T
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	88 INS_T_DEPTH=$advanced_config.assembly.INS_T_DEPTH
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	89 DEL_T_DEPTH=$advanced_config.assembly.DEL_T_DEPTH
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	90 SILENCE_COMPLEX_INDELS=$advanced_config.assembly.SILENCE_COMPLEX_INDELS
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	91 MIN_AMBIG=$advanced_config.assembly.MIN_AMBIG
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	92 SSW_M=$advanced_config.assembly.SSW_M
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	93 SSW_X=$advanced_config.assembly.SSW_X
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	94 SSW_O=$advanced_config.assembly.SSW_O
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	95 SSW_E=$advanced_config.assembly.SSW_E
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	96 ALIGN_AMENDED=$advanced_config.assembly.ALIGN_AMENDED
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	97 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	98 #if $advanced_config.variant_calling == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	99 AUTO_F=$advanced_config.variant_calling.AUTO_F
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	100 MIN_FI=$advanced_config.variant_calling.MIN_FI
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	101 MIN_FD=$advanced_config.variant_calling.MIN_FD
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	102 MIN_F=$advanced_config.variant_calling.MIN_F
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	103 MIN_C=$advanced_config.variant_calling.MIN_C
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	104 MIN_AQ=$advanced_config.variant_calling.MIN_AQ
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	105 MIN_TCC=$advanced_config.variant_calling.MIN_TCC
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	106 MIN_CONF=$advanced_config.variant_calling.MIN_CONF
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	107 SIG_LEVEL=$advanced_config.variant_calling.SIG_LEVEL
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	108 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	109 #end if]]></configfile>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	110 </configfiles>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	111 <inputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	112 <conditional name="input_type_conditional">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	113 <param name="input_type" type="select" label="Input Type">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	114 <option value="single" selected="true">Single Dataset</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	115 <option value="paired_collection">Paired Collection</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	116 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	117 <when value="single">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	118 <param name="fastq_input1" type="data" format="fastq,fastq.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	119 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	120 <when value="paired_collection">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	121 <param name="fastq_input" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	122 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	123 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	124 <param name="module" type="select" label="Select analysis module">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	125 <option value="FLU" selected="true">FLU</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	126 <option value="FLU-utr">FLU-utr</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	127 <option value="FLU-pacbio">FLU-pacbio</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	128 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	129 <param name="optional_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Select additional IRMA outputs">
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	130 <option value="amended_consensus" selected="false">Amended consensus files: Include ambiguity codes for alleles, with second allele frequency greater 0.25</option>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	131 <option value="bam" selected="false">Bam: Alignment files of fastq against polished reference</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	132 <option value="vcf" selected="false">Vcf: Variation calling file per segment</option>
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	133 <option value="run_info" selected="false">Run info: Text file with run metadata</option>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	134 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	135 <conditional name="advanced_config">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	136 <param name="customize" type="select" label="Customize Advanced Settings?" help="Choosing Yes here, lets you overwrite advanced settings defined in IRMA's default configuration file.">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	137 <option value="no">No, use defaults for advanced settings</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	138 <option value="yes">Yes</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	139 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	140 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	141 <when value="yes">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	142 <conditional name="reference">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	143 <param name="customize" type="select" label="Customize Reference Settings" help="Choosing Yes here, lets you overwrite reference settings.">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	144 <option value="no">No, use defaults for reference settings</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	145 <option value="yes">Yes</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	146 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	147 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	148 <when value="yes">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	149 <param name="SKIP_E" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Skip reference elongation" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	150 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	151 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	152
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	153 <conditional name="read_gathering">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	154 <param name="customize" type="select" label="Customize settings to read gathering" help="Choosing Yes here, lets you overwrite read gathering settings.">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	155 <option value="no">No, use defaults for read gathering settings</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	156 <option value="yes">Yes</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	157 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	158 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	159 <when value="yes">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	160 <param name="MAX_ROUNDS" type="integer" min="1" max="20" value="5" label="Maximal rounds of read gathering"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	161 <param name="USE_MEDIAN" type="select" label="Use median or average for read gathering">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	162 <option value="0">Average</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	163 <option value="1" selected="true">Median</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	164 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	165 <param name="QUAL_THRESHOLD" type="integer" min="0" value="30" label="Minimum read statistic to keep (Phred)"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	166 <param name="MIN_LEN" type="integer" min="0" max="1000" value="125" label="Minimum read length to keep (bp)" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	167 <param name="INCL_CHIM" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Include chimera? Transposase adapter - clips 5' of the adapter on the forward strand and 3' on the reverse strand. applicable to NextTera pair-end reads" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	168 <param name="ADAPTER" type="text" value="AGATGTGTATAAGAGACAG" label="Adapter sequence">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	169 <validator type="regex">[CAGT]+</validator>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	170 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	171 <param name="ENFORCE_CLIPPED_LENGTH" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Reads are filtered for minimum length post adapter trimming" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	172
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	173 <param name="MERGE_SECONDARY" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Merge secondary data after the first round to the unmatched pool. Useful if co-infections are not expected." />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	174
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	175 <param name="RESIDUAL_ASSEMBLY_FACTOR" type="integer" min="0" max="100" value="0" label="The ratio of match read patterns to altmatch is measured, and if its less than factor, residual assembly is performed. Set 0 for off."/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	176 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	177 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	178 <conditional name="match_step">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	179 <param name="customize" type="select" label="Customize settings regarding the match step" help="Choosing Yes here, lets you overwrite match step settings.">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	180 <option value="no">No, use defaults for match step settings</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	181 <option value="yes">Yes</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	182 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	183 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	184 <when value="yes">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	185 <param name="MIN_RP" type="integer" min="0" value="15" label="Minimum read pattern count to continue"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	186 <param name="MIN_RC" type="integer" min="0" value="15" label="Minimum read count to continue"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	187 <param name="MIN_BLAT_MATCH" type="integer" min="0" value="0" label="Minimum read pattern count to continue"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	188 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	189 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	190 <conditional name="sort_step">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	191 <param name="customize" type="select" label="Customize settings regarding the sort step" help="Choosing Yes here, lets you overwrite sort step settings.">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	192 <option value="no">No, use defaults for sort step settings</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	193 <option value="yes">Yes</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	194 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	195 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	196 <when value="yes">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	197 <param name="SORT_PROG" type="select" label="Select program used for sorting">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	198 <option value="LABEL">LABEL</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	199 <option value="BLAT" selected="true">BLAT</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	200 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	201 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	202 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	203 <conditional name="align_step">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	204 <param name="customize" type="select" label="Customize settings regarding the alignment step" help="Choosing Yes here, lets you overwrite align step settings.">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	205 <option value="no">No, use defaults for align step settings</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	206 <option value="yes">Yes</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	207 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	208 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	209 <when value="yes">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	210 <param name="ALIGN_PROG" type="select" label="Select program used for alignment">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	211 <option value="BLAT">BLAT</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	212 <option value="SAM" selected="true">SAM</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	213 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	214 <param name="DEL_TYPE" type="select" label="How to handle deletions in rough alignment">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	215 <option value="" selected="true">Default</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	216 <option value="NNN">NNN</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	217 <option value="REF">REF</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	218 <option value="DEL" >DEL</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	219 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	220 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	221 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	222 <conditional name="assembly">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	223 <param name="customize" type="select" label="Customize settings regarding the assembly" help="Choosing Yes here, lets you overwrite assembly settings.">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	224 <option value="no">No, use defaults for assembly settings</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	225 <option value="yes">Yes</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	226 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	227 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	228 <when value="yes">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	229 <param name="MAX_ITER_ASSEM" type="integer" min="1" value="5" label="Maximal assembly iteration"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	230 <!-- true and false values are inverted for the next param because we're asking the opposite question of what we need to configure -->
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	231 <param name="NO_MERGE" type="boolean" falsevalue="1" truevalue="0" checked="true" label="Merge read pairs?" help="Merging read pairs after final assembly provides error detection and correction." />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	232 <param name="INS_T" type="float" min="0" max="1" value="0.25" label="The minimum frequency threshold for insertion refinement"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	233 <param name="DEL_T" type="float" min="0" max="1" value="0.6" label="The minimum frequency threshold for deletion refinement"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	234 <param name="INS_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for insertion refinement"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	235 <param name="DEL_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for deletion refinement"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	236 <param name="SILENCE_COMPLEX_INDELS" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Silences reads with complex indels (having 4 indels with at least one greater than 9)" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	237 <param name="MIN_AMBIG" type="float" min="0" max="1" value="0.25" label="The minimum called SNV frequency for mixed base in amended consensus folder"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	238 <param name="SSW_M" type="integer" min="1" value="2" label="The smith-waterman match score"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	239 <param name="SSW_X" type="integer" min="1" value="5" label="The smith-waterman mismatch penalty"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	240 <param name="SSW_O" type="integer" min="1" value="10" label="The smith-waterman gap open penalty"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	241 <param name="SSW_E" type="integer" min="1" value="1" label="The smith-waterman gap extension penalty"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	242 <param name="ALIGN_AMENDED" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Do global alignment of the amended consensus to the HMM profile" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	243 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	244 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	245 <conditional name="variant_calling">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	246 <param name="customize" type="select" label="Customize settings regarding the variant calling" help="Choosing Yes here, lets you overwrite variant calling settings.">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	247 <option value="no">No, use defaults for variant calling settings</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	248 <option value="yes">Yes</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	249 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	250 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	251 <when value="yes">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	252 <param name="AUTO_F" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Automatically adjust frequency threshold" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	253 <param name="MIN_FI" type="float" min="0" max="1" value="0.005" label="The minimum insertion variant frequency"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	254 <param name="MIN_FD" type="float" min="0" max="1" value="0.005" label="The minimum deletion variant frequency"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	255 <param name="MIN_F" type="float" min="0" max="1" value="0.008" label="The minimum frequency for single nucleotide variants"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	256 <param name="MIN_C" type="integer" min="1" value="2" label="The minimum count for variants"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	257 <param name="MIN_AQ" type="integer" min="1" value="24" label="The minimum average variant quality (does not apply to deletions)"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	258 <param name="MIN_TCC" type="integer" min="1" value="100" label="The minimum non-ambiguous column coverage"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	259 <param name="MIN_CONF" type="float" min="0" max="1" value="0.80" label="The minimum confidence"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	260 <param name="SIG_LEVEL" type="select" label="The significance test level for variant calling">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	261 <option value="0.999" selected="true">99.9%</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	262 <option value="0.99" >99%</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	263 <option value="0.95" >95%</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	264 <option value="0.90" >90%</option>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	265 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	266 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	267 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	268 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	269 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	270 </inputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	271 <outputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	272 <collection name="consensus_collection" type="list" label="Fasta Consensus Sequences">
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	273 <data name="PB2" format="fasta" from_work_dir="resultDir/A_PB2.fasta" label="PB2"/>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	274 <data name="PB1" format="fasta" from_work_dir="resultDir/A_PB1.fasta" label="PB1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	275 <data name="PA" format="fasta" from_work_dir="resultDir/A_PA.fasta" label="PA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	276 <data name="HA" format="fasta" from_work_dir="resultDir/A_HA.fasta" label="HA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	277 <data name="NP" format="fasta" from_work_dir="resultDir/A_NP.fasta" label="NP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	278 <data name="NA" format="fasta" from_work_dir="resultDir/A_NA.fasta" label="NA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	279 <data name="MP" format="fasta" from_work_dir="resultDir/A_MP.fasta" label="MP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	280 <data name="NS" format="fasta" from_work_dir="resultDir/A_NS.fasta" label="NS"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	281 </collection>
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1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	283 <collection name="amended_collection" type="list" label="Amended Fasta Consensus">
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	284 <filter>optional_outputs and 'amended_consensus' in optional_outputs</filter>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	285 <data name="PB2" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_1.fa" label="PB2"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	286 <data name="PB1" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_2.fa" label="PB1"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	287 <data name="PA" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_3.fa" label="PA"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	288 <data name="HA" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_4.fa" label="HA"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	289 <data name="NP" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_5.fa" label="NP"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	290 <data name="NA" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_6.fa" label="NA"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	291 <data name="MP" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_7.fa" label="MP"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	292 <data name="NS" format="fasta" from_work_dir="resultDir/amended_consensus/resultDir_8.fa" label="NS"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	293 </collection>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	294 <collection name="bam_collection" type="list" label="Alignment files (bam)">
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1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	296 <data name="PB2" format="bam" from_work_dir="resultDir/A_PB2.bam" label="PB2"/>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	297 <data name="PB1" format="bam" from_work_dir="resultDir/A_PB1.bam" label="PB1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	298 <data name="PA" format="bam" from_work_dir="resultDir/A_PA.bam" label="PA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	299 <data name="HA" format="bam" from_work_dir="resultDir/A_HA.bam" label="HA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	300 <data name="NP" format="bam" from_work_dir="resultDir/A_NP.bam" label="NP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	301 <data name="NA" format="bam" from_work_dir="resultDir/A_NA.bam" label="NA"/>
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3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	304 </collection>
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1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	307 <data name="PB2" format="vcf" from_work_dir="resultDir/A_PB2.vcf" label="PB2"/>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	308 <data name="PB1" format="vcf" from_work_dir="resultDir/A_PB1.vcf" label="PB1"/>
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3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	313 <data name="MP" format="vcf" from_work_dir="resultDir/A_MP.vcf" label="MP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	314 <data name="NS" format="vcf" from_work_dir="resultDir/A_NS.vcf" label="NS"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	315 </collection>
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	316 <data name="run_info" label="IRMA run info" format="txt" from_work_dir="resultDir/logs/run_info.txt">
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	317 <filter>optional_outputs and 'run_info' in optional_outputs</filter>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	318 </data>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	319 </outputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	320 <tests>
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3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	322 <conditional name="input_type_conditional">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	323 <param name="fastq_input1" value="test_reads.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	324 <param name="input_type" value="single" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	325 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	326 <conditional name="advanced_config">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	327 <param name="customize" value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	328 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	329 <param name="module" value="FLU-utr" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	330 <param name="optional_outputs" value="vcf,bam"/>
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3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	332 <element name="HA">
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3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	339 <test expect_num_outputs="18">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	340 <param name="module" value="FLU"/>
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3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	342 <conditional name="input_type_conditional">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	343 <param name="input_type" value="paired_collection"/>
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3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	348 </collection>
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3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	356 </element>
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3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	359 </test>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	360 <test expect_num_outputs="9">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	361 <param name="module" value="FLU-utr"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	362 <conditional name="input_type_conditional">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	363 <param name="input_type" value="paired_collection"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	364 <param name="fastq_input">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	365 <collection type="paired">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	366 <element name="forward" value="test_reads.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	367 <element name="reverse" value="test_reads_copy.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	368 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	369 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	370 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	371 <conditional name="advanced_config">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	372 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	373 <conditional name="reference">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	374 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	375 <param name="SKIP_E" value="0"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	376 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	377 <conditional name="read_gathering">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	378 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	379 <param name="MAX_ROUNDS" value="1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	380 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	381 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	382 <output_collection name="consensus_collection" type="list" count="8">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	383 <element name="HA">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	384 <assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	385 <has_n_lines n="2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	386 </assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	387 </element>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	388 </output_collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	389 </test>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	390 <test expect_num_outputs="27">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	391 <param name="module" value="FLU"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	392 <param name="optional_outputs" value="bam,vcf"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	393 <conditional name="input_type_conditional">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	394 <param name="input_type" value="paired_collection"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	395 <param name="fastq_input">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	396 <collection type="paired">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	397 <element name="forward" value="test_reads.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	398 <element name="reverse" value="test_reads_copy.fq" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	399 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	400 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	401 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	402 <conditional name="advanced_config">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	403 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	404 <conditional name="reference">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	405 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	406 <param name="SKIP_E" value="true"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	407 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	408 <conditional name="read_gathering">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	409 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	410 <param name="MAX_ROUNDS" value="3"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	411 <param name="USE_MEDIAN" value="1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	412 <param name="QUAL_THRESHOLD" value="30"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	413 <param name="MIN_LEN" value="125"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	414 <param name="INCL_CHIM" value="false"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	415 <param name="ADAPTER" value="AGATGTGTATAAGAGACAG"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	416 <param name="ENFORCE_CLIPPED_LENGTH" value="true"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	417 <param name="MERGE_SECONDARY" value="false"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	418 <param name="RESIDUAL_ASSEMBLY_FACTOR" value="0"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	419 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	420 <conditional name="match_step">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	421 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	422 <param name="MIN_RP" value="15"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	423 <param name="MIN_RC" value="15"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	424 <param name="MIN_BLAT_MATCH" value="0"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	425 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	426 <conditional name="sort_step">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	427 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	428 <param name="SORT_PROG" value="LABEL"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	429 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	430 <conditional name="align_step">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	431 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	432 <param name="ALIGN_PROG" value="SAM"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	433 <param name="DEL_TYPE" value=""/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	434 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	435 <conditional name="assembly">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	436 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	437 <param name="MAX_ITER_ASSEM" value="5"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	438 <param name="NO_MERGE" value="false"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	439 <param name="INS_T" value="0.25"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	440 <param name="DEL_T" value="0.6"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	441 <param name="INS_T_DEPTH" value="1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	442 <param name="DEL_T_DEPTH" value="1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	443 <param name="SILENCE_COMPLEX_INDELS" value="true"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	444 <param name="MIN_AMBIG" value="0.25"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	445 <param name="SSW_M" value="2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	446 <param name="SSW_X" value="5"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	447 <param name="SSW_O" value="10"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	448 <param name="SSW_E" value="1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	449 <param name="ALIGN_AMENDED" value="false"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	450 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	451 <conditional name="variant_calling">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	452 <param name="customize" value="yes"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	453 <param name="AUTO_F" value="true"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	454 <param name="MIN_FI" value="0.005"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	455 <param name="MIN_FD" value="0.005"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	456 <param name="MIN_F" value="0.008"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	457 <param name="MIN_C" value="2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	458 <param name="MIN_AQ" value="24"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	459 <param name="MIN_TCC" value="100"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	460 <param name="MIN_CONF" value="0.80"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	461 <param name="SIG_LEVEL" value="0.999"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	462 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	463 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	464 <output_collection name="consensus_collection" type="list" count="8">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	465 <element name="HA">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	466 <assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	467 <has_n_lines n="2"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	468 </assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	469 </element>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	470 </output_collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	471 <output_collection name="bam_collection" type="list" count="8" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	472 <output_collection name="vcf_collection" type="list" count="8" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	473 </test>
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	474 <test expect_num_outputs="19">
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	475 <conditional name="input_type_conditional">
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	476 <param name="fastq_input1" value="test_reads.fq" />
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	477 <param name="input_type" value="single" />
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	478 </conditional>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	479 <conditional name="advanced_config">
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	480 <param name="customize" value="no" />
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	481 </conditional>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	482 <param name="module" value="FLU-utr" />
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	483 <param name="optional_outputs" value="amended_consensus,run_info"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	484 <output_collection name="consensus_collection" type="list">
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	485 <element name="HA">
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	486 <assert_contents>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	487 <has_n_lines n="2"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	488 </assert_contents>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	489 </element>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	490 </output_collection>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	491 <output_collection name="amended_collection" type="list">
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	492 <element name="HA">
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	493 <assert_contents>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	494 <has_n_lines n="2"/>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	495 </assert_contents>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	496 </element>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	497 </output_collection>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	498 </test>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	499 </tests>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	500 <help><![CDATA[
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	501 .. class:: infomark
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	502
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	503 What it does
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	504
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	505 IRMA (Iterative Refinement Meta-Assembler) can be used to obtain robust assembly, variant calling, and phasing of highly variable RNA viruses.
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	506 These are obtained after an iterative assembly approach. Visit https://wonder.cdc.gov/amd/flu/irma/ for more information.
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	507 IRMA offers modules for influenza, RSV, ebolavirus and coronavirus, but this galaxy wrapper currently only supports influenza modules.
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	508
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	509 Inputs
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	510
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	511 Specify the module and provide your read data.
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	512
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	513 Outputs
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	514
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	515 The default output of the tool is a collection of consensus sequences in FASTA format.
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	516
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	517 Optionally, collections of read mapping and variant calling results can be produced as additional outputs.
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	518
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	519 Settings
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	520
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	521 IRMA provides carefully chosen default settings for its different analysis modes.
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	522 Advanced(!) users have the option to override these through the advanced config section.
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	523
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	524 .. class:: Warning mark
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	525
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	526 By enabling any section of the advanced configuration options you will override the default settings for all parameters in that section, and the default values of a section may not be IRMA's defaults for the selected module, but reflect IRMA's global defaults.
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	527
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	528 https://wonder.cdc.gov/amd/flu/irma/configuration.html provides more information about configuration parameters.
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	529 ]]></help>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	530 <citations>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	531 <citation type="doi">10.1186/s12864-016-3030-6</citation>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	532 </citations>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	533 </tool>

Mercurial > repos > iuc > irma

annotate irma.xml @ 2:69ce61289a2a draft