irma: irma.xml annotate

annotate irma.xml @ 3:205a59cb55f1 draft default tip

planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34

author	iuc
date	Wed, 29 Jan 2025 08:19:15 +0000
parents	69ce61289a2a
children

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>
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	5 <token name="@VERSION_SUFFIX@">3</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 '${input_type_conditional.fastq_input.reverse}'
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	42 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	43 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	44 resultDir &&
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	45 ## IRMA does not write empty output files
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	46 ## so the following script makes sure all expected outputs exist unconditionally
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	47 python3 '$__tool_directory__/createMissingFiles.py'
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	48 ]]></command>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	49 <configfiles>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	50 <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	51 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	52 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	53 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	54 ASSEM_PROG="MINIMAP2"
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	55 GRID_ON=0
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	56 SKIP_E=$SKIP_E
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	57 SORT_PROG="BLAT" ## LABEL is not working in galaxy docker.
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	58 #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	59 #if $advanced_config.read_gathering == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	60 MAX_ROUNDS=$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	61 USE_MEDIAN=$advanced_config.read_gathering.USE_MEDIAN
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	62 QUAL_THRESHOLD=$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	63 MIN_LEN=$advanced_config.read_gathering.MIN_LEN
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	64 INCL_CHIM=$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	65 ADAPTER=$advanced_config.read_gathering.ADAPTER
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	66 ENFORCE_CLIPPED_LENGTH=$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	67 MERGE_SECONDARY=$advanced_config.read_gathering.MERGE_SECONDARY
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	68 RESIDUAL_ASSEMBLY_FACTOR=$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	69 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	70 #if $advanced_config.match_step == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	71 MIN_RP=$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	72 MIN_RC=$advanced_config.match_step.MIN_RC
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	73 MIN_BLAT_MATCH=$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	74 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	75 #if $advanced_config.align_step == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	76 ALIGN_PROG=$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	77 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	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 $advanced_config.assembly == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	80 MAX_ITER_ASSEM=$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	81 NO_MERGE=$advanced_config.assembly.NO_MERGE
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	82 INS_T=$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	83 DEL_T=$advanced_config.assembly.DEL_T
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	84 INS_T_DEPTH=$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	85 DEL_T_DEPTH=$advanced_config.assembly.DEL_T_DEPTH
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	86 SILENCE_COMPLEX_INDELS=$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	87 MIN_AMBIG=$advanced_config.assembly.MIN_AMBIG
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	88 ALIGN_AMENDED=$advanced_config.assembly.ALIGN_AMENDED
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	89 MM2_A=$advanced_config.assembly.MM2_A
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	90 MM2_B=$advanced_config.assembly.MM2_B
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	91 MM2_O=$advanced_config.assembly.MM2_O
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	92 #if $module == "FLU-avian":
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	93 ## respect user choice of A,B,O,E, but configure short read presets otherwise
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	94 MM2_E="$advanced_config.assembly.MM2_E -x sr"
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	95 #else:
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	96 MM2_E=$advanced_config.assembly.MM2_E
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	97 #end if
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	98 #else:
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	99 #if $module == "FLU-avian":
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	100 configure short read presets for minimap2 overwriting irma module defaults where necessary
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	101 MM2_A=2
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	102 MM2_B=8
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	103 MM2_O="12,32"
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	104 MM2_E="2,1 -x sr"
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	105 #end if
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	106 #end if
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	107 #if $advanced_config.variant_calling == 'yes':
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	108 AUTO_F=$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	109 MIN_FI=$advanced_config.variant_calling.MIN_FI
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	110 MIN_FD=$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	111 MIN_F=$advanced_config.variant_calling.MIN_F
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	112 MIN_C=$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	113 MIN_AQ=$advanced_config.variant_calling.MIN_AQ
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	114 MIN_TCC=$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	115 MIN_CONF=$advanced_config.variant_calling.MIN_CONF
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	116 SIG_LEVEL=$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	117 #end if
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	118 #end if
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	119 ]]></configfile>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	120 </configfiles>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	121 <inputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	122 <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	123 <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	124 <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	125 <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	126 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	127 <when value="single">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	128 <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	129 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	130 <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	131 <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	132 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	133 </conditional>
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	134 <param name="module" type="select" label="Select platform">
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	135 <option value="FLU-avian" selected="true">Illumina</option>
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	136 <option value="FLU-minion">MinIon</option>
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	137 <option value="FLU-pacbio">PacBio</option>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	138 </param>
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	139 <param name="SKIP_E" type="boolean" falsevalue="1" truevalue="0" checked="true" label="Assemble UTRs, by elongation of reference" />
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	140 <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	141 <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	142 <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	143 <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	144 <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	145 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	146 <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	147 <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	148 <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	149 <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	150 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	151 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	152 <when value="yes">
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="align_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 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	192 <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	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="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	198 <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	199 <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	200 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	201 <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	202 <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	203 <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	204 <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	205 <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	206 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	207 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	208 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	209 <conditional name="assembly">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	210 <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	211 <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	212 <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	213 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	214 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	215 <when value="yes">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	216 <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	217 <!-- 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	218 <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	219 <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	220 <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	221 <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	222 <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	223 <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	224 <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"/>
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	225 <param name="MM2_A" type="integer" min="1" value="2" label="The minimap2 match score"/>
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	226 <param name="MM2_B" type="integer" min="1" value="8" label="The minimap2 mismatch penalty"/>
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	227 <param name="MM2_O" type="integer" min="1" value="10" label="The minimap2 gap open penalty"/>
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	228 <param name="MM2_E" type="integer" min="1" value="1" label="The minimap2 gap extension penalty"/>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	229 <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	230 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	231 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	232 <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	233 <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	234 <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	235 <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	236 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	237 <when value="no" />
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	238 <when value="yes">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	239 <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	240 <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	241 <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	242 <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	243 <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	244 <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	245 <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	246 <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	247 <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	248 <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	249 <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	250 <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	251 <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	252 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	253 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	254 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	255 </when>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	256 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	257 </inputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	258 <outputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 <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	267 <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	268 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	269 <!-- optional outputs-->
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 <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	279 <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	280 </collection>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	281 <collection name="bam_collection" type="list" label="Alignment files (bam)">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	282 <filter>optional_outputs and 'bam' in optional_outputs</filter>
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	283 <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	284 <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	285 <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	286 <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	287 <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	288 <data name="NA" format="bam" from_work_dir="resultDir/A_NA.bam" label="NA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	289 <data name="MP" format="bam" from_work_dir="resultDir/A_MP.bam" label="MP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	290 <data name="NS" format="bam" from_work_dir="resultDir/A_NS.bam" label="NS"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	291 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	292 <collection name="vcf_collection" type="list" label="Variant calling files (VCF)">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	293 <filter>optional_outputs and 'vcf' in optional_outputs</filter>
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	294 <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	295 <data name="PB1" format="vcf" from_work_dir="resultDir/A_PB1.vcf" label="PB1"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	296 <data name="PA" format="vcf" from_work_dir="resultDir/A_PA.vcf" label="PA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	297 <data name="HA" format="vcf" from_work_dir="resultDir/A_HA.vcf" label="HA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	298 <data name="NP" format="vcf" from_work_dir="resultDir/A_NP.vcf" label="NP"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	299 <data name="NA" format="vcf" from_work_dir="resultDir/A_NA.vcf" label="NA"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	300 <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	301 <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	302 </collection>
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	303 <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	304 <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	305 </data>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	306 </outputs>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	307 <tests>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	308 <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	309 <conditional name="input_type_conditional">
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	310 <param name="fastq_input1" value="forward.fastqsanger" />
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	311 <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	312 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	313 <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	314 <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	315 </conditional>
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	316 <param name="module" value="FLU-avian" />
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	317 <param name="SKIP_E" value="1" />
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	318 <param name="optional_outputs" value="vcf,bam"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	319 <output_collection name="consensus_collection" type="list">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	320 <element name="HA">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	321 <assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	322 <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	323 </assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	324 </element>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	325 </output_collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	326 </test>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	327 <test expect_num_outputs="18">
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	328 <param name="module" value="FLU-avian" />
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	329 <param name="SKIP_E" value="1" />
0 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="bam"/>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	331 <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	332 <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	333 <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	334 <collection type="paired">
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	335 <element name="forward" value="forward.fastqsanger" />
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	336 <element name="reverse" value="reverse.fastqsanger" />
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	337 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	338 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	339 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	340 <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	341 <element name="HA">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	342 <assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	343 <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	344 </assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	345 </element>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	346 </output_collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	347 <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	348 </test>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	349 <test expect_num_outputs="9">
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	350 <param name="module" value="FLU-avian" />
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	351 <param name="SKIP_E" value="1" />
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	352 <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	353 <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	354 <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	355 <collection type="paired">
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	356 <element name="forward" value="forward.fastqsanger" />
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	357 <element name="reverse" value="reverse.fastqsanger" />
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	358 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	359 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	360 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	361 <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	362 <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	363 <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	364 <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	365 <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	366 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	367 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	368 <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	369 <element name="HA">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	370 <assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	371 <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	372 </assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	373 </element>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	374 </output_collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	375 </test>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	376 <test expect_num_outputs="27">
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	377 <param name="module" value="FLU-pacbio" />
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	378 <param name="SKIP_E" value="0" />
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	379 <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	380 <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	381 <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	382 <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	383 <collection type="paired">
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	384 <element name="forward" value="forward.fastqsanger" />
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	385 <element name="reverse" value="reverse.fastqsanger" />
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	386 </collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	387 </param>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	388 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	389 <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	390 <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	391 <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	392 <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	393 <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	394 <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	395 <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	396 <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	397 <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	398 <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	399 <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	400 <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	401 <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	402 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	403 <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	404 <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	405 <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	406 <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	407 <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	408 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	409 <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	410 <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	411 <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	412 <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	413 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	414 <conditional name="assembly">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	415 <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	416 <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	417 <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	418 <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	419 <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	420 <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	421 <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	422 <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	423 <param name="MIN_AMBIG" value="0.25"/>
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	424 <param name="MM2_A" value="2"/>
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	425 <param name="MM2_B" value="7"/>
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	426 <param name="MM2_O" value="12"/>
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	427 <param name="MM2_E" value="2"/>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	428 <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	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="variant_calling">
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="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	433 <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	434 <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	435 <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	436 <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	437 <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	438 <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	439 <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	440 <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	441 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	442 </conditional>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	443 <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	444 <element name="HA">
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	445 <assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	446 <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	447 </assert_contents>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	448 </element>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	449 </output_collection>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	450 <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	451 <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	452 </test>
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	453 <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	454 <conditional name="input_type_conditional">
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	455 <param name="fastq_input1" value="forward.fastqsanger" />
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	456 <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	457 </conditional>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	458 <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	459 <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	460 </conditional>
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	461 <param name="module" value="FLU-avian" />
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	462 <param name="SKIP_E" value="1" />
1 736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	463 <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	464 <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	465 <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	466 <assert_contents>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	467 <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	468 </assert_contents>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	469 </element>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	470 </output_collection>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	471 <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	472 <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	473 <assert_contents>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	474 <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	475 </assert_contents>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	476 </element>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	477 </output_collection>
736090e99c59 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 6b8463ba27d0c91b736d579b0891632d4c032402 iuc parents: 0 diff changeset	478 </test>
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	479 </tests>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	480 <help><![CDATA[
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	481 .. class:: infomark
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	482
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	483 What it does
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	484
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	485 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	486 These are obtained after an iterative assembly approach. Visit https://wonder.cdc.gov/amd/flu/irma/ for more information.
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	487 IRMA offers modules for influenza, RSV, ebolavirus and coronavirus, but this Galaxy wrapper currently only supports influenza modules.
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	488
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	489 Inputs
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	490
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	491 Specify the sequencing platform and provide your read data.
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	492
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	493 Outputs
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	494
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	495 The default output of the tool is a collection of majority consensus sequences in FASTA format.
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	496
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	497 Optionally, collections of ambiguous consensus sequences, of read mapping and variant calling results can be produced as additional outputs.
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	498
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	499 Settings
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	500
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	501 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	502 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	503
3 205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	504 This wrapper always uses minimap2 at the assembly step (even where the IRMA command line tool would default to SSW). For MinIon and PacBio data it uses minimap2's default long reads settings with IRMA-specific modifications of -A, -B, -O and -E parameters. For Illumina data minimap2 is run with its short-reads preset (-x sr) configuration. For all platforms, the minimap2 options -A (match score), -B (mismatch penalty), -O (gap open penalty) and -E (gap extension penalty) are user-configurable via Advanced settings -> Assembly settings.
205a59cb55f1 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34 iuc parents: 2 diff changeset	505
0 3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	506 .. class:: Warning mark
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	507
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	508 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	509
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	510 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	511 ]]></help>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	512 <citations>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	513 <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	514 </citations>
3d86c05cd838 planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c iuc parents: diff changeset	515 </tool>

Mercurial > repos > iuc > irma

annotate irma.xml @ 3:205a59cb55f1 draft default tip