--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/irma.xml	Sat Nov 09 13:53:38 2024 +0000
@@ -0,0 +1,491 @@
+<tool id="irma" name="IRMA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
+    <description>Construct robust assemblies of highly variable RNA viruses</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.2.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">irma-virus</xref> 
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">irma</requirement>
+        <requirement type="package" version="3.12">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+## handle gz inputs
+#if $input_type == 'single'
+  #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz')
+    ln -sf '${input_type_conditional.fastq_input1}' file1.fastq.gz &&
+  #end if
+#elif $input_type == 'paired_collection'
+  #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz')
+    ln -sf '${input_type_conditional.fastq_input.forward}' file1.fastq.gz &&
+    ln -sf '${input_type_conditional.fastq_input.reverse}'  file2.fastq.gz &&
+  #end if
+#end if
+
+## irma command
+IRMA '${module}'
+#if $input_type_conditional.input_type == 'single'
+  #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz')
+    file1.fastq.gz
+  #else
+    '${input_type_conditional.fastq_input1}'
+  #end if
+#elif $input_type_conditional.input_type == 'paired_collection'
+  #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz')
+    file1.fastq.gz
+    file2.fastq.gz
+  #else
+    '${input_type_conditional.fastq_input.forward}'
+    '${input_type_conditional.fastq_input.reverse}'
+  #end if
+#end if
+resultDir &&
+## IRMA does not write empty output files
+## so the following script makes sure all expected outputs exist unconditionally
+python3 '$__tool_directory__/createMissingFiles.py' &&
+cat irma_config.sh
+    ]]></command>
+    <configfiles>
+        <configfile filename='irma_config.sh'><![CDATA[
+SINGLE_LOCAL_PROC=\${GALAXY_SLOTS:-1}
+DOUBLE_LOCAL_PROC=\$((SINGLE_LOCAL_PROC/2 + (SINGLE_LOCAL_PROC==1)))
+TMP=\$TMPDIR
+#if $advanced_config.customize == 'yes':
+  #if $advanced_config.reference == 'yes':
+SKIP_E=$advanced_config.reference.SKIP_E
+  #end if
+  #if $advanced_config.read_gathering == 'yes':
+MAX_ROUNDS=$advanced_config.read_gathering.MAX_ROUNDS		                        
+USE_MEDIAN=$advanced_config.read_gathering.USE_MEDIAN		                        
+QUAL_THRESHOLD=$advanced_config.read_gathering.QUAL_THRESHOLD	                    
+MIN_LEN=$advanced_config.read_gathering.MIN_LEN         		                    
+INCL_CHIM=$advanced_config.read_gathering.INCL_CHIM     		                    
+ADAPTER=$advanced_config.read_gathering.ADAPTER                              
+ENFORCE_CLIPPED_LENGTH=$advanced_config.read_gathering.ENFORCE_CLIPPED_LENGTH
+MERGE_SECONDARY=$advanced_config.read_gathering.MERGE_SECONDARY         		    
+RESIDUAL_ASSEMBLY_FACTOR=$advanced_config.read_gathering.RESIDUAL_ASSEMBLY_FACTOR   
+  #end if
+  #if $advanced_config.match_step == 'yes':
+MIN_RP=$advanced_config.match_step.MIN_RP    
+MIN_RC=$advanced_config.match_step.MIN_RC
+MIN_BLAT_MATCH=$advanced_config.match_step.MIN_BLAT_MATCH
+  #end if
+  #if $advanced_config.sort_step == 'yes':
+SORT_PROG=$advanced_config.sort_step.SORT_PROG
+  #end if
+  #if $advanced_config.align_step == 'yes':
+ALIGN_PROG=$advanced_config.align_step.ALIGN_PROG
+DEL_TYPE=$advanced_config.align_step.DEL_TYPE
+  #end if
+  #if $advanced_config.assembly == 'yes':
+MAX_ITER_ASSEM=$advanced_config.assembly.MAX_ITER_ASSEM
+NO_MERGE=$advanced_config.assembly.NO_MERGE            
+INS_T=$advanced_config.assembly.INS_T
+DEL_T=$advanced_config.assembly.DEL_T
+INS_T_DEPTH=$advanced_config.assembly.INS_T_DEPTH
+DEL_T_DEPTH=$advanced_config.assembly.DEL_T_DEPTH
+SILENCE_COMPLEX_INDELS=$advanced_config.assembly.SILENCE_COMPLEX_INDELS
+MIN_AMBIG=$advanced_config.assembly.MIN_AMBIG
+SSW_M=$advanced_config.assembly.SSW_M
+SSW_X=$advanced_config.assembly.SSW_X
+SSW_O=$advanced_config.assembly.SSW_O
+SSW_E=$advanced_config.assembly.SSW_E
+ALIGN_AMENDED=$advanced_config.assembly.ALIGN_AMENDED
+  #end if
+  #if $advanced_config.variant_calling == 'yes':
+AUTO_F=$advanced_config.variant_calling.AUTO_F
+MIN_FI=$advanced_config.variant_calling.MIN_FI
+MIN_FD=$advanced_config.variant_calling.MIN_FD
+MIN_F=$advanced_config.variant_calling.MIN_F
+MIN_C=$advanced_config.variant_calling.MIN_C
+MIN_AQ=$advanced_config.variant_calling.MIN_AQ
+MIN_TCC=$advanced_config.variant_calling.MIN_TCC
+MIN_CONF=$advanced_config.variant_calling.MIN_CONF
+SIG_LEVEL=$advanced_config.variant_calling.SIG_LEVEL
+  #end if
+#end if]]></configfile>
+    </configfiles>
+    <inputs>
+        <conditional name="input_type_conditional">
+            <param name="input_type" type="select" label="Input Type">
+                <option value="single" selected="true">Single Dataset</option>
+                <option value="paired_collection">Paired Collection</option>
+            </param>
+            <when value="single">
+                 <param name="fastq_input1" type="data" format="fastq,fastq.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
+            </when>
+            <when value="paired_collection">
+                 <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"/>
+            </when>
+        </conditional>
+        <param name="module" type="select" label="Select analysis module">
+            <option value="FLU" selected="true">FLU</option>
+            <option value="FLU-utr">FLU-utr</option>
+            <option value="FLU-pacbio">FLU-pacbio</option>
+        </param>
+        <param name="optional_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Select additional IRMA outputs">
+            <option value="bam" selected="false">Bam: Alignment files of fastq against polished reference</option>
+            <option value="vcf" selected="false">Vcf: Variation calling file per segment</option>
+        </param>
+        <conditional name="advanced_config">
+            <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.">
+                <option value="no">No, use defaults for advanced settings</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <conditional name="reference">
+                    <param name="customize" type="select" label="Customize Reference Settings" help="Choosing Yes here, lets you overwrite reference settings.">
+                        <option value="no">No, use defaults for reference settings</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="SKIP_E" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Skip reference elongation" />
+                    </when>
+                </conditional>
+
+                <conditional name="read_gathering">
+                    <param name="customize" type="select" label="Customize settings to read gathering" help="Choosing Yes here, lets you overwrite read gathering settings.">
+                        <option value="no">No, use defaults for read gathering settings</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="MAX_ROUNDS" type="integer" min="1" max="20" value="5" label="Maximal rounds of read gathering"/>
+                        <param name="USE_MEDIAN" type="select" label="Use median or average for read gathering">
+                            <option value="0">Average</option>
+                            <option value="1" selected="true">Median</option>
+                        </param>
+                        <param name="QUAL_THRESHOLD" type="integer" min="0" value="30" label="Minimum read statistic to keep (Phred)"/>
+                        <param name="MIN_LEN" type="integer" min="0" max="1000" value="125" label="Minimum read length to keep (bp)" />
+                        <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" />
+                        <param name="ADAPTER" type="text" value="AGATGTGTATAAGAGACAG" label="Adapter sequence">
+                            <validator type="regex">[CAGT]+</validator> 
+                        </param>
+                        <param name="ENFORCE_CLIPPED_LENGTH" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Reads are filtered for minimum length post adapter trimming" />
+                        
+                        <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." />
+                        
+                        <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."/>
+                    </when>
+                </conditional>
+                <conditional name="match_step">
+                    <param name="customize" type="select" label="Customize settings regarding the match step" help="Choosing Yes here, lets you overwrite match step settings.">
+                        <option value="no">No, use defaults for match step settings</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="MIN_RP" type="integer" min="0" value="15" label="Minimum read pattern count to continue"/>
+                        <param name="MIN_RC" type="integer" min="0" value="15" label="Minimum read count to continue"/>
+                        <param name="MIN_BLAT_MATCH" type="integer" min="0" value="0" label="Minimum read pattern count to continue"/>
+                    </when>
+                </conditional>
+                <conditional name="sort_step">
+                    <param name="customize" type="select" label="Customize settings regarding the sort step" help="Choosing Yes here, lets you overwrite sort step settings.">
+                        <option value="no">No, use defaults for sort step settings</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="SORT_PROG" type="select" label="Select program used for sorting">
+                            <option value="LABEL">LABEL</option>
+                            <option value="BLAT" selected="true">BLAT</option>
+                        </param>
+                    </when>
+                </conditional>
+                <conditional name="align_step">
+                    <param name="customize" type="select" label="Customize settings regarding the alignment step" help="Choosing Yes here, lets you overwrite align step settings.">
+                        <option value="no">No, use defaults for align step settings</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="ALIGN_PROG" type="select" label="Select program used for alignment">
+                            <option value="BLAT">BLAT</option>
+                            <option value="SAM" selected="true">SAM</option>
+                        </param>
+                        <param name="DEL_TYPE" type="select" label="How to handle deletions in rough alignment">
+                            <option value="" selected="true">Default</option>
+                            <option value="NNN">NNN</option>
+                            <option value="REF">REF</option>
+                            <option value="DEL" >DEL</option>
+                        </param>
+                    </when>
+                </conditional>
+                <conditional name="assembly">
+                    <param name="customize" type="select" label="Customize settings regarding the assembly" help="Choosing Yes here, lets you overwrite assembly settings.">
+                        <option value="no">No, use defaults for assembly settings</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="MAX_ITER_ASSEM" type="integer" min="1" value="5" label="Maximal assembly iteration"/>
+                        <!-- true and false values are inverted for the next param because we're asking the opposite question of what we need to configure -->
+                        <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." />
+                        <param name="INS_T" type="float" min="0" max="1" value="0.25" label="The minimum frequency threshold for insertion refinement"/>
+                        <param name="DEL_T" type="float" min="0" max="1" value="0.6" label="The minimum frequency threshold for deletion refinement"/>
+                        <param name="INS_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for insertion refinement"/>
+                        <param name="DEL_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for deletion refinement"/>
+                        <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)" />
+                        <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"/>
+                        <param name="SSW_M" type="integer" min="1" value="2" label="The smith-waterman match score"/>
+                        <param name="SSW_X" type="integer" min="1" value="5" label="The smith-waterman mismatch penalty"/>
+                        <param name="SSW_O" type="integer" min="1" value="10" label="The smith-waterman gap open penalty"/>
+                        <param name="SSW_E" type="integer" min="1" value="1" label="The smith-waterman gap extension penalty"/>
+                        <param name="ALIGN_AMENDED" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Do global alignment of the amended consensus to the HMM profile" />
+                    </when>
+                </conditional>
+                <conditional name="variant_calling">
+                    <param name="customize" type="select" label="Customize settings regarding the variant calling" help="Choosing Yes here, lets you overwrite variant calling settings.">
+                        <option value="no">No, use defaults for variant calling settings</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="AUTO_F" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Automatically adjust frequency threshold" />
+                        <param name="MIN_FI" type="float" min="0" max="1" value="0.005" label="The minimum insertion variant frequency"/>
+                        <param name="MIN_FD" type="float" min="0" max="1" value="0.005" label="The minimum deletion variant frequency"/>
+                        <param name="MIN_F" type="float" min="0" max="1" value="0.008" label="The minimum frequency for single nucleotide variants"/>
+                        <param name="MIN_C" type="integer" min="1" value="2" label="The minimum count for variants"/>
+                        <param name="MIN_AQ" type="integer" min="1" value="24" label="The minimum average variant quality (does not apply to deletions)"/>
+                        <param name="MIN_TCC" type="integer" min="1" value="100" label="The minimum non-ambiguous column coverage"/>
+                        <param name="MIN_CONF" type="float" min="0" max="1" value="0.80" label="The minimum confidence"/>
+                        <param name="SIG_LEVEL" type="select" label="The significance test level for variant calling">
+                            <option value="0.999" selected="true">99.9%</option>
+                            <option value="0.99" >99%</option>
+                            <option value="0.95" >95%</option>
+                            <option value="0.90" >90%</option>
+                        </param>
+                    </when>
+                </conditional>          
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <collection name="consensus_collection" type="list" label="Fasta Consensus Sequences">
+            <data name="PB1" format="fasta" from_work_dir="resultDir/A_PB1.fasta" label="PB1"/>
+            <data name="PB2" format="fasta" from_work_dir="resultDir/A_PB2.fasta" label="PB2"/>
+            <data name="PA" format="fasta" from_work_dir="resultDir/A_PA.fasta" label="PA"/>
+            <data name="HA" format="fasta" from_work_dir="resultDir/A_HA.fasta" label="HA"/>
+            <data name="NP" format="fasta" from_work_dir="resultDir/A_NP.fasta" label="NP"/>
+            <data name="NA" format="fasta" from_work_dir="resultDir/A_NA.fasta" label="NA"/>
+            <data name="MP" format="fasta" from_work_dir="resultDir/A_MP.fasta" label="MP"/>
+            <data name="NS" format="fasta" from_work_dir="resultDir/A_NS.fasta" label="NS"/>
+        </collection>
+        <!-- optional outputs-->
+        <collection name="bam_collection" type="list" label="Alignment files (bam)">
+            <filter>optional_outputs and 'bam' in optional_outputs</filter>
+            <data name="PB1" format="bam" from_work_dir="resultDir/A_PB1.bam" label="PB1"/>
+            <data name="PB2" format="bam" from_work_dir="resultDir/A_PB2.bam" label="PB2"/>
+            <data name="PA" format="bam" from_work_dir="resultDir/A_PA.bam" label="PA"/>
+            <data name="HA" format="bam" from_work_dir="resultDir/A_HA.bam" label="HA"/>
+            <data name="NP" format="bam" from_work_dir="resultDir/A_NP.bam" label="NP"/>
+            <data name="NA" format="bam" from_work_dir="resultDir/A_NA.bam" label="NA"/>
+            <data name="MP" format="bam" from_work_dir="resultDir/A_MP.bam" label="MP"/>
+            <data name="NS" format="bam" from_work_dir="resultDir/A_NS.bam" label="NS"/>
+        </collection>
+        <collection name="vcf_collection" type="list" label="Variant calling files (VCF)">
+            <filter>optional_outputs and 'vcf' in optional_outputs</filter>
+            <data name="PB1" format="vcf" from_work_dir="resultDir/A_PB1.vcf" label="PB1"/>
+            <data name="PB2" format="vcf" from_work_dir="resultDir/A_PB2.vcf" label="PB2"/>
+            <data name="PA" format="vcf" from_work_dir="resultDir/A_PA.vcf" label="PA"/>
+            <data name="HA" format="vcf" from_work_dir="resultDir/A_HA.vcf" label="HA"/>
+            <data name="NP" format="vcf" from_work_dir="resultDir/A_NP.vcf" label="NP"/>
+            <data name="NA" format="vcf" from_work_dir="resultDir/A_NA.vcf" label="NA"/>
+            <data name="MP" format="vcf" from_work_dir="resultDir/A_MP.vcf" label="MP"/>
+            <data name="NS" format="vcf" from_work_dir="resultDir/A_NS.vcf" label="NS"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="27">
+            <conditional name="input_type_conditional">
+                <param name="fastq_input1" value="test_reads.fq" />
+                <param name="input_type" value="single" />
+            </conditional>
+            <conditional name="advanced_config">
+                <param name="customize" value="no" />
+            </conditional>
+            <param name="module" value="FLU-utr" />
+            <param name="optional_outputs" value="vcf,bam"/>
+            <output_collection name="consensus_collection" type="list">
+                <element name="HA">
+                  <assert_contents>
+                    <has_n_lines n="2"/>
+                  </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="18">
+            <param name="module" value="FLU"/>
+            <param name="optional_outputs" value="bam"/>
+            <conditional name="input_type_conditional">
+                <param name="input_type" value="paired_collection"/>
+                <param name="fastq_input">
+                    <collection type="paired">
+                        <element name="forward" value="test_reads.fq" />
+                        <element name="reverse" value="test_reads_copy.fq" />
+                    </collection>
+                </param>
+            </conditional>
+            <output_collection name="consensus_collection" type="list" count="8">
+                <element name="HA">
+                    <assert_contents>
+                        <has_n_lines n="2"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="bam_collection" type="list" count="8" />
+        </test>
+        <test expect_num_outputs="9">
+            <param name="module" value="FLU-utr"/>
+            <conditional name="input_type_conditional">
+                <param name="input_type" value="paired_collection"/>
+                <param name="fastq_input">
+                    <collection type="paired">
+                        <element name="forward" value="test_reads.fq" />
+                        <element name="reverse" value="test_reads_copy.fq" />
+                    </collection>
+                </param>
+            </conditional>
+            <conditional name="advanced_config">
+                <param name="customize" value="yes"/>
+                <conditional name="reference">
+                    <param name="customize" value="yes"/>
+                    <param name="SKIP_E" value="0"/>
+                </conditional>
+                <conditional name="read_gathering">
+                    <param name="customize" value="yes"/>
+                    <param name="MAX_ROUNDS" value="1"/>
+                </conditional>
+            </conditional>
+            <output_collection name="consensus_collection" type="list" count="8">
+                <element name="HA">
+                    <assert_contents>
+                        <has_n_lines n="2"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="27">
+            <param name="module" value="FLU"/>
+            <param name="optional_outputs" value="bam,vcf"/>
+            <conditional name="input_type_conditional">
+                <param name="input_type" value="paired_collection"/>
+                <param name="fastq_input">
+                    <collection type="paired">
+                        <element name="forward" value="test_reads.fq" />
+                        <element name="reverse" value="test_reads_copy.fq" />
+                    </collection>
+                </param>
+            </conditional>
+            <conditional name="advanced_config">
+                <param name="customize" value="yes"/>
+                <conditional name="reference">
+                    <param name="customize" value="yes"/>
+                    <param name="SKIP_E" value="true"/>
+                </conditional>
+                <conditional name="read_gathering">
+                    <param name="customize" value="yes"/>
+                    <param name="MAX_ROUNDS" value="3"/>
+                    <param name="USE_MEDIAN" value="1"/>
+                    <param name="QUAL_THRESHOLD" value="30"/>
+                    <param name="MIN_LEN" value="125"/>
+                    <param name="INCL_CHIM" value="false"/>
+                    <param name="ADAPTER" value="AGATGTGTATAAGAGACAG"/>
+                    <param name="ENFORCE_CLIPPED_LENGTH" value="true"/>
+                    <param name="MERGE_SECONDARY" value="false"/>
+                    <param name="RESIDUAL_ASSEMBLY_FACTOR" value="0"/>
+                </conditional>
+                <conditional name="match_step">
+                    <param name="customize" value="yes"/>
+                    <param name="MIN_RP" value="15"/>
+                    <param name="MIN_RC" value="15"/>
+                    <param name="MIN_BLAT_MATCH" value="0"/>
+                </conditional>
+                <conditional name="sort_step">
+                    <param name="customize" value="yes"/>
+                    <param name="SORT_PROG" value="LABEL"/>
+                </conditional>
+                <conditional name="align_step">
+                    <param name="customize" value="yes"/>
+                    <param name="ALIGN_PROG" value="SAM"/>
+                    <param name="DEL_TYPE" value=""/>
+                </conditional>
+                <conditional name="assembly">
+                    <param name="customize" value="yes"/>
+                    <param name="MAX_ITER_ASSEM" value="5"/>
+                    <param name="NO_MERGE" value="false"/>
+                    <param name="INS_T" value="0.25"/>
+                    <param name="DEL_T" value="0.6"/>
+                    <param name="INS_T_DEPTH" value="1"/>
+                    <param name="DEL_T_DEPTH" value="1"/>
+                    <param name="SILENCE_COMPLEX_INDELS" value="true"/>
+                    <param name="MIN_AMBIG" value="0.25"/>
+                    <param name="SSW_M" value="2"/>
+                    <param name="SSW_X" value="5"/>
+                    <param name="SSW_O" value="10"/>
+                    <param name="SSW_E" value="1"/>
+                    <param name="ALIGN_AMENDED" value="false"/>
+                </conditional>
+                <conditional name="variant_calling">
+                    <param name="customize" value="yes"/>
+                    <param name="AUTO_F" value="true"/>
+                    <param name="MIN_FI" value="0.005"/>
+                    <param name="MIN_FD" value="0.005"/>
+                    <param name="MIN_F" value="0.008"/>
+                    <param name="MIN_C" value="2"/>
+                    <param name="MIN_AQ" value="24"/>
+                    <param name="MIN_TCC" value="100"/>
+                    <param name="MIN_CONF" value="0.80"/>
+                    <param name="SIG_LEVEL" value="0.999"/>
+                </conditional>
+            </conditional>
+            <output_collection name="consensus_collection" type="list" count="8">
+                <element name="HA">
+                    <assert_contents>
+                        <has_n_lines n="2"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="bam_collection" type="list" count="8" />
+            <output_collection name="vcf_collection" type="list" count="8" />
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+IRMA (Iterative Refinement Meta-Assembler) can be used to obtain robust assembly, variant calling, and phasing of highly variable RNA viruses.
+These are obtained after an iterative assembly approach. Visit https://wonder.cdc.gov/amd/flu/irma/ for more information.
+IRMA offers modules for influenza, RSV, ebolavirus and coronavirus, but this galaxy wrapper currently only supports influenza modules.
+
+**Inputs**
+
+Specify the module and provide your read data.
+
+**Outputs**
+
+The default output of the tool is a collection of consensus sequences in FASTA format.
+
+Optionally, collections of read mapping and variant calling results can be produced as additional outputs.
+
+**Settings**
+
+IRMA provides carefully chosen default settings for its different analysis modes.
+Advanced(!) users have the option to override these through the advanced config section.
+
+.. class:: Warning mark
+
+    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.
+
+https://wonder.cdc.gov/amd/flu/irma/configuration.html provides more information about configuration parameters.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/s12864-016-3030-6</citation>
+    </citations>
+</tool>