diff macros.xml @ 20:45795f582ae9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
author iuc
date Tue, 27 Aug 2024 14:11:53 +0000
parents 42ce70172b72
children
line wrap: on
line diff
--- a/macros.xml	Wed Feb 14 09:04:09 2024 +0000
+++ b/macros.xml	Tue Aug 27 14:11:53 2024 +0000
@@ -5,7 +5,7 @@
     the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
     <!-- STAR version to be used -->
     <token name="@TOOL_VERSION@">2.7.11a</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.01</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
@@ -17,16 +17,14 @@
     <token name="@IDX_VERSION@">2.7.4a</token>
     <token name="@IDX_VERSION_SUFFIX@">2</token>
     <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
-
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">star</requirement>
             <requirement type="package" version="1.18">samtools</requirement>
             <requirement type="package" version="1.13">gzip</requirement>
-            <yield />
+            <yield/>
         </requirements>
     </xml>
-
     <xml name="edam">
         <edam_topics>
             <edam_topic>topic_3170</edam_topic>
@@ -36,20 +34,16 @@
             <edam_operation>operation_0292</edam_operation>
         </edam_operations>
     </xml>
-
     <xml name="index_selection" token_with_gene_model="0">
-        <param argument="--genomeDir" type="select"
-        label="Select reference genome"
-        help="If your genome of interest is not listed, contact the Galaxy team">
+        <param argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
             <options from_data_table="@IDX_DATA_TABLE@">
-                <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
-                <filter type="static_value" column="5" value="@IDX_VERSION@" />
-                <filter type="sort_by" column="2" />
-                <validator type="no_options" message="No indexes are available for the selected input dataset" />
+                <filter type="static_value" column="4" value="@WITH_GENE_MODEL@"/>
+                <filter type="static_value" column="5" value="@IDX_VERSION@"/>
+                <filter type="sort_by" column="2"/>
+                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
             </options>
         </param>
     </xml>
-
     <token name="@FASTQ_GZ_OPTION@">
         --readFilesCommand zcat
     </token>
@@ -59,9 +53,9 @@
         </citations>
     </xml>
     <xml name="SJDBOPTIONS">
-         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
-         <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'."/>
-         <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
+        <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
+        <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'."/>
+        <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
     </xml>
     <xml name="dbKeyActions">
         <actions>
@@ -80,7 +74,7 @@
             </when>
             <when value="history">
                 <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
+                    <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey"/>
                 </action>
             </when>
         </conditional>
@@ -135,7 +129,7 @@
         &&
     #end if
     ]]></token>
-    <token name="@REFGENOMEHANDLING@" ><![CDATA[
+    <token name="@REFGENOMEHANDLING@"><![CDATA[
     --runThreadN \${GALAXY_SLOTS:-4}
     --genomeLoad NoSharedMemory
     --genomeDir
@@ -154,7 +148,7 @@
         #end if
     #end if
     ]]></token>
-    <token name="@READSHANDLING@" ><![CDATA[
+    <token name="@READSHANDLING@"><![CDATA[
     ## Check that the input pairs are of the same type
     ## otherwise STARsolo will run for a long time and then error out.
     ## We consume either repeats of two inputs R1 + R2
@@ -183,59 +177,57 @@
         @FASTQ_GZ_OPTION@
     #end if
     ]]></token>
-    <token name="@LIMITS@" ><![CDATA[
+    <token name="@LIMITS@"><![CDATA[
         --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000))
         --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000))
         --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000))
     ]]></token>
     <xml name="ref_selection">
-        <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome" />
-          <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
+        <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome"/>
+        <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
     </xml>
-    <xml name="stdio" >
+    <xml name="stdio">
         <stdio>
             <regex match="FATAL error" source="both" level="fatal"/>
             <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
             <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
             <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
-            <yield />
+            <yield/>
         </stdio>
     </xml>
     <xml name="input_selection">
-        <conditional name="input_types" >
-            <param name="use" type="select" label="Input Type" >
-                <option value="repeat" >Separate barcode and cDNA reads</option>
-                <option value="list_paired" >Paired collection of barcode and cDNA reads</option>
+        <conditional name="input_types">
+            <param name="use" type="select" label="Input Type">
+                <option value="repeat">Separate barcode and cDNA reads</option>
+                <option value="list_paired">Paired collection of barcode and cDNA reads</option>
             </param>
             <when value="repeat">
-                <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data"  multiple="true"
-                label="RNA-Seq FASTQ/FASTA file, Barcode reads" />
-                <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data"  multiple="true"
-                label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
+                <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/>
+                <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true" label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
             </when>
             <when value="list_paired">
-                <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" />
+                <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs"/>
             </when>
         </conditional>
     </xml>
     <xml name="input_selection_smart_seq">
-        <conditional name="input_types_smart_seq" >
-            <param name="use" type="select" label="Input Type" >
-                <option value="list_single_end" >Single-end FASTQ collection</option>
-                <option value="list_paired_end" >Paired FASTQ collection</option>
+        <conditional name="input_types_smart_seq">
+            <param name="use" type="select" label="Input Type">
+                <option value="list_single_end">Single-end FASTQ collection</option>
+                <option value="list_paired_end">Paired FASTQ collection</option>
             </param>
             <when value="list_single_end">
-                <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files" />
+                <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files"/>
             </when>
             <when value="list_paired_end">
-                <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
+                <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files"/>
             </when>
         </conditional>
     </xml>
     <xml name="umidedup_options">
         <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other (1MM_All)</option>
-        <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
-        <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
+        <option value="1MM_Directional_UMItools">Directional method from the UMI-tool</option>
+        <option value="1MM_Directional">Directional with stringent UMI deduplication</option>
     </xml>
     <xml name="anchor_types">
         <option value="0">Read start</option>
@@ -244,16 +236,16 @@
         <option value="3">Adapter end</option>
     </xml>
     <xml name="cb_match_wl_common">
-        <option value="Exact" >Exact</option>
-        <option value="1MM" >Single match (1MM)</option>
+        <option value="Exact">Exact</option>
+        <option value="1MM">Single match (1MM)</option>
     </xml>
     <xml name="cb_match_wl_cellranger">
-        <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2, 1MM_multi)</option>
-        <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option>
-        <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option>
+        <option value="1MM_multi" selected="true">Multiple matches (CellRanger 2, 1MM_multi)</option>
+        <option value="1MM_multi_pseudocounts">Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option>
+        <option value="1MM_multi_Nbase_pseudocounts">Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option>
     </xml>
     <xml name="solo_adapter_params">
-        <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
+        <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes.">
             <sanitizer>
                 <valid initial="string.digits">
                     <add value="-"/>
@@ -265,11 +257,11 @@
                 </valid>
             </sanitizer>
         </param>
-        <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence" />
-        <param argument="--clipAdapterType" type="select" >
-            <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option>
-            <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
-            <option value="None" >No adapter clipping</option>
+        <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence"/>
+        <param argument="--clipAdapterType" type="select">
+            <option value="Hamming" selected="true">Adapter clipping based on Hamming distance</option>
+            <option value="CellRanger4">5p and 3p adapter clipping similar to CellRanger4</option>
+            <option value="None">No adapter clipping</option>
         </param>
     </xml>
     <xml name="common_SAM_attributes">
@@ -284,14 +276,14 @@
     </xml>
     <xml name="limits">
         <section name="junction_limits" title="Junction Limits" expanded="false">
-            <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
-            <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
-            <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
+            <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)"/>
+            <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions"/>
+            <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly."/>
         </section>
     </xml>
     <xml name="outCountActions">
         <actions>
-            <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
+            <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand"/>
             <expand macro="dbKeyAction"/>
         </actions>
     </xml>
@@ -304,7 +296,7 @@
             </param>
             <when value="None">
                 <!-- This is necessary for the filtering of output -->
-                <param name="outWigStrand" type="hidden" value="false" />
+                <param name="outWigStrand" type="hidden" value="false"/>
             </when>
             <when value="bedGraph">
                 <expand macro="outWigParams"/>
@@ -352,73 +344,92 @@
     <xml name="outWigOutputs">
         <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out">
             <filter>outWig['outWigType'] != "None"</filter>
-            <expand macro="dbKeyActions" />
+            <expand macro="dbKeyActions"/>
             <change_format>
-                <when input="outWig.outWigType" value="wiggle" format="wig" />
+                <when input="outWig.outWigType" value="wiggle" format="wig"/>
             </change_format>
         </data>
         <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out">
             <filter>outWig['outWigType'] != "None"</filter>
-            <expand macro="dbKeyActions" />
+            <expand macro="dbKeyActions"/>
             <change_format>
-                <when input="outWig.outWigType" value="wiggle" format="wig" />
+                <when input="outWig.outWigType" value="wiggle" format="wig"/>
             </change_format>
         </data>
         <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">
             <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
-            <expand macro="dbKeyActions" />
+            <expand macro="dbKeyActions"/>
             <change_format>
-                <when input="outWig.outWigType" value="wiggle" format="wig" />
+                <when input="outWig.outWigType" value="wiggle" format="wig"/>
             </change_format>
         </data>
         <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">
             <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
-            <expand macro="dbKeyActions" />
+            <expand macro="dbKeyActions"/>
             <change_format>
-                <when input="outWig.outWigType" value="wiggle" format="wig" />
+                <when input="outWig.outWigType" value="wiggle" format="wig"/>
             </change_format>
         </data>
     </xml>
     <xml name="quantMode">
         <conditional name="quantmode_output">
-            <param argument="--quantMode" type="select"
-            label="Per gene/transcript output"
-            help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
+            <param argument="--quantMode" type="select" label="Per gene/transcript output" help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
                 <option value="-">No per gene or transcript output</option>
                 <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
                 <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
                 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
             </param>
-            <when value="-" />
-            <when value="GeneCounts" />
+            <when value="-"/>
+            <when value="GeneCounts"/>
             <when value="TranscriptomeSAM">
-                <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
-                label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
-                help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
+                <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled."/>
             </when>
             <when value="TranscriptomeSAM GeneCounts">
-                <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
-                label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
-                help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
+                <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled."/>
             </when>
         </conditional>
     </xml>
     <xml name="quantModeNoGTF">
         <conditional name="quantmode_output">
-            <param argument="--quantMode" type="select"
-            label="Per gene/transcript output">
+            <param argument="--quantMode" type="select" label="Per gene/transcript output">
                 <option value="-">No per gene or transcript output as no GTF was provided</option>
             </param>
-            <when value="-" />
+            <when value="-"/>
         </conditional>
     </xml>
     <xml name="outSAMmapqUnique">
         <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value
         - according to SAM/BAM specs it means "undefined".
         - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->
-        <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"
-        label="MAPQ value for unique mappers"
-        help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is
-used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />
+        <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255" label="MAPQ value for unique mappers" help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is used: &gt;=5 mappings =&gt; MAPQ=0; 3-4 mappings =&gt; MAPQ=1; 2 mappings =&gt; MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2."/>
+    </xml>
+    <xml name="wasp">
+        <!--
+            This is re-implementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker,
+            Yoav Gilad and Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12,
+            1061–1063 (2015) https://www.nature.com/articles/nmeth.3582. WASP filtering is activated
+            with "waspOutputMode SAMtag".
+            -->
+        <conditional name="wasp_conditional">
+            <param argument="--waspOutputMode" type="select" label="Actiavte WASP filtering">
+                <help><![CDATA[This is a reimplementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker,
+                    Yoav Gilad and Jonathan K Pritchard. https://doi.org/10.1038/nmeth.3582. This option will add the vW tag to the SAM output. vW:i:1 means
+                    alignment passed WASP filtering, and all other values mean it did not:<br/>
+                    - vW:i:2 = multi-mapping read<br/>
+                    - vW:i:3 = variant base in the read is N (non-ACGT)<br/>
+                    - vW:i:4 = remapped read did not map <br/>
+                    - vW:i:5 = remapped read multi-maps <br/>
+                    - vW:i:6 = remapped read maps to a different locus <br/>
+                    - vW:i:7 = read overlaps too many variants <br/>
+                    ]]>
+                </help>
+                <option value="" selected="true">No WASP filtering</option>
+                <option value="wasp_mode">Activate WASP filtering</option>
+            </param>
+            <when value="wasp_mode">
+                <param argument="--varVCFfile" type="data" format="vcf" label="VCF file with personal variants" help="Each variant is expected to have a genotype with two alleles. The VCF file needs to have the 10th column with genotype recorded as 0/1, 1/0, 1/1 (or | instead of /)"/>
+            </when>
+            <when value=""/>
+        </conditional>
     </xml>
 </macros>