--- a/manta.xml	Tue Jun 09 06:23:39 2020 -0400
+++ b/manta.xml	Thu Jun 08 17:36:38 2023 +0000
@@ -1,7 +1,5 @@
-<tool id="manta" name="Manta" version="@WRAPPER_VERSION@">
-
+<tool id="manta" name="Manta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.</description>
-
     <macros>
         <import>manta_macros.xml</import>
     </macros>
@@ -9,7 +7,6 @@
     <expand macro="stdio"/>
 
     <command detect_errors="exit_code"><![CDATA[
-    @VERSION@
     @pipefail@
     @set_reference_fasta_filename@
     #set run_dir = './MantaWorkflow'
@@ -29,7 +26,7 @@
     #end if
     #if str( $set_configuration.set_configuration_switch ) == "Customized":
         rm ./configManta.py.ini &&
-        python $__tool_directory__/customConfigManta.py
+        python '$__tool_directory__/customConfigManta.py'
         --minCandidateVariantSize '$set_configuration.minCandidateVariantSize'
         --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize'
         --minEdgeObservations '$set_configuration.minEdgeObservations'
@@ -46,22 +43,22 @@
         --useOverlapPairEvidence '$set_configuration.useOverlapPairEvidence' &&
     #end if
     
-    configManta.py --referenceFasta='${reference_fasta_filename}'
-                   --config='./configManta.py.ini'
-                   #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
-                       --bam='normal.bam'
-                   #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
-                       --bam='normal.bam'
-                       --tumorBam='tumor.bam'
-                   #end if
-                      --runDir='${run_dir}'
-                      --scanSizeMb=${advanced.scanSizeMb}
-                      --callMemMb=${advanced.callMemMb} &&
+    configManta.py
+        --referenceFasta='${reference_fasta_filename}'
+        --config='./configManta.py.ini'
+        #if str( $bam_input.bam_input_selector ) == "not_tumor_bam":
+            --bam='normal.bam'
+        #else if str( $bam_input.bam_input_selector ) == "tumor_bam":
+            --bam='normal.bam'
+            --tumorBam='tumor.bam'
+        #end if
+        --runDir='${run_dir}'
+        --scanSizeMb=${advanced.scanSizeMb}
+        --callMemMb=${advanced.callMemMb} &&
 
     python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4}
 
     ]]></command>
-
     <inputs>
         <expand macro="reference_source_conditional" />
         <conditional name="bam_input">
@@ -143,30 +140,30 @@
     </outputs>
     <tests>
         <test>
-                <param name="reference_source_selector" value="cached"/>
-                <param name="index" value="hg19"/>
-                <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
-                <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
-                <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
-                <param name="set_configuration_switch" value="Default_config_file"/>
-                <param name="callMemMb" value="1000"/>
-                <param name="candidateSmallIndels_check" value="True"/>
-                <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
-                <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
+            <param name="reference_source_selector" value="cached"/>
+            <param name="index" value="hg19"/>
+            <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
+            <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
+            <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
+            <param name="set_configuration_switch" value="Default_config_file"/>
+            <param name="callMemMb" value="1000"/>
+            <param name="candidateSmallIndels_check" value="True"/>
+            <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
+            <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
         </test>
-         <test>
-                <param name="reference_source_selector" value="cached"/>
-                <param name="index" value="hg19"/>
-                <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
-                <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
-                <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
-                <param name="set_configuration_switch" value="Customized"/>
-                <param name="callMemMb" value="1000"/>
-                <param name="candidateSmallIndels_check" value="True"/>
-                <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
-                <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
+        <test>
+            <param name="reference_source_selector" value="cached"/>
+            <param name="index" value="hg19"/>
+            <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
+            <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
+            <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
+            <param name="set_configuration_switch" value="Customized"/>
+            <param name="callMemMb" value="1000"/>
+            <param name="candidateSmallIndels_check" value="True"/>
+            <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="6"/>
+            <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
         </test>
-       <test>
+        <test>
                 <param name="reference_source_selector" value="cached"/>
                 <param name="index" value="hg19"/>
                 <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
@@ -252,78 +249,8 @@
   can execute the workflow on a single node or through
   sge and resume any interrupted execution.
 
-**Options**
-  --version             show program's version number and exit
-  -h, --help            show this help message and exit
-  --config=FILE         provide a configuration file to override defaults in
-                        global config file (/home/lpanunzi/Desktop/Hackaton_GC
-                        C2019/manta_sv/manta/bin/configManta.py.ini)
-  --allHelp             show all extended/hidden options
-**Workflow options**
-    --bam=FILE, --normalBam=FILE
-                        Normal sample BAM or CRAM file. May be specified more
-                        than once, multiple inputs will be treated as each BAM
-                        file representing a different sample. [optional] (no
-                        default)
-    --tumorBam=FILE, --tumourBam=FILE
-                        Tumor sample BAM or CRAM file. Only up to one tumor
-                        bam file accepted. [optional] (no default)
-    --exome             Set options for WES input: turn off depth filters
-    --rna               Set options for RNA-Seq input. Must specify exactly
-                        one bam input file
-    --unstrandedRNA     Set if RNA-Seq input is unstranded: Allows splice-
-                        junctions on either strand
-    --referenceFasta=FILE
-                        samtools-indexed reference fasta file [required]
-    --runDir=DIR        Name of directory to be created where all workflow
-                        scripts and output will be written. Each analysis
-                        requires a separate directory. (default:
-                        MantaWorkflow)
-    --callRegions=FILE  Optionally provide a bgzip-compressed/tabix-indexed
-                        BED file containing the set of regions to call. No VCF
-                        output will be provided outside of these regions. The
-                        full genome will still be used to estimate statistics
-                        from the input (such as expected fragment size
-                        distribution). Only one BED file may be specified.
-                        (default: call the entire genome)
-**Extended options**
-    These options are either unlikely to be reset after initial site
-    configuration or only of interest for workflow development/debugging.
-    They will not be printed here if a default exists unless --allHelp is
-    specified
-    
-    --existingAlignStatsFile=FILE
-                        Pre-calculated alignment statistics file. Skips
-                        alignment stats calculation.
-    --useExistingChromDepths
-                        Use pre-calculated chromosome depths.
-    --candidateBins=candidateBins
-                        Provide the total number of tasks which candidate
-                        generation  will be sub-divided into. (default: 256)
-    --retainTempFiles   Keep all temporary files (for workflow debugging)
-    --generateEvidenceBam
-                        Generate a bam of supporting reads for all SVs
-    --outputContig      Output assembled contig sequences in VCF file
-    --scanSizeMb=INT    Maximum sequence region size (in megabases) scanned by
-                        each task during SV Locus graph generation. (default:
-                        12)
-    --region=REGION     Limit the analysis to a region of the genome for
-                        debugging purposes. If this argument is provided
-                        multiple times all specified regions will be analyzed
-                        together. All regions must be non-overlapping to get a
-                        meaningful result. Examples: '--region chr20' (whole
-                        chromosome), '--region chr2:100-2000 --region
-                        chr3:2500-3000' (two regions)'. If this option is
-                        specified (one or more times) together with the
-                        --callRegions BED file, then all region arguments will
-                        be intersected with the callRegions BED track.
-    --callMemMb=INT     Set default task memory requirement (in megabytes) for
-                        common tasks. This may benefit an analysis of unusual
-                        depth, chimera rate, etc.. 'Common' tasks refers to
-                        most compute intensive scatter-phase tasks of graph
-                        creation and candidate generation.
 
-    For further info see: https://github.com/Illumina/manta
+For further info see: https://github.com/Illumina/manta
 
   ]]></help>
     <citations>