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changeset 8:bebb4f9eba4f draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 097dc42275535b1ace343a7842d0dcfbb6ef6f38
author artbio
date Fri, 16 Jan 2026 17:19:22 +0000
parents 555971edd46e
children
files manta.xml manta_macros.xml
diffstat 2 files changed, 76 insertions(+), 79 deletions(-) [+]
line wrap: on
line diff
--- a/manta.xml	Tue Feb 20 08:31:27 2024 +0000
+++ b/manta.xml	Fri Jan 16 17:19:22 2026 +0000
@@ -96,7 +96,7 @@
             <when value="Default_config_file">
             </when>
             <when value="Custom_config_file">
-                <param format="ini" name="CustomConfigFile" type="data" label="config file"/>
+                <param format="txt" name="CustomConfigFile" type="data" label="config file"/>
             </when>
             <when value="Customized">
                 <param name="minCandidateVariantSize" type="integer" value="8" label="minCandidateVariantSize" help="Run discovery and candidate reporting for all SVs/indels at or above this size."/>
@@ -138,73 +138,99 @@
             <filter>bam_input['bam_input_selector'] == 'tumor_bam'</filter>
         </data>
     </outputs>
+
     <tests>
         <test expect_num_outputs="3">
-            <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="reference_source|reference_source_selector" value="cached"/>
+            <param name="reference_source|index" value="hg19"/>
+
+            <param name="bam_input|bam_input_selector" value="tumor_bam" dbkey="hg19"/>
+            <param name="bam_input|normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
+            <param name="bam_input|tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
+
+            <param name="set_configuration|set_configuration_switch" value="Default_config_file"/>
+            
+            <param name="advanced|callMemMb" value="1000"/>
+            
             <param name="candidateSmallIndels_check" value="True"/>
             <output name="conf_file" file="conf_file_1.ini" ftype="txt"/>
             <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 expect_num_outputs="3">
-            <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="reference_source|reference_source_selector" value="cached"/>
+            <param name="reference_source|index" value="hg19"/>
+
+            <param name="bam_input|bam_input_selector" value="tumor_bam" dbkey="hg19"/>
+            <param name="bam_input|normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
+            <param name="bam_input|tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
+
+            <param name="set_configuration|set_configuration_switch" value="Customized"/>
+            
+            <param name="advanced|callMemMb" value="1000"/>
+            
             <param name="candidateSmallIndels_check" value="True"/>
             <output name="conf_file" file="conf_file_2.ini" ftype="txt"/>
             <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 expect_num_outputs="3">
-                <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="conf_file" file="conf_file_3.ini" ftype="txt"/>
-                <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|reference_source_selector" value="cached"/>
+            <param name="reference_source|index" value="hg19"/>
+
+            <param name="bam_input|bam_input_selector" value="tumor_bam" dbkey="hg19"/>
+            <param name="bam_input|normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
+            <param name="bam_input|tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
+
+            <param name="set_configuration|set_configuration_switch" value="Default_config_file"/>
+            
+            <param name="advanced|callMemMb" value="1000"/>
+            
+            <param name="candidateSmallIndels_check" value="True"/>
+            <output name="conf_file" file="conf_file_3.ini" ftype="txt"/>
+            <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 expect_num_outputs="3">
-                <param name="reference_source_selector" value="history"/>
-                <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
-                <param name="bam_input_selector" value="tumor_bam"/>
-                <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="candidateSV_check" value="True"/>
-                <output name="conf_file" file="conf_file_4.ini" ftype="txt"/>
-                <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="6"/>
-                <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
+            <param name="reference_source|reference_source_selector" value="history"/>
+            <param name="reference_source|ref_file" ftype="fasta" value="hg19_region.fa"/>
+
+            <param name="bam_input|bam_input_selector" value="tumor_bam"/>
+            <param name="bam_input|normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
+            <param name="bam_input|tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
+
+            <param name="set_configuration|set_configuration_switch" value="Default_config_file"/>
+            
+            <param name="advanced|callMemMb" value="1000"/>
+            
+            <param name="candidateSV_check" value="True"/>
+            <output name="conf_file" file="conf_file_4.ini" ftype="txt"/>
+            <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="6"/>
+            <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="6"/>
         </test>
+
         <test expect_num_outputs="3">
-                <param name="reference_source_selector" value="history"/>
-                <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
-                <param name="bam_input_selector" value="tumor_bam"/>
-                <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="conf_file" file="conf_file_5.ini" ftype="txt"/>
-                <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|reference_source_selector" value="history"/>
+            <param name="reference_source|ref_file" ftype="fasta" value="hg19_region.fa"/>
+
+            <param name="bam_input|bam_input_selector" value="tumor_bam"/>
+            <param name="bam_input|normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
+            <param name="bam_input|tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
+
+            <param name="set_configuration|set_configuration_switch" value="Default_config_file"/>
+            
+            <param name="advanced|callMemMb" value="1000"/>
+            
+            <param name="candidateSmallIndels_check" value="True"/>
+            <output name="conf_file" file="conf_file_5.ini" ftype="txt"/>
+            <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>
     </tests>
+
     <help><![CDATA[
 **Outputs**
   The primary Manta outputs are a set of VCF 4.1 files. Currently there are 3 VCF files
--- a/manta_macros.xml	Tue Feb 20 08:31:27 2024 +0000
+++ b/manta_macros.xml	Fri Jan 16 17:19:22 2026 +0000
@@ -1,7 +1,7 @@
 <macros>
 
     <token name="@TOOL_VERSION@">1.6</token>
-    <token name="@VERSION_SUFFIX@">9</token>
+    <token name="@VERSION_SUFFIX@">10</token>
     <token name="@PROFILE@">20.05</token>
     <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
 
@@ -30,7 +30,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">manta</requirement>
-            <requirement type="package" version="1.7">samtools</requirement>
+            <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
     </xml>
 
@@ -65,33 +65,4 @@
             </when>
         </conditional>
     </macro>
-
-    <macro name="manta_configuration">
-        <conditional name="configuration">
-            <param name="configuration_switch" type="select" label="How do you want to configure manta?">
-                <option value="Custom_config_file">Upload a different config file</option>
-                <option value="Customized">Customize the options</option>
-            </param>
-            <when value="Custom_config_file">
-                <param format="ini" name="CustomConfigFile" type="data" label="config file"/>
-            </when>
-            <when value="Customized">
-                <param name="minCandidateVariantSize" type="integer" value="8" label="minCandidateVariantSize" help="Run discovery and candidate reporting for all SVs/indels at or above this size."/>
-                <param name="rnaMinCandidateVariantSize" type="integer" value="1000" label="rnaMinCandidateVariantSize" help="Separate option (to provide different default) used for runs in RNA-mode."/>
-                <param name="minEdgeObservations" type="integer" value="3" label="minEdgeObservations" help="Remove all edges from the graph unless they're supported by this many 'observations'."/>
-                <param name="graphNodeMaxEdgeCount" type="integer" value="10" label="graphNodeMaxEdgeCount" help="If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge."/>
-                <param name="minCandidateSpanningCount" type="integer" value="3" label="minCandidateSpanningCount" help="Run discovery and candidate reporting for all SVs/indels with at least this many spanning support observations."/>
-                <param name="minScoredVariantSize" type="integer" value="50" label="minScoredVariantSize" help="After candidate identification, only score and report SVs/indels at or above this size."/>
-                <param name="minDiploidVariantScore" type="integer" value="10" label="minDiploidVariantScore" help="Minimum VCF 'QUAL' score for a variant to be included in the diploid vcf."/>
-                <param name="minPassDiploidVariantScore" type="integer" value="20" label="minPassDiploidVariantScore" help="VCF 'QUAL' score below which a variant is marked as filtered in the diploid vcf."/>
-                <param name="minPassDiploidGTScore" type="integer" value="15" label="minPassDiploidGTScore" help="Minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf."/>
-                <param name="minSomaticScore" type="integer" value="10" label="minSomaticScore" help="Somatic quality scores below this level are not included in the somatic vcf."/>
-                <param name="minPassSomaticScore" type="integer" value="30" label="minPassSomaticScore" help="Somatic quality scores below this level are filtered in the somatic vcf."/>
-                <param name="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" type="integer" value="1" label="enableRemoteReadRetrievalForInsertionsInGermlineCallingModes" help="Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote locations with poor mapping quality. This feature can be enabled/disabled separately for germline and cancer calling below."/>
-                <param name="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" type="integer" value="0" label="enableRemoteReadRetrievalForInsertionsInCancerCallingModes" help="Here 'CancerCallingModes' includes tumor-normal subtraction and tumor-only calling. 'GermlineCallingModes' includes all other calling modes."/>
-                <param name="useOverlapPairEvidence" type="integer" value="0" label="useOverlapPairEvidence" help="Set if an overlapping read pair will be considered as evidence. Set this value &lt;= 0 to skip overlapping read pairs."/>
-            </when>
-        </conditional>
-    </macro>
-
 </macros>