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changeset 3:3242dbeea69c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 00d6705a08a9d9cc9093846b730c4dec247cf5e7
author iuc
date Sat, 18 May 2024 20:34:13 +0000
parents b4b6b660293a
children
files irissv.xml macros.xml test-data/test_out.vcf
diffstat 3 files changed, 13 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/irissv.xml	Wed Jul 06 07:07:21 2022 +0000
+++ b/irissv.xml	Sat May 18 20:34:13 2024 +0000
@@ -1,12 +1,10 @@
-<tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Refine insertion sequences</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-
     <expand macro="requirements"/>
     <expand macro="version_command"/>
-
     <command detect_errors="aggressive"><![CDATA[
     @REF_FASTA@
 
@@ -43,20 +41,19 @@
         <!--
             Optional arguments
         -->
-        <param argument="padding_before" type="integer" value="1" min="1" label="The number of bases to output before the variant in REF/ALT fields" />
-        <param argument="padding_after" type="integer" value="0" min="0" label="The number of bases to output after the variant in REF/ALT fields" />
-        <param argument="genome_buffer" type="integer" value="100000" min="1" label="The genome region on each side of the SV to align assembled reads to" />
-        <param argument="min_ins_length" type="integer" value="30" min="1" label="The min length allowed for a refined insertion sequence" />
-        <param argument="max_ins_dist" type="integer" value="100" min="0" label="The max distance a refined insertion call can be from its old position" />
-        <param argument="max_out_length" type="integer" value="100000" min="0" label="The max length of variant which will be output" />
-        <param argument="max_len_change" type="float" value="0.25" min="0.0" label="The max proportion by which a variant's length can change" />
-        
+        <param argument="padding_before" type="integer" min="1" value="1" label="The number of bases to output before the variant in REF/ALT fields"/>
+        <param argument="padding_after" type="integer" min="0" value="0" label="The number of bases to output after the variant in REF/ALT fields"/>
+        <param argument="genome_buffer" type="integer" min="1" value="100000" label="The genome region on each side of the SV to align assembled reads to"/>
+        <param argument="min_ins_length" type="integer" min="1" value="30" label="The min length allowed for a refined insertion sequence"/>
+        <param argument="max_ins_dist" type="integer" min="0" value="100" label="The max distance a refined insertion call can be from its old position"/>
+        <param argument="max_out_length" type="integer" min="0" value="100000" label="The max length of variant which will be output"/>
+        <param argument="max_len_change" type="float" min="0.0" value="0.25" label="The max proportion by which a variant's length can change"/>
         <param name="aligner" type="select">
             <option value="" selected="true">Use minimap2 for mapping</option>
             <option value="--pacbio" selected="true">Use minimap2 for mapping in PacBio mode</option>
             <option value="--hifi">Use minimap2 in hifi mode</option>
         </param>
-        <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding" />
+        <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding"/>
         <!--
             Flags
         -->
@@ -76,7 +73,7 @@
         <test expect_num_outputs="1">
             <conditional name="reference_source">
                 <param name="reference_source_selector" value="history"/>
-                <param name="ref_file" ftype="fasta.gz" value="genome.fa.gz"/>
+                <param name="ref_file" value="genome.fa.gz" ftype="fasta.gz"/>
             </conditional>
             <param name="in_vcf" value="sniffles.vcf"/>
             <param name="in_bam" value="iris.bam"/>
--- a/macros.xml	Wed Jul 06 07:07:21 2022 +0000
+++ b/macros.xml	Sat May 18 20:34:13 2024 +0000
@@ -1,10 +1,9 @@
-<?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.0.4</token>
+    <token name="@TOOL_VERSION@">1.0.5</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.9">samtools</requirement>
+            <requirement type="package" version="1.19.2">samtools</requirement>
             <requirement type="package" version="@TOOL_VERSION@">irissv</requirement>
         </requirements>
     </xml>
@@ -22,11 +21,9 @@
             }</citation>
         </citations>
     </xml>
-
     <!--
         command
     -->
-
     <token name="@REF_FASTA@"><![CDATA[
         #if $reference_source.reference_source_selector == 'history':
             #set reference = $reference_source.ref_file
@@ -41,7 +38,6 @@
             ln -sf '$reference' reference &&
         #end if
     ]]></token>
-
     <xml name="reference">
         <conditional name="reference_source">
             <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
@@ -65,7 +61,6 @@
     <!--
         Help
     -->
-
     <token name="@WID@"><![CDATA[
 *irissv*, or Implement for Refining Insertion Sequences is a tool which corrects the sequences of structural variant calls (currently only insertions). It uses FalconSense to obtain consensus sequences of the reads surrounding each variant and aligns these sequences back to the reference at the insertion site, resulting in an insertion which takes into account the aggregate information of all supporting reads.
     ]]></token>
--- a/test-data/test_out.vcf	Wed Jul 06 07:07:21 2022 +0000
+++ b/test-data/test_out.vcf	Sat May 18 20:34:13 2024 +0000
@@ -35,5 +35,5 @@
 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads">
 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	aln_sorted.bam
-chr1	6932	0	A	ATGGGGGGAGGCCCCCCCCGGGGGGGGGCCCCCCCCAGGGGGGGGGCCCCCCCCGGGGGGGGCCCCCCCCCGGGGGG	.	PASS	PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=chr1;END=6932;STD_quant_start=0.000000;STD_quant_stop=1.346291;Kurtosis_quant_start=8.663097;Kurtosis_quant_stop=3.560172;SVTYPE=INS;RNAMES=CHR1_1354_+,CHR1_1732_-,CHR1_2052_-,CHR1_2093_-,CHR1_2095_+,CHR1_2109_-,CHR1_2620_+,CHR1_2797_-,CHR1_3081_-,CHR1_3198_+,CHR1_3222_-,CHR1_3277_+,CHR1_3405_+,CHR1_3951_+,CHR1_3993_+,CHR1_4076_+,CHR1_4421_+,CHR1_4453_+,CHR1_4485_-,CHR1_4606_+,CHR1_4654_-,CHR1_4663_+,CHR1_4698_+,CHR1_4981_-,CHR1_5004_+,CHR1_5087_-,CHR1_5139_+,CHR1_5805_-,CHR1_5942_-,CHR1_5979_-,CHR1_601_-,CHR1_686_-;SUPTYPE=AL,SR;SVLEN=76;STRANDS=+-;RE=32;REF_strand=32;AF=1;IRIS_PROCESSED=1;IRIS_REFINED=1	GT:DR:DV	1/1:0:32
+chr1	6930	0	A	AGGGGGGCGGCCCCCCCCGGGGGGGGCCCCCCCCCGGGGGGGGGCCCCCCCGCGGGGGGGGGCCCCCCCCGGGGG	.	PASS	PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=chr1;END=6930;STD_quant_start=0.000000;STD_quant_stop=1.346291;Kurtosis_quant_start=8.663097;Kurtosis_quant_stop=3.560172;SVTYPE=INS;RNAMES=CHR1_1354_+,CHR1_1732_-,CHR1_2052_-,CHR1_2093_-,CHR1_2095_+,CHR1_2109_-,CHR1_2620_+,CHR1_2797_-,CHR1_3081_-,CHR1_3198_+,CHR1_3222_-,CHR1_3277_+,CHR1_3405_+,CHR1_3951_+,CHR1_3993_+,CHR1_4076_+,CHR1_4421_+,CHR1_4453_+,CHR1_4485_-,CHR1_4606_+,CHR1_4654_-,CHR1_4663_+,CHR1_4698_+,CHR1_4981_-,CHR1_5004_+,CHR1_5087_-,CHR1_5139_+,CHR1_5805_-,CHR1_5942_-,CHR1_5979_-,CHR1_601_-,CHR1_686_-;SUPTYPE=AL,SR;SVLEN=74;STRANDS=+-;RE=32;REF_strand=32;AF=1;IRIS_PROCESSED=1;IRIS_REFINED=0	GT:DR:DV	1/1:0:32
 chr1	13790	1	CACCATGTTGGCCAAGATGTTCTCGATCTCCTGACCTTGTGATCTGCCTGCCTCGTCCTCCCAAAGTGCTG	C	.	PASS	PRECISE;SVMETHOD=Snifflesv1.0.11;CHR2=chr1;END=13860;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=5.511580;Kurtosis_quant_stop=7.842635;SVTYPE=DEL;RNAMES=CHR1_10314_-,CHR1_10536_-,CHR1_10726_+,CHR1_10836_-,CHR1_10943_-,CHR1_11036_+,CHR1_11496_+,CHR1_11511_+,CHR1_11624_+,CHR1_11653_-,CHR1_11724_+,CHR1_11735_-,CHR1_11742_+,CHR1_11912_+,CHR1_11924_-,CHR1_12188_+,CHR1_12517_+,CHR1_12570_-,CHR1_12685_+,CHR1_13137_+,CHR1_13143_+,CHR1_13164_+,CHR1_13172_+,CHR1_13264_+,CHR1_13410_+,CHR1_13416_+,CHR1_13449_-,CHR1_320_+,CHR1_3277_+,CHR1_4421_+,CHR1_4654_-,CHR1_5139_+,CHR1_5979_-,CHR1_7604_-,CHR1_7697_+,CHR1_7747_-,CHR1_7838_-,CHR1_8144_+,CHR1_8491_-,CHR1_8598_+,CHR1_9029_+,CHR1_9687_-,CHR1_9723_+,CHR1_9750_+,CHR1_9968_-;SUPTYPE=AL;SVLEN=-70;STRANDS=+-;RE=45;REF_strand=45;AF=1;IRIS_PROCESSED=1;IRIS_REFINED=0	GT:DR:DV	1/1:0:45