diff irissv.xml @ 3:3242dbeea69c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 00d6705a08a9d9cc9093846b730c4dec247cf5e7

--- 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"/>