diff irissv.xml @ 0:30fc9f2bcbe4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/irissv.xml	Tue Jan 19 20:30:21 2021 +0000
@@ -0,0 +1,118 @@
+<?xml version="1.0"?>
+<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="exit_code"><![CDATA[
+    @REF_FASTA@
+
+    iris
+        genome_in=reference.fa
+        vcf_in='${in_vcf}'
+        reads_in='${in_bam}'
+        vcf_out='${out_vcf}'
+        threads=\${GALAXY_SLOTS:-4}
+        padding_before='${padding_before}'
+        padding_after='${padding_after}'
+        genome_buffer='${genome_buffer}'
+        min_ins_length='${min_ins_length}'
+        max_ins_dist='${max_ins_dist}'
+        max_out_length='${max_out_length}'
+        max_len_change='${max_len_change}'
+        '${aligner}'
+        '${rerunracon}'
+        '${also_deletions}'
+        '${keep_long_variants}'
+    ]]></command>
+    <inputs>
+        <!--
+            Required arguments
+        -->
+        <expand macro="reference"/>
+        <param name="in_vcf" type="data" format="vcf" label="The VCF file with variant calls/supporting reads"/>
+        <param name="in_bam" type="data" format="bam" label="The BAM file containing the reads"/>
+        <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
+        <!-- <param name="output_log" type="boolean" label="Output log file?" checked="true"/> -->
+        <!--
+            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 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" />
+        <!--
+            Flags
+        -->
+        <param argument="--also_deletions" type="boolean" truevalue="also_deletions" falsevalue="" checked="false" label="also try to refine deletion positions/lengths"/>
+        <param argument="--keep_long_variants" type="boolean" truevalue="--keep_long_variants" falsevalue="" checked="false" label="output original VCF line for very long variants instead of ignoring them"/>
+    </inputs>
+    <outputs>
+        <!-- standard -->
+        <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}: Result"/>
+        <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
+        <!-- <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
+            <filter>output_log</filter>
+        </data> -->
+    </outputs>
+    <tests>
+        <!-- #1 default -->
+        <test expect_num_outputs="1">
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history"/>
+                <param name="ref_file" ftype="fasta" value="genome.fa"/>
+            </conditional>
+            <param name="in_vcf" value="sniffles.vcf"/>
+            <param name="in_bam" value="iris.bam"/>
+            <output name="out_vcf" file="test_out.vcf"/>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="ref_file" value="iris"/>
+            </conditional>
+            <param name="in_vcf" value="sniffles.vcf"/>
+            <param name="in_bam" value="iris.bam"/>
+            <output name="out_vcf" file="test_out.vcf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+
+**Input**
+
+- FASTA file containing the reference genome
+
+- VCF file with variant calls & supporting reads determined by Sniffles
+
+- BAM file containing the reads
+
+**Output**
+
+- VCF file with refined insertion sequences
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>