Mercurial > repos > iuc > irissv
diff irissv.xml @ 0:30fc9f2bcbe4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
author | iuc |
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date | Tue, 19 Jan 2021 20:30:21 +0000 |
parents | |
children | 1d4f065fa0ef |
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--- /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>