Mercurial > repos > iuc > get_hrun
comparison get_hrun.xml @ 0:ccb3b00e6405 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
| author | iuc |
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| date | Tue, 02 Mar 2021 21:35:15 +0000 |
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| children |
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| -1:000000000000 | 0:ccb3b00e6405 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="get_hrun" name="Get homopolymer run length" version="@VERSION@+galaxy0" profile="@PROFILE@" license="MIT"> | |
| 3 <description>Annotate indel variants with homopolymer context</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 ln -s '${reference}' ref.fa && | |
| 10 samtools faidx ref.fa && | |
| 11 python '${__tool_directory__}/get_hrun.py' --reference ref.fa --in-vcf '${in_vcf}' --out-vcf '${out_vcf}' | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param argument="--in-vcf" type="data" format="vcf" label="Input VCF"/> | |
| 15 <param argument="--reference" type="data" format="fasta" label="Input Reference FASTA"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}"/> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="in_vcf" value="in.vcf"/> | |
| 23 <param name="reference" value="reference.fasta"/> | |
| 24 <output name="out_vcf" value="out.vcf"/> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help><![CDATA[ | |
| 28 .. class:: infomark | |
| 29 | |
| 30 **What it does** | |
| 31 | |
| 32 @WID@ | |
| 33 | |
| 34 **Inputs** | |
| 35 - VCF file | |
| 36 - Reference file for that VCF | |
| 37 **Outputs** | |
| 38 - VCF with annotated homopolymers | |
| 39 ]]></help> | |
| 40 <expand macro="citations"/> | |
| 41 </tool> |