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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit a64e791889cae72cf8cf029de8c65fa35d91b16d"
author | iuc |
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date | Fri, 15 Oct 2021 14:56:03 +0000 |
parents | f8564b2d7f63 |
children | 5c55448d0f33 |
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<?xml version="1.0"?> <tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>De novo assembly of Oxford Nanopore Technologies data</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="version_command"/> <!--TODO in future version : enable CUDA support for racon polishing--> <command detect_errors="exit_code"><![CDATA[ #if $input_reads.is_of_type("fasta") ln -s '$input_reads' ./input.fa && #set input = "input.fa" #elif $input_reads.is_of_type("fasta.gz") ln -s '$input_reads' ./input.fa.gz && #set input = "input.fa.gz" #elif $input_reads.is_of_type("fastq") ln -s '$input_reads' ./input.fq && #set input = "input.fq" #elif $input_reads.is_of_type("fastq.gz") ln -s '$input_reads' ./input.fq.gz && #set input = "input.fq.gz" #end if raven --kmer-len '$kmer_len' --window-len '$window_len' --frequency '$frequency' --polishing-rounds '$polishing_rounds' --match '$match' --mismatch '$mismatch' --gap '$gap' $graphical_fragment_assembly --disable-checkpoints -t \${GALAXY_SLOTS:-4} '$input' > '$out_fasta' ]]></command> <inputs> <param name="input_reads" type="data" format="fasta,fastq,fasta.gz,fastq.gz"/> <param argument="--kmer-len" type="integer" value="15" label="Length of minimizers used to find overlaps"/> <param argument="--window-len" type="integer" value="5" label="Length of sliding window from which minimizers are sampled"/> <param argument="--frequency" type="float" value="0.001" label="Threshold for ignoring most frequent minimizers"/> <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/> <param argument="--match" type="integer" value="3"/> <param argument="--mismatch" type="integer" value="-5"/> <param argument="--gap" type="integer" value="-4" max="-1"/> <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/> </inputs> <outputs> <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa"> <filter>graphical_fragment_assembly</filter> </data> <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)" /> </outputs> <tests> <test expect_num_outputs="2"> <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> <output name="out_gfa"> <assert_contents> <has_n_lines n="2"/> <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/> </assert_contents> </output> <output name="out_fasta"> <assert_contents> <has_n_lines n="2"/> <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/> </assert_contents> </output> </test> <!-- <test expect_num_outputs="1"> <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> <param name="graphical_fragment_assembly" value="false"/> <output name="out_fasta"> <assert_contents> <has_n_lines n="2"/> <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/> </assert_contents> </output> </test> --> </tests> <help><![CDATA[ .. class:: infomark **What it does** @WID@ **Input** - fasta / fastq / fasta.gz / fastq.gz data **Output** - Assembled genome (FASTA) - Graphical fragment assembly (optional) (.txt) **References** @REFERENCES@ ]]></help> <expand macro="citations"/> </tool>