Mercurial > repos > nml > seqtk_nml
diff seqtk_nml.xml @ 0:e1867440ed36 draft
planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
author | nml |
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date | Tue, 19 Sep 2017 16:37:42 -0400 |
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children | f49992c79fe4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_nml.xml Tue Sep 19 16:37:42 2017 -0400 @@ -0,0 +1,113 @@ +<tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.0"> + <description>Runs seqTK sample if raw coverage is above user defined threshold </description> + <requirements> + <requirement type="package" version="1.2">seqtk</requirement> + <requirement type="package" version="1.6.924">perl-bioperl</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Unknown error has occured"/> + </stdio> + <command> + perl $__tool_directory__/seqtk_nml.pl --ref $fastar + + #if $single_or_paired.type == "single" + --type single + --forward $input_se + --cov $coverage + --out_forward $output + --log $log + #elif $single_or_paired.type == "paired" + --type paired + --forward $single_or_paired.forward_pe + --reverse $single_or_paired.reverse_pe + --cov $coverage + --out_forward $output + --out_reverse $output_rev + --log $log + #else + collection + $single_or_paired.fastq_collection.forward $single_or_paired.fastq_collection.reverse + $coverage $output_collection.forward $output_collection.reverse + #end if + + </command> + <inputs> + <conditional name="single_or_paired"> + <param name="type" type="select" label="Read type"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + <option value="collection">Collection Paired-end</option> + </param> + <when value="single"> + <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/> + </when> + <when value="paired"> + <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/> + <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/> + </when> + <when value="collection"> + <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" /> + </when> + </conditional> + <param name="fastar" type="data" label="Fasta Reference File" format="fasta" /> + <param name="coverage" type="integer" label="Desired Coverage" value="50" /> + </inputs> + <outputs> + <data format="fastqsanger" name="output" label="SubSampled Fastq" > + <filter>single_or_paired['type']!="collection"</filter> + </data> + <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse"> + <filter>single_or_paired['type']=="paired"</filter> + </data> + <collection name="output_collection" type="paired" label="SubSampled Fastqs"> + <data name="forward" format="fastqsanger"/> + <data name="reverse" format="fastqsanger"/> + <filter>single_or_paired['type']=="collection"</filter> + </collection> + <data format="txt" name="log" label="Log file"/> + </outputs> + + <tests> + <test> + <param name="type" value="paired" /> + <param name="forward_pe" value="inputforward.fastq" /> + <param name="reverse_pe" value="inputreverse.fastq" /> + <param name="fastar" value="testref.fasta"/> + <param name="coverage" value="50" /> + <output name="output" file="outputforward.fastq" /> + <output name="output_rev" file="outputreverse.fastq" /> + <output name="log" file="lognosample.log" /> + </test> + <test> + <param name="type" value="paired" /> + <param name="forward_pe" value="inputforward.fastq" /> + <param name="reverse_pe" value="inputreverse.fastq" /> + <param name="fastar" value="testref.fasta"/> + <param name="coverage" value="25" /> + <output name="output" file="outputdownsamepleforward.fastq" /> + <output name="output_rev" file="outputdownsameplereverse.fastq" /> + <output name="log" file="logdownsample.log" /> + </test> + </tests> + <help> +What it does +============ + +Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads. + + +Usage +===== + +**Parameters** + - Fastq reads (single end, paired end, or paired end collection) + - Fasta reference file + +**Options** + - Desired coverage (50) + </help> + <citations> + <citation type="doi">doi.org/10.1371/journal.pone.0163962</citation> + </citations> +</tool> +