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bridger.xml |
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| diff -r 000000000000 -r 38461a69ece5 bridger.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bridger.xml Fri Dec 02 04:13:24 2016 -0500 |
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| @@ -0,0 +1,104 @@ +<tool id="bridger" name="bridger" version="v1"> + <description>de novo assembly of RNA-Seq data</description> + <requirements> + <container type="docker">ycogne/bridger</container> + </requirements> + <command> + /usr/bin/Bridger_r2014-12-01/Bridger.pl + + #if $inputs.paired_or_single == "paired": + + --left $inputs.left_input + + --right $inputs.right_input + + #if $inputs.left_input.is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + + #if $inputs.strand.is_strand_specific: + --SS_lib_type $inputs.strand.library_type + #end if + + + + #else: + --single $inputs.input + + #if $inputs.input.is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + + #if $inputs.strand.is_strand_specific: + --SS_lib_type $inputs.strand.library_type + #end if + #end if + + --CPU $additional_params.CPU_usage + -k $additional_params.kmer_used + + -o /home/results/Bridger 2>1 ; + mv /home/results/Bridger/Bridger.fasta $assembled_transcripts + + + + </command> + <inputs> + <conditional name="inputs"> + <param name="paired_or_single" type="select" label="Paired or Single-end data?"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + <when value="paired"> + <param format="fasta,fastqsanger,fastq" argument="--left" name="left_input" type="data" label="Left/Forward strand reads" help=""/> + <param format="fasta,fastqsanger,fastq" argument="--right" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> + <conditional name="strand"> + <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> + <when value="false"> + </when> + <when value="true"> + <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> + <option value="FR">Forward-Reverse</option> + <option value="RF">Reverse-Forward</option> + </param> + </when> + </conditional> + </when> + <when value="single"> + <param format="fasta,fastqsanger,fastq" name="input" argument="--single" type="data" label="Single-end reads" help=""/> + <conditional name="strand"> + <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> + <when value="false"> + </when> + <when value="true"> + <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> + <option value="F">F</option> + <option value="R">R</option> + </param> + </when> + </conditional> + </when> + </conditional> + + <section name="additional_params" title="Additional Options" expanded="False"> + <param name="CPU_usage" argument="--CPU_usage" type="integer" optional="true" value="3" min="1" label="Number of CPU" help="Number of CPU use by the software"/> + <param name="kmer_used" argument="-k" type="integer" optional="true" value="25" min="10" label="Kmer length" help="Kmer length"/> + + </section> + + </inputs> + <outputs> + + <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" /> + + </outputs> + <help> + https://github.com/fmaguire/Bridger_Assembler + </help> + + +</tool> |