Mercurial > repos > iuc > art
diff art_illumina.xml @ 0:b98d6fffd00b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
author | iuc |
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date | Thu, 11 Jun 2015 11:51:06 -0400 |
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children | a12ce5668966 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/art_illumina.xml Thu Jun 11 11:51:06 2015 -0400 @@ -0,0 +1,158 @@ +<tool id="art_illumina" name="ART Illumina" version="2014.11.03.0"> + <description>simulates sequencing data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <command><![CDATA[ +art_illumina + +#if str($sam) == "-s": + --samout +#end if + +#if not str($aln) == "-a": + --noALN +#end if + +#if str($generate.choice) == "paired_end": + --paired + --mflen $generate.fragment_size + --sdev $generate.fragment_sd +#else if str($generate.choice) == "mate_pair": + --matepair + --mflen $generate.fragment_size + --sdev $generate.fragment_sd +#end if + +--in $input_seq_file +--len $read_length +--fcov $fold_coverage + +$amplicon + +--insRate $insRate +--insRate2 $insRate2 +--delRate $delRate +--delRate2 $delRate2 + +#if $rndSeed and $rndSeed > -1: + --rndSeed $rndSeed +#end if + +--out output; +]]></command> + <inputs> + <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/> + <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/> + <param label="length of reads to be simulated" name="read_length" type="integer" value="100"/> + <param label="amplicon sequencing simulation" name="amplicon" type="boolean" truevalue="--amplicon" falsevalue="" /> + + <conditional name="generate"> + <param name="choice" type="select" label="Type of data to generate"> + <option value="single_end">Single-End</option> + <option value="paired_end">Paired-End</option> + <option value="mate_pair">Mate-Pair</option> + </param> + <when value="single_end"> + </when> + <when value="paired_end"> + <expand macro="frag_len_sd" /> + </when> + <when value="mate_pair"> + <expand macro="frag_len_sd" /> + </when> + </conditional> + + <expand macro="aln" /> + <expand macro="sam" /> + + <param label="the first-read insertion rate" help="(--insRate)" name="insRate" type="float" value="0.00009" /> + <param label="the second-read insertion rate" help="(--insRate2)" name="insRate2" type="float" value="0.00015" /> + <param label="the first-read deletion rate" help="(--delRate)" name="delRate" type="float" value="0.00011" /> + <param label="the second-read deletion rate" help="(--delRate2)" name="delRate2" type="float" value="0.00023" /> + + <expand macro="rndSeed" /> + <!-- todo: id, errfree, masN, qShift(2), sepProf --> + </inputs> + <outputs> + <!-- Single End --> + <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of Illumina sequencing of $input_seq_file.name"> + <filter>generate['choice'] == "single_end"</filter> + </data> + + <!-- Paired End --> + <data format="fastq" name="output_fq1_paired" from_work_dir="output1.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Forward)"> + <filter>generate['choice'] != "single_end"</filter> + </data> + <data format="fastq" name="output_fq2_paired" from_work_dir="output2.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Reverse)"> + <filter>generate['choice'] != "single_end"</filter> + </data> + <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated Illumina data to $input_seq_file.name"> + <filter>sam</filter> + </data> + + <!-- Single End --> + <data format="aln" name="output_aln1_single" from_work_dir="output.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name"> + <filter>aln and generate['choice'] == "single_end"</filter> + </data> + + <!-- paired end --> + <data format="aln" name="output_aln1_paired" from_work_dir="output1.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name"> + <filter>aln and generate['choice'] != "single_end"</filter> + </data> + <data format="aln" name="output_aln2_paired" from_work_dir="output2.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name"> + <filter>aln and generate['choice'] != "single_end"</filter> + </data> + </outputs> + <tests> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="read_length" value="200" /> + <param name="choice" value="single_end" /> + <param name="aln" value="True" /> + <param name="sam" value="True" /> + + <output name="output_fq1_single" file="art.illumina.01.fq" /> + <output name="output_aln1_single" file="art.illumina.01.aln" lines_diff="2"/> + <output name="output_sam" file="art.illumina.01.sam" lines_diff="2"/> + </test> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="read_length" value="200" /> + <param name="choice" value="paired_end" /> + <param name="fragment_size" value="300" /> + <param name="fragment_sd" value="10" /> + <param name="aln" value="True" /> + <param name="sam" value="True" /> + + <output name="output_fq1_paired" file="art.illumina.021.fq" /> + <output name="output_fq2_paired" file="art.illumina.022.fq" /> + <output name="output_aln1_paired" file="art.illumina.021.aln" lines_diff="2"/> + <output name="output_aln2_paired" file="art.illumina.022.aln" lines_diff="2"/> + <output name="output_sam" file="art.illumina.02.sam" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ +Art Illumina Simulator +====================== + +ART (art_Illumina Q version) is a simulation program to generate sequence read +data of Illumina sequencers. ART generates reads according to the empirical +read quality profile summarized from large real read data. ART has been using +for testing or benchmarking a variety of methods or tools for next-generation +sequencing data analysis, including read alignment, de novo assembly, detection +of SNP, CNV, or other structure variation. + +art_Illumina can generate single-end, paired-end, mate-pair reads, and +amplicon sequencing simulation of Illumina sequencing platform. Its outputs +include FASTQ read, ALN and/or SAM alignment files. + + ]]></help> + <expand macro="citation" /> +</tool> +