Mercurial > repos > iuc > art
diff art_454.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 |
parents | |
children | a12ce5668966 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/art_454.xml Thu Jun 11 11:51:06 2015 -0400 @@ -0,0 +1,155 @@ +<tool id="art_454" name="ART 454" version="2014.11.03.0"> + <description>simulates pyrosequencing data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <command><![CDATA[ +art_454 $t + +$aln +$sam + +#if $rndSeed and $rndSeed > -1: +-r $rndSeed +#end if + +#if $c +-c $c +#end if + +#if $generate.amplicon.use_amplicon == "amplicon_true": + #if $generate.choice == "single_end": + -A + #else: + -B + #end if +#end if + +$input_seq_file +output + +#if $generate.choice == "single_end": + $fold_coverage +#else: + $fold_coverage + $generate.fragment_size + $generate.fragment_sd +#end if + +#if $generate.amplicon.use_amplicon == "amplicon_true": + #if $generate.choice == "single_end": + $generate.amplicon.reads_per_amplicon + #else: + $generate.amplicon.read_pairs_per_amplicon + #end if +#end if +; +]]></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"/> + + <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> + </param> + <when value="single_end"> + <expand macro="amplicon" /> + </when> + <when value="paired_end"> + <expand macro="frag_len_sd" /> + <expand macro="amplicon_pair" /> + </when> + </conditional> + + + <expand macro="sam" /> + <expand macro="aln" /> + + <param type="boolean" label="indicate to simulate reads from the built-in GS FLX Titanium profile (-t)" name="t" truevalue="-t" falsevalue="" optional="true" /> + <param label="specify the number of flow cycles by the sequencer [100 for GS-FLX, 200 for GS-FLX Titanium] (-c)" name="c" type="integer" value="100" optional="true" /> + + <expand macro="rndSeed" /> + </inputs> + <outputs> + <!-- Single End --> + <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of 454 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 454 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 454 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 454 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 454 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 454 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 454 data to $input_seq_file.name"> + <filter>generate['choice'] != "single_end" and generate['amplicon']['use_amplicon'] == "amplicon_true"</filter> + </data> + </outputs> + <tests> + <!-- Single End tests --> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="choice" value="single_end" /> + <output name="output_fq1_single" file="art.454.01.fq" /> + </test> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="choice" value="single_end" /> + <param name="sam" value="True" /> + <output name="output_fq1_single" file="art.454.01.fq" /> + <output name="output_sam" file="art.454.01.sam" lines_diff="2"/> + </test> + <!-- Paired End tests --> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="fold_coverage" value="20" /> + <param name="choice" value="paired_end" /> + <param name="fragment_size" value="105" /> + <param name="fragment_sd" value="5" /> + <param name="sam" value="True" /> + <output name="output_fq1_paired" file="art.454.021.fq" /> + <output name="output_fq2_paired" file="art.454.022.fq" /> + <output name="output_sam" file="art.454.02.sam" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ +Art 454 Pyrosequencing Simulator +================================ + +ART_454 is a simulation program to generate sequence read data of Roche 454 +Pyrosequencing sequencers. ART generates reads according to the empirical read +quality profile and the calibrated error profile of uncall/overcall +homopolymers from real 454 read data. ART has been using for testing or +benchmarking a variety of method or tools for next-generation sequencing data +analysis, including read alignment, de novo assembly, detection of SNP, CNV, or +other structure variation. + +art_454 can generate both single-end and paired-end of 454 sequencing platform. +Besides for regular genome DNA and cDNA sequencing simulation, art_454 also +supports amplicon sequencing. The reference sequences can be either DNA or RNA. + ]]></help> + <expand macro="citation" /> +</tool> +