Mercurial > repos > iuc > art
diff art_solid.xml @ 0:b98d6fffd00b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
| author | iuc |
|---|---|
| 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_solid.xml Thu Jun 11 11:51:06 2015 -0400 @@ -0,0 +1,161 @@ +<tool id="art_solid" name="ART SOLiD" version="2014.11.03.0"> + <description>simulates SOLiD data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <command><![CDATA[ +art_SOLiD + +$sam + +#if $rndSeed and $rndSeed > -1: + -r $rndSeed +#end if + +#if $generate.amplicon.use_amplicon == "amplicon_true": + -A + + #if $generate.choice == "single_end": + s + #else if $generate.choice == "paired_end": + p + #else: + m + #end if + +#end if + +$input_seq_file +output + +#if $generate.choice == "single_end": + $generate.LEN_READ + $fold_coverage +#else if $generate.choice == "paired_end": + $generate.LEN_READ_F3 + $generate.LEN_READ_F5 + $fold_coverage + $generate.fragment_size + $generate.fragment_sd +#else: + $generate.LEN_READ + $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> + <option value="paired_end">Mate Pair</option> + </param> + <when value="single_end"> + <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" /> + <expand macro="amplicon" /> + </when> + <when value="paired_end"> + <param name="LEN_READ_F3" type="integer" label="Length of F3 reads" value="100" /> + <param name="LEN_READ_F5" type="integer" label="Length of F5 reads" value="100" /> + <expand macro="frag_len_sd" /> + <expand macro="amplicon_pair" /> + </when> + <when value="mate_pair"> + <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" /> + <expand macro="frag_len_sd" /> + <expand macro="amplicon_pair" /> + </when> + </conditional> + + <expand macro="sam" /> + <expand macro="rndSeed" /> + + </inputs> + <outputs> + + <!-- Single End --> + <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of SOLiD 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="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F3)"> + <filter>generate['choice'] == "paired_end"</filter> + </data> + <data format="fastq" name="output_fq2_paired" from_work_dir="output_F5.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F5)"> + <filter>generate['choice'] == "paired_end"</filter> + </data> + + <!-- Mate Pair --> + <data format="fastq" name="output_fq1_mate" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Forward)"> + <filter>generate['choice'] == "mate_pair"</filter> + </data> + <data format="fastq" name="output_fq2_mate" from_work_dir="output_R3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Reverse)"> + <filter>generate['choice'] == "mate_pair"</filter> + </data> + + <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated SOLiD data to $input_seq_file.name"> + <filter>sam</filter> + </data> + <!-- todo? map file --> + </outputs> + <tests> + <!-- Single End tests --> + <test> + <param name="rndSeed" value="42" /> + <param name="input_seq_file" value="input.fa" /> + <param name="LEN_READ" value="25" /> + <param name="fold_coverage" value="10" /> + <param name="choice" value="single_end" /> + <param name="sam" value="False" /> + + <output name="output_fq1_single" file="art.solid.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="paired_end" /> + <param name="LEN_READ_F3" value="50" /> + <param name="LEN_READ_F5" value="50" /> + <param name="fragment_size" value="75" /> + <param name="fragment_sd" value="10" /> + <param name="sam" value="True" /> + + <output name="output_fq1_paired" file="art.solid.02_F3.fq" /> + <output name="output_fq2_paired" file="art.solid.02_F5.fq" /> + <output name="output_sam" file="art.solid.02.sam" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ +Art SOLiD Simulator +=================== + +ART_SOLiD is a simulation program to generate sequence read data of SOLiD +sequencing reads. ART generates reads according to a SOLiD read error profile. +The built-in error profile is an empiricial error profile summarized from large +SOLiD sequencing 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_SOLiD can generate both single-end, matepair, and paired-end of SOLiD +sequencing platform. art_SOLiD also support amplicon sequencing simulation with +RNA references. + ]]></help> + <expand macro="citation" /> +</tool> +