Mercurial > repos > iuc > art
annotate art_454.xml @ 5:7d6f5eef1245 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 321bb0b81c749a898c0b59447a5a87d68c4dd058
| author | iuc |
|---|---|
| date | Sun, 14 Jun 2015 22:49:32 -0400 |
| parents | 03a48ad6b460 |
| children | 3f163b178c5c |
| rev | line source |
|---|---|
| 0 | 1 <tool id="art_454" name="ART 454" version="2014.11.03.0"> |
| 2 <description>simulates pyrosequencing data</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
|
5
7d6f5eef1245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 321bb0b81c749a898c0b59447a5a87d68c4dd058
iuc
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0
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changeset
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6 <expand macro="requirements"/> |
| 0 | 7 <expand macro="stdio" /> |
| 8 <command><![CDATA[ | |
| 9 art_454 $t | |
| 10 | |
| 11 $aln | |
| 12 $sam | |
| 13 | |
| 14 #if $rndSeed and $rndSeed > -1: | |
| 15 -r $rndSeed | |
| 16 #end if | |
| 17 | |
| 18 #if $c | |
| 19 -c $c | |
| 20 #end if | |
| 21 | |
| 22 #if $generate.amplicon.use_amplicon == "amplicon_true": | |
| 23 #if $generate.choice == "single_end": | |
| 24 -A | |
| 25 #else: | |
| 26 -B | |
| 27 #end if | |
| 28 #end if | |
| 29 | |
| 30 $input_seq_file | |
| 31 output | |
| 32 | |
| 33 #if $generate.choice == "single_end": | |
| 34 $fold_coverage | |
| 35 #else: | |
| 36 $fold_coverage | |
| 37 $generate.fragment_size | |
| 38 $generate.fragment_sd | |
| 39 #end if | |
| 40 | |
| 41 #if $generate.amplicon.use_amplicon == "amplicon_true": | |
| 42 #if $generate.choice == "single_end": | |
| 43 $generate.amplicon.reads_per_amplicon | |
| 44 #else: | |
| 45 $generate.amplicon.read_pairs_per_amplicon | |
| 46 #end if | |
| 47 #end if | |
| 48 ; | |
| 49 ]]></command> | |
| 50 <inputs> | |
| 51 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/> | |
| 52 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/> | |
| 53 | |
| 54 <conditional name="generate"> | |
| 55 <param name="choice" type="select" label="Type of data to generate"> | |
| 56 <option value="single_end">Single-End</option> | |
| 57 <option value="paired_end">Paired-End</option> | |
| 58 </param> | |
| 59 <when value="single_end"> | |
| 60 <expand macro="amplicon" /> | |
| 61 </when> | |
| 62 <when value="paired_end"> | |
| 63 <expand macro="frag_len_sd" /> | |
| 64 <expand macro="amplicon_pair" /> | |
| 65 </when> | |
| 66 </conditional> | |
| 67 | |
| 68 | |
| 69 <expand macro="sam" /> | |
| 70 <expand macro="aln" /> | |
| 71 | |
| 72 <param type="boolean" label="indicate to simulate reads from the built-in GS FLX Titanium profile (-t)" name="t" truevalue="-t" falsevalue="" optional="true" /> | |
| 73 <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" /> | |
| 74 | |
| 75 <expand macro="rndSeed" /> | |
| 76 </inputs> | |
| 77 <outputs> | |
| 78 <!-- Single End --> | |
| 79 <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of 454 sequencing of $input_seq_file.name"> | |
| 80 <filter>generate['choice'] == "single_end"</filter> | |
| 81 </data> | |
| 82 | |
| 83 <!-- Paired End --> | |
| 84 <data format="fastq" name="output_fq1_paired" from_work_dir="output1.fq" label="Simulated of 454 sequencing of $input_seq_file.name (Forward)"> | |
| 85 <filter>generate['choice'] != "single_end"</filter> | |
| 86 </data> | |
| 87 <data format="fastq" name="output_fq2_paired" from_work_dir="output2.fq" label="Simulated of 454 sequencing of $input_seq_file.name (Reverse)"> | |
| 88 <filter>generate['choice'] != "single_end"</filter> | |
| 89 </data> | |
| 90 <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated 454 data to $input_seq_file.name"> | |
| 91 <filter>sam</filter> | |
| 92 </data> | |
| 93 | |
| 94 <!-- Single End --> | |
| 95 <data format="aln" name="output_aln1_single" from_work_dir="output.aln" label="Alignment of Simulated 454 data to $input_seq_file.name"> | |
| 96 <filter>aln and generate['choice'] == "single_end"</filter> | |
| 97 </data> | |
| 98 <!-- Paired End --> | |
| 99 <data format="aln" name="output_aln1_paired" from_work_dir="output1.aln" label="Alignment of Simulated 454 data to $input_seq_file.name"> | |
| 100 <filter>aln and generate['choice'] != "single_end"</filter> | |
| 101 </data> | |
| 102 <data format="aln" name="output_aln2_paired" from_work_dir="output2.aln" label="Alignment of Simulated 454 data to $input_seq_file.name"> | |
| 103 <filter>generate['choice'] != "single_end" and generate['amplicon']['use_amplicon'] == "amplicon_true"</filter> | |
| 104 </data> | |
| 105 </outputs> | |
| 106 <tests> | |
| 107 <!-- Single End tests --> | |
| 108 <test> | |
| 109 <param name="rndSeed" value="42" /> | |
| 110 <param name="input_seq_file" value="input.fa" /> | |
| 111 <param name="fold_coverage" value="20" /> | |
| 112 <param name="choice" value="single_end" /> | |
| 113 <output name="output_fq1_single" file="art.454.01.fq" /> | |
| 114 </test> | |
| 115 <test> | |
| 116 <param name="rndSeed" value="42" /> | |
| 117 <param name="input_seq_file" value="input.fa" /> | |
| 118 <param name="fold_coverage" value="20" /> | |
| 119 <param name="choice" value="single_end" /> | |
| 120 <param name="sam" value="True" /> | |
| 121 <output name="output_fq1_single" file="art.454.01.fq" /> | |
| 122 <output name="output_sam" file="art.454.01.sam" lines_diff="2"/> | |
| 123 </test> | |
| 124 <!-- Paired End tests --> | |
| 125 <test> | |
| 126 <param name="rndSeed" value="42" /> | |
| 127 <param name="input_seq_file" value="input.fa" /> | |
| 128 <param name="fold_coverage" value="20" /> | |
| 129 <param name="choice" value="paired_end" /> | |
| 130 <param name="fragment_size" value="105" /> | |
| 131 <param name="fragment_sd" value="5" /> | |
| 132 <param name="sam" value="True" /> | |
| 133 <output name="output_fq1_paired" file="art.454.021.fq" /> | |
| 134 <output name="output_fq2_paired" file="art.454.022.fq" /> | |
| 135 <output name="output_sam" file="art.454.02.sam" lines_diff="2"/> | |
| 136 </test> | |
| 137 </tests> | |
| 138 <help><![CDATA[ | |
| 139 Art 454 Pyrosequencing Simulator | |
| 140 ================================ | |
| 141 | |
| 142 ART_454 is a simulation program to generate sequence read data of Roche 454 | |
| 143 Pyrosequencing sequencers. ART generates reads according to the empirical read | |
| 144 quality profile and the calibrated error profile of uncall/overcall | |
| 145 homopolymers from real 454 read data. ART has been using for testing or | |
| 146 benchmarking a variety of method or tools for next-generation sequencing data | |
| 147 analysis, including read alignment, de novo assembly, detection of SNP, CNV, or | |
| 148 other structure variation. | |
| 149 | |
| 150 art_454 can generate both single-end and paired-end of 454 sequencing platform. | |
| 151 Besides for regular genome DNA and cDNA sequencing simulation, art_454 also | |
| 152 supports amplicon sequencing. The reference sequences can be either DNA or RNA. | |
| 153 ]]></help> | |
| 154 <expand macro="citation" /> | |
| 155 </tool> | |
| 156 |