Mercurial > repos > iuc > art
annotate art_solid.xml @ 7:3f163b178c5c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
| author | iuc |
|---|---|
| date | Tue, 28 Jun 2016 11:32:06 -0400 |
| parents | 7d6f5eef1245 |
| children | 56591ec04525 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="art_solid" name="ART SOLiD" version="2014.11.03.0"> |
| 2 <description>simulates SOLiD data</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
|
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7d6f5eef1245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 321bb0b81c749a898c0b59447a5a87d68c4dd058
iuc
parents:
0
diff
changeset
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6 <expand macro="requirements"/> |
| 0 | 7 <expand macro="stdio" /> |
| 8 <command><![CDATA[ | |
| 9 art_SOLiD | |
| 10 | |
| 11 $sam | |
| 12 | |
| 13 #if $rndSeed and $rndSeed > -1: | |
| 14 -r $rndSeed | |
| 15 #end if | |
| 16 | |
| 17 #if $generate.amplicon.use_amplicon == "amplicon_true": | |
| 18 -A | |
| 19 | |
| 20 #if $generate.choice == "single_end": | |
| 21 s | |
| 22 #else if $generate.choice == "paired_end": | |
| 23 p | |
| 24 #else: | |
| 25 m | |
| 26 #end if | |
| 27 | |
| 28 #end if | |
| 29 | |
| 30 $input_seq_file | |
| 31 output | |
| 32 | |
| 33 #if $generate.choice == "single_end": | |
| 34 $generate.LEN_READ | |
| 35 $fold_coverage | |
| 36 #else if $generate.choice == "paired_end": | |
| 37 $generate.LEN_READ_F3 | |
| 38 $generate.LEN_READ_F5 | |
| 39 $fold_coverage | |
| 40 $generate.fragment_size | |
| 41 $generate.fragment_sd | |
| 42 #else: | |
| 43 $generate.LEN_READ | |
| 44 $fold_coverage | |
| 45 $generate.fragment_size | |
| 46 $generate.fragment_sd | |
| 47 #end if | |
| 48 | |
| 49 #if $generate.amplicon.use_amplicon == "amplicon_true": | |
| 50 #if $generate.choice == "single_end": | |
| 51 $generate.amplicon.reads_per_amplicon | |
| 52 #else: | |
| 53 $generate.amplicon.read_pairs_per_amplicon | |
| 54 #end if | |
| 55 #end if | |
| 56 ]]></command> | |
| 57 <inputs> | |
| 58 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/> | |
| 59 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/> | |
| 60 | |
| 61 <conditional name="generate"> | |
| 62 <param name="choice" type="select" label="Type of data to generate"> | |
| 63 <option value="single_end">Single-End</option> | |
| 64 <option value="paired_end">Paired-End</option> | |
| 65 <option value="paired_end">Mate Pair</option> | |
| 66 </param> | |
| 67 <when value="single_end"> | |
| 68 <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" /> | |
| 69 <expand macro="amplicon" /> | |
| 70 </when> | |
| 71 <when value="paired_end"> | |
| 72 <param name="LEN_READ_F3" type="integer" label="Length of F3 reads" value="100" /> | |
| 73 <param name="LEN_READ_F5" type="integer" label="Length of F5 reads" value="100" /> | |
| 74 <expand macro="frag_len_sd" /> | |
| 75 <expand macro="amplicon_pair" /> | |
| 76 </when> | |
| 77 <when value="mate_pair"> | |
| 78 <param name="LEN_READ" type="integer" label="Length of F3/R3 reads" value="100" /> | |
| 79 <expand macro="frag_len_sd" /> | |
| 80 <expand macro="amplicon_pair" /> | |
| 81 </when> | |
| 82 </conditional> | |
| 83 | |
| 84 <expand macro="sam" /> | |
| 85 <expand macro="rndSeed" /> | |
| 86 | |
| 87 </inputs> | |
| 88 <outputs> | |
| 89 | |
| 90 <!-- Single End --> | |
| 91 <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name"> | |
| 92 <filter>generate['choice'] == "single_end"</filter> | |
| 93 </data> | |
| 94 | |
| 95 <!-- Paired End --> | |
| 96 <data format="fastq" name="output_fq1_paired" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F3)"> | |
| 97 <filter>generate['choice'] == "paired_end"</filter> | |
| 98 </data> | |
| 99 <data format="fastq" name="output_fq2_paired" from_work_dir="output_F5.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (F5)"> | |
| 100 <filter>generate['choice'] == "paired_end"</filter> | |
| 101 </data> | |
| 102 | |
| 103 <!-- Mate Pair --> | |
| 104 <data format="fastq" name="output_fq1_mate" from_work_dir="output_F3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Forward)"> | |
| 105 <filter>generate['choice'] == "mate_pair"</filter> | |
| 106 </data> | |
| 107 <data format="fastq" name="output_fq2_mate" from_work_dir="output_R3.fq" label="Simulated of SOLiD sequencing of $input_seq_file.name (Reverse)"> | |
| 108 <filter>generate['choice'] == "mate_pair"</filter> | |
| 109 </data> | |
| 110 | |
| 111 <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated SOLiD data to $input_seq_file.name"> | |
| 112 <filter>sam</filter> | |
| 113 </data> | |
| 114 <!-- todo? map file --> | |
| 115 </outputs> | |
| 116 <tests> | |
| 117 <!-- Single End tests --> | |
| 118 <test> | |
| 119 <param name="rndSeed" value="42" /> | |
| 120 <param name="input_seq_file" value="input.fa" /> | |
| 121 <param name="LEN_READ" value="25" /> | |
| 122 <param name="fold_coverage" value="10" /> | |
| 123 <param name="choice" value="single_end" /> | |
| 124 <param name="sam" value="False" /> | |
| 125 | |
|
7
3f163b178c5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
parents:
5
diff
changeset
|
126 <output name="output_fq1_single" file="art.solid.01.fq" compare="sim_size" delta="5000" /> |
| 0 | 127 </test> |
| 128 <test> | |
| 129 <param name="rndSeed" value="42" /> | |
| 130 <param name="input_seq_file" value="input.fa" /> | |
| 131 <param name="fold_coverage" value="20" /> | |
| 132 <param name="choice" value="paired_end" /> | |
| 133 <param name="LEN_READ_F3" value="50" /> | |
| 134 <param name="LEN_READ_F5" value="50" /> | |
| 135 <param name="fragment_size" value="75" /> | |
| 136 <param name="fragment_sd" value="10" /> | |
| 137 <param name="sam" value="True" /> | |
| 138 | |
|
7
3f163b178c5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
parents:
5
diff
changeset
|
139 <output name="output_fq1_paired" file="art.solid.02_F3.fq" compare="sim_size" delta="5000" /> |
|
3f163b178c5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
parents:
5
diff
changeset
|
140 <output name="output_fq2_paired" file="art.solid.02_F5.fq" compare="sim_size" delta="5000" /> |
|
3f163b178c5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
parents:
5
diff
changeset
|
141 <output name="output_sam" file="art.solid.02.sam" compare="sim_size" delta="5000"/> |
| 0 | 142 </test> |
| 143 </tests> | |
| 144 <help><![CDATA[ | |
| 145 Art SOLiD Simulator | |
| 146 =================== | |
| 147 | |
| 148 ART_SOLiD is a simulation program to generate sequence read data of SOLiD | |
| 149 sequencing reads. ART generates reads according to a SOLiD read error profile. | |
| 150 The built-in error profile is an empiricial error profile summarized from large | |
| 151 SOLiD sequencing data. ART has been using for testing or benchmarking a variety | |
| 152 of method or tools for next-generation sequencing data analysis, including read | |
| 153 alignment, de novo assembly, detection of SNP, CNV, or other structure | |
| 154 variation. | |
| 155 | |
| 156 art_SOLiD can generate both single-end, matepair, and paired-end of SOLiD | |
| 157 sequencing platform. art_SOLiD also support amplicon sequencing simulation with | |
| 158 RNA references. | |
| 159 ]]></help> | |
| 160 <expand macro="citation" /> | |
| 161 </tool> | |
| 162 |