Mercurial > repos > iuc > pear
annotate pear.xml @ 2:2f804526f5fd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit d43478961a586d7cda1fb37358c5a26a0ffa1a15
author | iuc |
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date | Thu, 09 Nov 2017 07:28:37 -0500 |
parents | 240f611a46f3 |
children | b4c6f054210a |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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1 <tool id="iuc_pear" name="Pear" version="0.9.6.1"> |
0 | 2 <description>Paired-End read merger</description> |
3 <requirements> | |
4 <requirement type="package" version="0.9.6">pear</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range="1:" /> | |
8 <exit_code range=":-1" /> | |
9 <regex match="Error:" /> | |
10 <regex match="Exception:" /> | |
11 </stdio> | |
12 <command> | |
13 <![CDATA[ | |
14 pear | |
15 #if str( $library.type ) == "paired": | |
16 -f "$library.forward" | |
17 -r "$library.reverse" | |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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18 #if $library.forward.is_of_type( 'fastqillumina' ): |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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19 --phred-base 64 |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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20 #else: |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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21 --phred-base 33 |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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22 #end if |
0 | 23 #else |
24 ## prepare collection | |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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25 -f "$library.input_collection.forward" |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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26 -r "$library.input_collection.reverse" |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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27 #if $library.input_collection.forward.is_of_type( 'fastqillumina' ): |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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28 --phred-base 64 |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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29 #else: |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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30 --phred-base 33 |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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31 #end if |
0 | 32 #end if |
33 | |
34 --output pear | |
35 --p-value $pvalue | |
36 --min-overlap $min_overlap | |
37 #if int($max_assembly_length) > 0: | |
38 --max-asm-length $max_assembly_length | |
39 #end if | |
40 --min-asm-length $min_assembly_length | |
41 --min-trim-length $min_trim_length | |
42 --quality-theshold $quality_threshold | |
43 --max-uncalled-base $max_uncalled_base | |
44 --test-method $test_method | |
45 --empirical-freqs $empirical_freqs | |
46 -j "\${GALAXY_SLOTS:-8}" | |
47 --score-method $score_method | |
48 --cap $cap | |
49 $nbase | |
50 ]]> | |
51 </command> | |
52 <inputs> | |
53 <conditional name="library"> | |
54 <param name="type" type="select" label="Dataset type"> | |
55 <option value="paired">Paired-end</option> | |
56 <option value="paired_collection">Paired-end Dataset Collection</option> | |
57 </param> | |
58 <when value="paired"> | |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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59 <param name="forward" type="data" format="fastqillumina,fastqsanger" |
0 | 60 label="Name of file that contains the forward paired-end reads" help="-f" /> |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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61 <param name="reverse" type="data" format="fastqillumina,fastqsanger" |
0 | 62 label="Name of file that contains the reverse paired-end reads" help="-r" /> |
63 </when> | |
64 <when value="paired_collection"> | |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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65 <param name="input_collection" format="fastqillumina,fastqsanger" |
0 | 66 type="data_collection" collection_type="paired" |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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67 label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" /> |
0 | 68 </when> |
69 </conditional> | |
70 | |
71 <!-- optional --> | |
72 <param name="pvalue" type="float" value="0.01" min="0" optional="True" max="1" label="Specify a p-value for the statistical test" | |
73 help="If the computed p-value of a possible assembly exceeds the specified p-value then the paired-end read will not be assembled. Setting 1.0 disables the test. (--p-value)" /> | |
74 | |
75 <param name="min_overlap" type="integer" value="10" optional="True" label="Minimum overlap size" | |
76 help="The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles. (--min-overlap)" /> | |
77 | |
78 <param name="max_assembly_length" type="integer" value="0" optional="True" label="Maximum possible length of the assembled sequences" | |
79 help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)" /> | |
80 | |
81 <param name="min_assembly_length" type="integer" value="50" optional="True" label="Minimum possible length of the assembled sequences" | |
82 help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)" /> | |
83 | |
84 <param name="min_trim_length" type="integer" value="1" optional="True" label="Minimum length of reads after trimming the low quality part" | |
85 help="See option -q. (--min-trim-length)" /> | |
86 | |
87 <param name="quality_threshold" type="integer" value="0" optional="True" label="Quality score threshold for trimming the low quality part of a read" | |
88 help="If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed. (--quality-threshold)" /> | |
89 | |
90 <param name="max_uncalled_base" type="float" value="1.0" min="0" optional="True" max="1" label="Maximal proportion of uncalled bases in a read" | |
91 help="Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases. The other extreme setting is 1 which causes PEAR to process all reads independent on the number of uncalled bases. (--max-uncalled-base)" /> | |
92 | |
93 <param name="cap" type="integer" value="40" optional="True" label="Specify the upper bound for the resulting quality score" | |
94 help="If set to zero, capping is disabled. (--cap)" /> | |
95 | |
96 <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)"> | |
97 <option value="1" selected="True">Given the minimum allowed overlap, test using the highest OES (1)</option> | |
98 <option value="2">Use the acceptance probability (2)</option> | |
99 </param> | |
100 | |
101 <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" | |
102 label="Disable empirical base frequencies" help="(--empirical-freqs)" /> | |
103 <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false" | |
104 label="Use N base if uncertain" help="When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases. (--nbase)" /> | |
105 | |
106 <param name="score_method" type="select" label="Scoring method" help="(--score-method)"> | |
107 <option value="1">OES with +1 for match and -1 for mismatch</option> | |
108 <option value="2" selected="True">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option> | |
109 <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option> | |
110 </param> | |
111 | |
112 <param name="outputs" type="select" display="checkboxes" optional="False" multiple="True" label="Output files"> | |
113 <option value="assembled" selected="True">Assembled reads</option> | |
114 <option value="forward">Forward unassembled reads</option> | |
115 <option value="reverse">Reverse unassembled reads</option> | |
116 <option value="discarded">Discarded reads</option> | |
117 </param> | |
118 </inputs> | |
119 <outputs> | |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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120 <data format="input" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> |
0 | 121 <filter>'assembled' in outputs</filter> |
122 </data> | |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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123 <data format="input" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> |
0 | 124 <filter>'forward' in outputs</filter> |
125 </data> | |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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126 <data format="input" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> |
0 | 127 <filter>'reverse' in outputs</filter> |
128 </data> | |
1
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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129 <data format="input" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> |
0 | 130 <filter>'discarded' in outputs</filter> |
131 </data> | |
132 </outputs> | |
133 <tests> | |
134 <test> | |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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135 <param name="forward" value="forward.fastq" ftype="fastqsanger" /> |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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136 <param name="reverse" value="reverse.fastq" ftype="fastqsanger" /> |
0 | 137 <param name="min_overlap" value="10" /> |
138 <param name="min_assembly_length" value="50" /> | |
139 <param name="cap" value="0" /> | |
140 <param name="outputs" value="assembled,forward" /> | |
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240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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0
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141 <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/> |
240f611a46f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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142 <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/> |
0 | 143 </test> |
144 </tests> | |
145 <help> | |
146 <![CDATA[ | |
147 | |
148 **What it does** | |
149 | |
150 PEAR_ is an ultrafast, memory-efficient and highly accurate pair-end read merger. | |
151 PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment | |
152 size as input. In addition, it implements a statistical test for minimizing false-positive results. | |
153 Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes | |
154 on a standard desktop computer. | |
155 | |
156 For more information please look at the documentation_ and `github repository`_. | |
157 | |
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2f804526f5fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit d43478961a586d7cda1fb37358c5a26a0ffa1a15
iuc
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158 .. _PEAR: https://sco.h-its.org/exelixis/web/software/pear/ |
2f804526f5fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit d43478961a586d7cda1fb37358c5a26a0ffa1a15
iuc
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159 .. _documentation: https://sco.h-its.org/exelixis/web/software/pear/doc.html |
0 | 160 |
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2f804526f5fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit d43478961a586d7cda1fb37358c5a26a0ffa1a15
iuc
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161 Please note that PEAR is released under the |
2f804526f5fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit d43478961a586d7cda1fb37358c5a26a0ffa1a15
iuc
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162 [CC Attribution-NonCommercial-ShareAlike](https://creativecommons.org/licenses/by-nc-sa/3.0/) license |
2f804526f5fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit d43478961a586d7cda1fb37358c5a26a0ffa1a15
iuc
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163 and that commercial partners should obtain a license. |
0 | 164 |
165 ]]> | |
166 </help> | |
167 <citations> | |
168 <citation type="doi">10.1093/bioinformatics/btt593</citation> | |
169 </citations> | |
170 </tool> |