Mercurial > repos > iuc > pear
annotate pear.xml @ 8:bb0164f44f3c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
| author | iuc |
|---|---|
| date | Wed, 09 Nov 2016 06:29:57 -0500 |
| parents | 5bbdf641a2d5 |
| children | 5d2d653c7cb0 |
| rev | line source |
|---|---|
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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1 <tool id="iuc_pear" name="Pear" version="0.9.6.1"> |
| 3 | 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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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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18 #if $library.forward.is_of_type( 'fastqillumina' ): |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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19 --phred-base 64 |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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20 #else: |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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21 --phred-base 33 |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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22 #end if |
| 3 | 23 #else |
| 24 ## prepare collection | |
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bb0164f44f3c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
parents:
7
diff
changeset
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25 -f "$library.input_collection.forward" |
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bb0164f44f3c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
parents:
7
diff
changeset
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26 -r "$library.input_collection.reverse" |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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27 #if $library.input_collection.forward.is_of_type( 'fastqillumina' ): |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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28 --phred-base 64 |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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29 #else: |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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30 --phred-base 33 |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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31 #end if |
| 3 | 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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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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59 <param name="forward" type="data" format="fastqillumina,fastqsanger" |
| 3 | 60 label="Name of file that contains the forward paired-end reads" help="-f" /> |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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61 <param name="reverse" type="data" format="fastqillumina,fastqsanger" |
| 3 | 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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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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65 <param name="input_collection" format="fastqillumina,fastqsanger" |
| 3 | 66 type="data_collection" collection_type="paired" |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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67 label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" /> |
| 3 | 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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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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120 <data format="input" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> |
| 3 | 121 <filter>'assembled' in outputs</filter> |
| 122 </data> | |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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123 <data format="input" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> |
| 3 | 124 <filter>'forward' in outputs</filter> |
| 125 </data> | |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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126 <data format="input" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> |
| 3 | 127 <filter>'reverse' in outputs</filter> |
| 128 </data> | |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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129 <data format="input" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> |
| 3 | 130 <filter>'discarded' in outputs</filter> |
| 131 </data> | |
| 132 </outputs> | |
| 133 <tests> | |
| 134 <test> | |
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7
5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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135 <param name="forward" value="forward.fastq" ftype="fastqsanger" /> |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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136 <param name="reverse" value="reverse.fastq" ftype="fastqsanger" /> |
| 3 | 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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7
5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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141 <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/> |
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5bbdf641a2d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
3
diff
changeset
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142 <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/> |
| 3 | 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 | |
| 158 .. _PEAR: http://sco.h-its.org/exelixis/web/software/pear/ | |
| 159 .. _documentation: http://sco.h-its.org/exelixis/web/software/pear/doc.html | |
| 160 .. _github repository: https://github.com/xflouris/PEAR | |
| 161 | |
| 162 | |
| 163 ]]> | |
| 164 </help> | |
| 165 <citations> | |
| 166 <citation type="doi">10.1093/bioinformatics/btt593</citation> | |
| 167 </citations> | |
| 168 </tool> |