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comparison correct_barcodes.xml @ 8:658eefb99fd7 draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
author nick
date Fri, 12 Jan 2018 19:18:41 -0500
parents e7b88ffb8294
children fa563fa9b330
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7:e7b88ffb8294 8:658eefb99fd7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.9"> 2 <tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.12">
3 <description>of duplex sequencing reads</description> 3 <description>of duplex sequencing reads</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.2.5">bowtie2</requirement> 5 <requirement type="package" version="1.1.2">bowtie</requirement>
6 <requirement type="package" version="0.1.18">samtools</requirement>
7 <requirement type="package" version="1.10">networkx</requirement> 6 <requirement type="package" version="1.10">networkx</requirement>
8 <requirement type="package" version="2.0.9">dunovo</requirement> 7 <requirement type="package" version="2.0.12">dunovo</requirement>
9 <!-- TODO: require Python 2.7 --> 8 <!-- TODO: require Python 2.7 -->
10 </requirements> 9 </requirements>
11 <version_command>correct.py --version</version_command> 10 <version_command>correct.py --version</version_command>
12 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
13 baralign.sh '$input' refdir correct.sam 12 baralign.sh -c $advanced.chunkmbs -t \${GALAXY_SLOTS:-1} '$input' refdir correct.sam
14 && samtools view -S -f 256 correct.sam 13 && correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos
15 | correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa 14 '$input' refdir/barcodes.fa correct.sam
16 > families.corrected.tsv 15 > families.corrected.tsv
17 && sort families.corrected.tsv 16 && sort families.corrected.tsv
18 > '$output' 17 > '$output'
19 ]]> 18 ]]>
20 </command> 19 </command>
21 <inputs> 20 <inputs>
22 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> 21 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
23 <param name="dist" type="integer" value="1" min="1" label="Maximum edit distance" help="Only use alignments where the barcodes differ by at most these many errors."/> 22 <param name="dist" type="integer" value="3" min="1" label="Maximum differences" help="Only use alignments where the barcodes differ by at most these many errors. Note that raising this beyond 3 probably probably won't have an effect, because of the inherent limit in bowtie's ability to match up distant barcodes."/>
24 <param name="mapq" type="integer" value="20" min="0" label="Minimum mapping quality" help="Only use alignments whose MAPQ is at least this."/> 23 <param name="mapq" type="integer" value="20" min="0" label="Minimum mapping quality" help="Only use alignments whose MAPQ is at least this."/>
25 <param name="pos" type="integer" value="2" min="0" label="Minimum start offset" help="Ignore alignments where the start positions differ by more than this."/> 24 <param name="pos" type="integer" value="2" min="0" label="Maximum start offset" help="Ignore alignments where the start positions differ by more than this."/>
26 <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time and memory taken to process it, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET"/> 25 <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time and memory taken to process it, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET"/>
26 <section name="advanced" title="Advanced Options" expanded="false">
27 <param name="chunkmbs" type="integer" value="512" min="16" label="bowtie --chunkmbs" help="This is the number of megabytes to give each bowtie thread for storing path descriptors. If you see warnings about &quot;Exhausted best-first chunk memory&quot; in stderr, you need to increase this."/>
28 </section>
27 </inputs> 29 </inputs>
28 <outputs> 30 <outputs>
29 <data name="output" format="tabular"/> 31 <data name="output" format="tabular"/>
30 </outputs> 32 </outputs>
31 <help> 33 <help>
32 34
33 **What it does** 35 **What it does**
34 36
35 This is for processing duplex sequencing data. This will correct duplex barcodes and create new, larger families. Errors in barcodes normally prevent them from being recognized as the same as the other barcodes in their family. Correcting these errors allows the original, full families to be reconstructed, saving reads which would otherwise be lost. This tool accomplishes this by doing an all vs. all alignment between the barcodes with bowtie2. This identifies ones which are identical except a few, small differences. 37 This is for processing duplex sequencing data. This will correct duplex barcodes and create new, larger families. Errors in barcodes normally prevent them from being recognized as the same as the other barcodes in their family. Correcting these errors allows the original, full families to be reconstructed, saving reads which would otherwise be lost. This tool accomplishes this by doing an all vs. all alignment between the barcodes with bowtie. This identifies ones which are identical except a few, small differences.
36 38
37 ----- 39 -----
38 40
39 **Input** 41 **Input**
40 42