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comparison align_families.xml @ 10:9dc43bf7d1db draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'230f018da2c0bc4eedc72e0f70eac0df1e85ebdb\n'-dirty
author nick
date Fri, 01 Jun 2018 17:55:23 -0400
parents fa563fa9b330
children 0f8e0dc73d1d
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9:fa563fa9b330 10:9dc43bf7d1db
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="align_families" name="Du Novo: Align families" version="2.14"> 2 <tool id="align_families" name="Du Novo: Align families" version="2.15">
3 <description>of duplex sequencing reads</description> 3 <description>of duplex sequencing reads</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="7.221">mafft</requirement> 5 <requirement type="package" version="7.221">mafft</requirement>
6 <requirement type="package" version="2.14">dunovo</requirement> 6 <requirement type="package" version="2.15">dunovo</requirement>
7 <!-- TODO: require Python 2.7 --> 7 <!-- TODO: require Python 2.7 -->
8 </requirements> 8 </requirements>
9 <version_command>align-families.py --version</version_command> 9 <version_command>align-families.py --version</version_command>
10 <command detect_errors="exit_code">align-families.py --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' &gt; '$output' 10 <command detect_errors="exit_code">align-families.py $check_ids --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
11 </command> 11 </command>
12 <inputs> 12 <inputs>
13 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> 13 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
14 <param name="aligner" type="select" value="mafft" label="Multiple sequence aligner" help="MAFFT is the original aligner Du Novo was published with in 2016. Kalign is much faster and has similar accuracy."> 14 <param name="aligner" type="select" value="mafft" label="Multiple sequence aligner" help="MAFFT is the original aligner Du Novo was published with in 2016. Kalign is much faster and has similar accuracy.">
15 <option value="kalign">Kalign2</option> 15 <option value="kalign">Kalign2</option>
16 <option value="mafft">MAFFT</option> 16 <option value="mafft">MAFFT</option>
17 </param> 17 </param>
18 <param name="check_ids" type="boolean" truevalue="" falsevalue="--no-check-ids" checked="True" label="Check read names" help="Make sure reads are properly paired up. The job will fail if there is a pair of reads where their ids aren't identical (minus any ending /1 or /2)."/>
18 <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 number of processes used, the time and memory taken to process it, the alignment algorithm selected, 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 names of the input and output datasets are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET."/> 19 <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 number of processes used, the time and memory taken to process it, the alignment algorithm selected, 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 names of the input and output datasets are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET."/>
19 </inputs> 20 </inputs>
20 <outputs> 21 <outputs>
21 <data name="output" format="tabular"/> 22 <data name="output" format="tabular"/>
22 </outputs> 23 </outputs>