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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
author thanhlv
date Thu, 22 Sep 2022 15:01:09 +0000
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b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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1 <tool id="polca" name="polca" version="@VERSION@">
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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2 <description> Minimal but speedy quality control for nanopore reads</description>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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3 <macros>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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4 <token name="@VERSION@">4.0.9</token>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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5 </macros>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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6 <requirements>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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7 <requirement type="package" version="@VERSION@">masurca</requirement>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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8 </requirements>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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9 <version_command>polca --version</version_command>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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10 <command detect_errors="exit_code"><![CDATA[
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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11 #if $short_reads.sr_type == 'paired'
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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12 ln -s '$short_read.R1' reads_1.fastq.gz &&
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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13 ln -s '$short_read.R2' reads_2.fastq.gz &&
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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14 #else if str($short_reads.sr_type) == "collection"
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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15 ln -s '$short_read.input1.forward' reads_1.fastq.gz &&
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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16 ln -s '$short_read.input1.reverse' reads_2.fastq.gz &&
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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17 #end if
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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18 ln -s '${contigs}' contigs &&
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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19 polca.sh -a contigs.fa
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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20 -r reads1.fastq.gz reads2.fastq.gz
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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21 -t \${GALAXY_SLOTS:-4}
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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22 -m 1G
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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23 $no_fix
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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24 ]]> </command>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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25
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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26 <inputs>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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27 <param name="contigs" type="data" format="fasta,fasta.gz" label="Assembly"/>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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28 <conditional name="short_reads">
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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29 <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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30 <option value="paired" selected="true">Paired End</option>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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31 <option value="collection">Paired Collection</option>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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32 </param>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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33 <when value="paired">
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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34 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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35 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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36 </when>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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37 <when value="collection">
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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38 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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39 </when>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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40 </conditional>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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41 <param argument="no_fix" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Do not fix errors when found." />
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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42 </inputs>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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43 <outputs>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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44 <data name="contigs" format="fasta" from_work_dir="contigs.PolcaCorrected.fa" label="${tool.name} on ${on_string} Polished assembly" />
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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45 <data name="report" format="fasta" from_work_dir="contigs.report" label="${tool.name} on ${on_string} Polished assembly" />
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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46 </outputs>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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47 <help><![CDATA[
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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48 ]]> </help>
b40614f1e3c7 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
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49 </tool>