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annotate nullarbor_prepare.xml @ 3:63ba2e9353bb draft default tip

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
author thanhlv
date Mon, 06 May 2019 08:05:32 -0400
parents f9c1aaf4f592
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f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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1 <tool id="nullarbor_prepare" name="Nullarbor prepare" version="@VERSION@">
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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2 <description>Prepare a tab file from a collection of paired-end reads</description>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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3 <macros>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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4 <import>macros.xml</import>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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5 </macros>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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6 <command detect_errors="exit_code"><![CDATA[
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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7 #for $input in $reads:
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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8 echo -e '$input.element_identifier''\t''$input[0]''\t''$input[1]' >> 'tab_file';
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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9 #end for
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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10 ]]></command>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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11
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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12 <inputs>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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13 <param name="reads" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="list:paired" label="Paired collection" help="Collection of reads, requires a mininum of 4 isolates to run (due to Roary)"/>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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14 </inputs>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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15 <outputs>
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thanhlv
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16 <data name="tab_file" format="tabular" label="${tool.name} on ${on_string}: Tab file" from_work_dir="tab_file"/>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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17 </outputs>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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18 <help><![CDATA[
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
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19 ]]></help>
f9c1aaf4f592 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/nullarbor commit 5215b942916d8c1186656f098cfdf4db52b5854b-dirty
thanhlv
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20 </tool>