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annotate augur_align.xml @ 1:892c6690a1e8 draft default tip

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
author dfornika
date Mon, 08 Apr 2019 13:27:08 -0400
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892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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1 <tool id="augur_align" name="augur align" version="@TOOL_VERSION@+galaxy0">
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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2 <description></description>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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3 <macros>
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4 <import>macros.xml</import>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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5 </macros>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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6 <requirements>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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7 <requirement type="package" version="@TOOL_VERSION@">augur</requirement>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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8 </requirements>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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9 <version_command>augur --version</version_command>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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10 <command detect_errors="exit_code"><![CDATA[
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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11 augur align
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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12 --nthreads \${GALAXY_SLOTS:-1}
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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13 --sequences '$sequences'
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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14 --reference-sequence '$reference_sequence'
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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15 $fill_gaps
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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16 --output 'output'
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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17 ]]></command>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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18 <inputs>
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19 <param name="sequences" type="data" format="fasta" label="Sequences"/>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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20 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence"/>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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21 <param name="fill_gaps" type="boolean" checked="false" truevalue="--fill-gaps" falsevalue="" label="Fill Gaps"/>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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22 </inputs>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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23 <outputs>
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24 <data name="pre_aligner_output" format="fasta" >
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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25 <discover_datasets pattern="output.pre_aligner.fasta" format="fasta" visible="true" />
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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26 </data>
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27 <data name="post_aligner_output" format="fasta" >
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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28 <discover_datasets pattern="output.post_aligner.fasta" format="fasta" visible="true" />
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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29 </data>
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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30 <data name="log" format="text" >
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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31 <discover_datasets pattern="*.log" format="text" visible="true" />
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32 </data>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="sequences" value="augur_align_test_0_sequences.input.fasta" />
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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37 <param name="reference_sequence" value="augur_align_test_0_reference_sequence.input.fasta" />
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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38 <param name="fill_gaps" value="false" />
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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39 <output name="pre_aligner_output" file="augur_align_test_0_pre_aligner_output.output.fasta" />
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40 <output name="post_aligner_output" file="augur_align_test_0_post_aligner_output.output.fasta" />
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41 </test>
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42 </tests>
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43 <help><![CDATA[
892c6690a1e8 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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44 Align multiple sequences from FASTA or VCF.
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45 ]]></help>
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46 <expand macro="citations" />
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47 </tool>