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annotate alignments-to-links.xml @ 13:8b1cf140bbd4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 0cfd88d16b0b20a66d4b21b037ddee6a8c440d88
author iuc
date Wed, 12 Apr 2023 15:08:23 +0000
parents 0ee66defe58b
children
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890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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1 <?xml version="1.0"?>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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2 <tool id="circos_aln_to_links" name="Circos: Alignments to links" version="@WRAPPER_VERSION@">
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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3 <description>reformats alignment files to prepare for Circos</description>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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4 <macros>
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5 <import>macros.xml</import>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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6 </macros>
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7 <edam_topics>
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8 <edam_topic>topic_0797</edam_topic>
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9 <edam_topic>topic_0092</edam_topic>
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10 </edam_topics>
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11 <edam_operations>
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12 <edam_operation>operation_1812</edam_operation>
74146c252453 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
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13 </edam_operations>
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0ee66defe58b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit b9ec351920dbc83fa14bd1f8cfdd0a6a19b89473"
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14 <expand macro="requirements">
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15 </expand>
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16 <command detect_errors="exit_code"><![CDATA[
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17 python '$__tool_directory__/alignments-to-links.py' '$input' '$input.ext' > '$output'
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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18 ]]></command>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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19 <inputs>
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20 <param name="input" type="data" format="maf,xmfa,stockholm" label="Alignment file (maf, xmfa, stockholm)" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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21 </inputs>
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22 <outputs>
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23 <data name="output" format="tabular" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input" value="alignments/1.maf" ftype="maf" />
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28 <output name="output" file="alignments/1.tab" ftype="tabular" />
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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29 </test>
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30 </tests>
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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31 <help><![CDATA[
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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32 Converts several standard alignment formats into a format appropriate for Circos plots.
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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33 ]]></help>
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34 <expand macro="citations" />
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35 </tool>