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annotate sylphtax_plugin.xml @ 30:26ee5e11ecbe draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
author iuc
date Thu, 15 Jan 2026 20:39:44 +0000
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30
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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1 <macros>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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2 <token name="@SYLPHTAX_COMMAND@"><![CDATA[
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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3 #for $file in $repeat.software_cond.input
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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4 @ESCAPE_IDENTIFIER@
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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5 #set file_path = os.path.join($software_dir, str($identifier) + '.sylphmpa')
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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6 ln -s '$file' '$file_path' &&
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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7 #end for
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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8 ]]></token>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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9 <xml name="sylphtax_form">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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10 <param name="input" type="data" format="tabular" multiple="true" label="Output of Sylph-tax" help="It should be the sylphmpa report from Sylph-tax"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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11 </xml>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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12 <xml name="sylphtax_test">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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13 <test expect_num_outputs="3">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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14 <repeat name="results">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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15 <conditional name="software_cond">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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16 <param name="software" value="sylphtax"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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17 <param name="input" value="sylphtax.sylphmpa"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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18 </conditional>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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19 </repeat>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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20 <param name="title" value="Title of the report"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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21 <param name="comment" value="Commment for the report"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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22 <param name="flat" value="true"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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23 <param name="export" value="true"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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24 <output name="html_report">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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25 <assert_contents>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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26 <has_text text="Title of the report"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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27 <has_text text="Commment for the report"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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28 <has_text text="Sylph-tax"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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29 </assert_contents>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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30 </output>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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31 <output_collection name="plots" type="list" count="8"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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32 </test>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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33 </xml>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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34 </macros>