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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
author iuc
date Tue, 05 Aug 2025 09:20:38 +0000
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f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
iuc
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1 <tool id="pimento_auto" name="PIMENTO Primer cutoff prediction" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENSE@">
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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2 <description>Infers primers by predicting optimal cutoff points from read conservation patterns</description>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
iuc
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3 <macros>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
iuc
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4 <import>macros.xml</import>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
iuc
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5 </macros>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
iuc
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6 <expand macro="creators"/>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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7 <expand macro="requirements"/>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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8 <command detect_errors="aggressive"><![CDATA[
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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9 pimento auto -i '$input' -st '$strand' -o sample
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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10 ]]></command>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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11 <inputs>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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12 <param name="input" type="data" label="Input reads" format="fastqsanger.gz"/>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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13 <param name="strand" type="select" label="Strand" format="fastqsanger.gz">
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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14 <option value="F">Forward</option>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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15 <option value="R">Reverse</option>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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16 <option value="FR">Both, forward and reverse</option>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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17 </param>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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18 </inputs>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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19 <outputs>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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20 <data name="output" label="${tool.name} on ${on_string}: Automatically inferred primers" format="fasta" from_work_dir="sample_auto_primers.fasta"/>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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21 </outputs>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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22 <tests>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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23 <test expect_num_outputs="1">
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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24 <param name="input" value="test.fastq.gz"/>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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25 <param name="strand" value="FR"/>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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26 <output name="output">
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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27 <assert_contents>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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28 <has_line line=">F_auto"/>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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29 <has_line line="CCTACGGGDGGCWGCAGT"/>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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30 <has_n_lines n="4"/>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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31 </assert_contents>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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32 </output>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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33 </test>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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34 </tests>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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35 <help><![CDATA[
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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36 Runs the primer cutoff strategy for primer inference. Using patterns of
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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37 base-conservation values for input reads, this strategy identifies potential
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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38 cutoff points where a primer sequence could end. An optimal choice of cutoff
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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39 based on the change in base-conservation before and after a cutoff is then
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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40 made. Finally a consensus sequence is generated using this cutoff point and
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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41 the input reads, which are saved to an output FASTA file.
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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42 ]]></help>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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43 <expand macro="citations"/>
f41d29b1a43e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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44 </tool>