Mercurial > repos > iuc > pimento_std

annotate std.xml @ 0:1ddab994fcee draft default tip

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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 09:21:07 +0000
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0
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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1 <tool id="pimento_std" name="PIMENTO Standard primer matching" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENSE@">
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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2 <description>Finds best-matching primers in reads using a fuzzy search against a standard primer library</description>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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3 <macros>
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4 <import>macros.xml</import>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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5 </macros>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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6 <expand macro="creators"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 #if $primers:
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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10 mkdir primers &&
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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11 cp '$primers' primers &&
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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12 pimento std -i '$input_reads' -p primers --minimum_primer_threshold $minimum_primer_threshold $merged -o sample
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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13 #else
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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14 pimento std -i '$input_reads' --minimum_primer_threshold $minimum_primer_threshold $merged -o sample
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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15 #end if
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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16 ]]></command>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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17 <inputs>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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18 <param name="input_reads" type="data" label="Input reads" format="fastqsanger.gz"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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19 <param name="primers" type="data" label="Input standard primers" format="fasta" optional="true"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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20 <param argument="--minimum_primer_threshold" type="float" value="0.6" min="0.1" max="1.0" label="Minimum primer threshold" help="Any primers with a read proportion lower than this threshold are disregarded"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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21 <param argument="--merged" type="boolean" truevalue="--merged" falsevalue="" help="Necessary if the input sequence file is made up of merged paired-end or single-end reads"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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22 </inputs>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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23 <outputs>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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24 <data name="fasta_output" label="${tool.name} on ${on_string}: FASTA containing best found single or pairs of primers" format="fasta" from_work_dir="sample_std_primers.fasta"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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25 <data name="best_found_primers" label="${tool.name} on ${on_string}: Best found primers" format="txt" from_work_dir="sample_std_primer_out.txt"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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26 <data name="searched_primers" label="${tool.name} on ${on_string}: Every single searched primer" format="txt" from_work_dir="all_standard_primer_proportions.txt"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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27 </outputs>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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28 <tests>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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29 <test expect_num_outputs="3">
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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30 <param name="input_reads" value="test.fastq.gz"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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31 <param name="minimum_primer_threshold" value="0.6"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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32 <param name="merged" value="true"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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33 <output name="fasta_output">
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34 <assert_contents>
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35 <has_line line=">341F"/>
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36 <has_line line="CCTACGGGNGGCWGCAG"/>
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37 <has_n_lines n="4"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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38 </assert_contents>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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39 </output>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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40 <output name="best_found_primers">
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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41 <assert_contents>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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42 <has_line line="V3-V4"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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43 <has_line line="341F: 0.984"/>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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44 <has_line line="805R: 0.948"/>
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45 </assert_contents>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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46 </output>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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47 <output name="searched_primers">
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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48 <assert_contents>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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49 <has_line line="V3;341F:0.984"/>
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50 <has_line line="V3;338F:0.0"/>
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51 <has_n_lines n="148"/>
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52 </assert_contents>
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53 </output>
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54 </test>
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55 </tests>
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56 <help><![CDATA[
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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57 Runs the standard primer matching strategy for primer inference. A library
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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58 of standard primers will be searched in input reads using fuzzy regex to
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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59 identify primers with high degrees of proportions. The best single, or pair,
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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60 of primers found will be outputted into a FASTA file (provided any were
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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61 indeed found). PIMENTO comes with its own standard primer library which will
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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62 be used as a default. Users can however give their own custom input library,
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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63 or extend the default library to suit their needs.
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64 ]]></help>
1ddab994fcee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento commit 69888afa40f5ac6a42fa9335cf61f0bb6387eb2f
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65 <expand macro="citations"/>
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66 </tool>