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annotate macros.xml @ 12:d60c3f704da0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f
author iuc
date Tue, 13 Aug 2024 12:18:39 +0000
parents c59d48774d03
children dbfc505896e9
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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1 <macros>
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2 <token name="@TOOL_VERSION@">0.23.4</token>
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3 <xml name="biotools">
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4 <xrefs>
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5 <xref type="bio.tools">
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6 fastp
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7 </xref>
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8 </xrefs>
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9 </xml>
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10 <xml name="adapter_trimming_options">
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11 <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False">
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12 <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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13 <expand macro="adapter_sequence" read_number="1" />
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14 <yield />
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15 </section>
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16 </xml>
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18 <xml name="global_trimming_options">
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19 <section name="global_trimming_options" title="Global trimming options" expanded="False">
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20 <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
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21 <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
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22 <yield/>
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23 </section>
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24 </xml>
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26 <xml name="global_trimming_options_paired">
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27 <expand macro="global_trimming_options">
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28 <param name="trim_front2" argument="-F" type="integer" optional="true" label="Trim front for input 2" help="Trimming how many bases in front for read2. If it's not specified, it will follow read1's settings."/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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29 <param name="trim_tail2" argument="-T" type="integer" optional="true" label="Trim tail for input 2" help="Trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings."/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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30 </expand>
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31 </xml>
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33 <xml name="adapter_sequence" token_read_number="1">
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34 <param argument="--adapter_sequence@READ_NUMBER@" type="text" optional="true" label="Adapter sequence for input @READ_NUMBER@" help="The adapter for read@READ_NUMBER@. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped.">
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35 <sanitizer>
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36 <valid>
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37 <add value="A"/>
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38 <add value="T"/>
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39 <add value="C"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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40 <add value="G"/>
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41 </valid>
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42 </sanitizer>
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43 </param>
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44 </xml>
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45
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46 <xml name="detect_adapter_for_pe">
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47 <param argument="--detect_adapter_for_pe" type="boolean" truevalue="--detect_adapter_for_pe" falsevalue="" checked="false" label="Adapter sequence auto-detection for paired-end" />
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48 </xml>
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49
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50 <xml name="in" token_read_number="1" token_argument="-i">
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51 <param name="in@READ_NUMBER@" argument="@ARGUMENT@" type="data" format="fastq,fastq.gz" label="Input @READ_NUMBER@" help="Input FASTQ file #@READ_NUMBER@"/>
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52 </xml>
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54 <xml name="poly_g_min_len">
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55 <param argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length"
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56 help="The minimum length to detect polyG in the read tail. 10 by default."/>
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57 </xml>
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58 </macros>