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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 48a5b169f1ea3d98761bfeaae135a808506e6cbb
author bgruening
date Wed, 05 Mar 2025 18:50:58 +0000
parents cd7e644cae1d
children
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cd7e644cae1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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1 <macros>
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2 <token name="@TOOL_VERSION@">0.6.7</token>
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eefb644655a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 48a5b169f1ea3d98761bfeaae135a808506e6cbb
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3 <token name="@VERSION_SUFFIX@">1</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">trim-galore</requirement>
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7 </requirements>
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8 </xml>
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9 <xml name="xrefs">
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10 <xrefs>
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11 <xref type="bio.tools">trim_galore</xref>
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12 </xrefs>
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13 </xml>
cd7e644cae1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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14 <xml name="adapter_trimming">
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15 <conditional name="trimming">
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16 <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">
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17 <option value="">Automatic detection</option>
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18 <option value="--illumina">Illumina universal</option>
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19 <option value="--nextera">Nextera transposase</option>
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20 <option value="--small_rna">Illumina small RNA adapters</option>
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21 <option value="user">User defined adapter sequence</option>
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22 </param>
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23 <when value=""/>
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24 <when value="--illumina"/>
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25 <when value="--nextera"/>
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26 <when value="--small_rna"/>
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27 <when value="user">
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28 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
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29 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
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30 </param>
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31 <yield/>
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32 </when>
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33 </conditional>
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34 </xml>
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35 <xml name="paired_adapter_trimming">
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36 <expand macro="adapter_trimming">
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37 <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
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38 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
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39 </param>
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40 </expand>
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41 <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
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42 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
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43 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
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44 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
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45 (--three_prime_clip_R1)</help>
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46 </param>
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47 <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 2">
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48 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
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49 adapter/quality trimming has been performed. This may remove some unwanted bias from
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50 the 3' end that is not directly related to adapter sequence or basecall quality.</help>
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51 </param>
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52 </xml>
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53 <xml name="citations">
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54 <citations>
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55 <citation type="bibtex">
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56 @misc{githubTrim_Galore,
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57 author = {Krueger, Felix},
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58 year = {2021},
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59 title = {Trim Galore},
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60 publisher = {GitHub},
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61 journal = {GitHub repository},
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62 url = {https://https://github.com/FelixKrueger/TrimGalore.com/fenderglass/Flye}}
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63 </citation>
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64 </citations>
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65 </xml>
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66 </macros>