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annotate edta_macros.xml @ 0:f1a157358d4d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
author bgruening
date Sun, 16 Oct 2022 12:41:19 +0000
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f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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1 <macros>
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2 <xml name="bio_tools">
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3 <xrefs>
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4 <xref type="bio.tools">edta</xref>
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5 </xrefs>
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6 </xml>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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7 <xml name="edta_main_param">
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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8 <!-- Genome to TE annotations -->
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9 <param argument="--genome" type="data" format="fasta" label="Genome File" help="The Genome FASTA file"/>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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10 <param argument ="--species" type="select" label="Which species should be used for identification of TIR candidates">
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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11 <option value="Others">Others</option>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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12 <option value="Rice">Rice</option>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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13 <option value="Maize">Maize</option>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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14 </param>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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15 <param argument="--step" type="select" label="Specify which steps you want to run EDTA">
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16 <option value="all">run the entire pipeline (all)</option>
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17 <option value="filter"> start from raw TEs to the end (filter)</option>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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18 <option value="final">Final</option>
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19 <option value="anno">Anno</option>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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20 </param>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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21 <param argument="--cds" type="data" format="fasta" label="Coding Sequence File" optional='true' help="Provide a FASTA file containing the coding sequence (no introns, UTRs, nor TEs) of this genome or its close relative."/>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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22 <param argument="--curatedlib" type="data" format="fasta" label="Curated Library File" optional='true' help="Provided a curated library to keep consistant naming and classification for known TEs. All TEs in this file will be trusted 100%, so please ONLY provide MANUALLY CURATED ones here."/>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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23 <param argument="--sensitive" type="boolean" truevalue="--sensitive 1" falsevalue="" label="Use RepeatModeler to identify remaining TEs" help="Use RepeatModeler to identify remaining TEs This step is very slow and MAY help to recover some TEs."/>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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24 <param name="mutation_rate" argument="--u" type="float" optional="True" label="Neutral Mutation Rate" help="Neutral mutation rate to calculate the age of intact LTR elements. Default: 1.3e-8 (per bp per year, from rice)"></param>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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25 <conditional name='anno_select'>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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26 <param name="anno" type="select" label="Would you like to perform whole-genome TE annotation after TE library construction?" argument='--a' help='Perform or not perform whole-genome TE annotation after TE library construction.'>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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27 <option value="yes">Yes</option>
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28 <option value="no">No</option>
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29 </param>
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30 <when value="yes">
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31 <param argument="--evaluate" type="boolean" truevalue="--evaluate 1" falsevalue="" label="Evaluate" help="Evaluate (1) classification consistency of the TE annotation " />
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32 <param name="exclude" argument="--exclude" type="data" format="bed" label="Exclude" help="Exclude bed format regions from TE annotation" optional="true"/>
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33 </when>
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34 <when value="no"></when>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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35 </conditional>
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36 </xml>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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37 <xml name="pan_edta">
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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38 <!-- Genome to TE annotations -->
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39 <param name="known_te" type='data' format="fasta" label="Genome File" optional='true' help="File of known TEs"></param>
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40 <repeat name="te_library" title="TE_Library">
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41 <param argument="--genome" type="data" format="fasta" label="Genome File" help="The Genome FASTA file"/>
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42 <param name='species' argument ="--species" type="select" label="Which species should be used for identification of TIR candidates">
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43 <option value="Others">Others</option>
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44 <option value="Rice">Rice</option>
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45 <option value="Maize">Maize</option>
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46 </param>
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47 <param argument="--cds" type="data" format="fasta" label="Coding Sequence File" optional='true' help="Provide a FASTA file containing the coding sequence (no introns, UTRs, nor TEs) of this genome or its close relative."/>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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48 <param argument="--curatedlib" type="data" format="fasta" label="Curated Library File" optional='true' help="Provided a curated library to keep consistant naming and classification for known TEs. All TEs in this file will be trusted 100%, so please ONLY provide MANUALLY CURATED ones here."/>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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49 <param argument="--sensitive" type="boolean" truevalue="--sensitive 1" falsevalue="" label="Use RepeatModeler to identify remaining TEs" help="Use RepeatModeler to identify remaining TEs This step is very slow and MAY help to recover some TEs."/>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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50 <param name="mutation_rate" argument="--u" type="float" optional="True" label="Neutral Mutation Rate" help="Neutral mutation rate to calculate the age of intact LTR elements. Default: 1.3e-8 (per bp per year, from rice)"></param>
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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51 <param argument="--evaluate" type="boolean" truevalue="--evaluate 1" falsevalue="" label="evaluate" help="Evaluate (1) classification consistency of the TE annotation " />
f1a157358d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
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52 <param argument="--exclude" type="data" format="bed" label="Exclude" help="Exclude bed format regions from TE annotation" optional="true"/>
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53 </repeat>
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54 </xml>
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55 <xml name="te_only">
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56 <!-- Find elements of a paticular TE type -->
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57 <param name="genome" argument="--genome" type="data" format="fasta" label="Genome File" help="The Genome FASTA file"/>
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58 <param name='species' argument ="--species" type="select" label="Which species should be used for identification of TIR candidates">
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59 <option value="Others">Others</option>
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60 <option value="Rice">Rice</option>
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61 <option value="Maize">Maize</option>
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62 </param>
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63 <param name="te_type" argument="--type" type="select" label="Which type of raw TE candidates do you want?">
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64 <option value="all">all</option>
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65 <option value="ltr">ltr</option>
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66 <option value="tir">tir</option>
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67 <option value="helitron">helitron</option>
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68 </param>
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69 </xml>
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70 </macros>