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comparison 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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-1:000000000000 0:f1a157358d4d
1 <macros>
2 <xml name="bio_tools">
3 <xrefs>
4 <xref type="bio.tools">edta</xref>
5 </xrefs>
6 </xml>
7 <xml name="edta_main_param">
8 <!-- Genome to TE annotations -->
9 <param argument="--genome" type="data" format="fasta" label="Genome File" help="The Genome FASTA file"/>
10 <param argument ="--species" type="select" label="Which species should be used for identification of TIR candidates">
11 <option value="Others">Others</option>
12 <option value="Rice">Rice</option>
13 <option value="Maize">Maize</option>
14 </param>
15 <param argument="--step" type="select" label="Specify which steps you want to run EDTA">
16 <option value="all">run the entire pipeline (all)</option>
17 <option value="filter"> start from raw TEs to the end (filter)</option>
18 <option value="final">Final</option>
19 <option value="anno">Anno</option>
20 </param>
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."/>
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."/>
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."/>
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>
25 <conditional name='anno_select'>
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.'>
27 <option value="yes">Yes</option>
28 <option value="no">No</option>
29 </param>
30 <when value="yes">
31 <param argument="--evaluate" type="boolean" truevalue="--evaluate 1" falsevalue="" label="Evaluate" help="Evaluate (1) classification consistency of the TE annotation " />
32 <param name="exclude" argument="--exclude" type="data" format="bed" label="Exclude" help="Exclude bed format regions from TE annotation" optional="true"/>
33 </when>
34 <when value="no"></when>
35 </conditional>
36 </xml>
37 <xml name="pan_edta">
38 <!-- Genome to TE annotations -->
39 <param name="known_te" type='data' format="fasta" label="Genome File" optional='true' help="File of known TEs"></param>
40 <repeat name="te_library" title="TE_Library">
41 <param argument="--genome" type="data" format="fasta" label="Genome File" help="The Genome FASTA file"/>
42 <param name='species' argument ="--species" type="select" label="Which species should be used for identification of TIR candidates">
43 <option value="Others">Others</option>
44 <option value="Rice">Rice</option>
45 <option value="Maize">Maize</option>
46 </param>
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."/>
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."/>
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."/>
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>
51 <param argument="--evaluate" type="boolean" truevalue="--evaluate 1" falsevalue="" label="evaluate" help="Evaluate (1) classification consistency of the TE annotation " />
52 <param argument="--exclude" type="data" format="bed" label="Exclude" help="Exclude bed format regions from TE annotation" optional="true"/>
53 </repeat>
54 </xml>
55 <xml name="te_only">
56 <!-- Find elements of a paticular TE type -->
57 <param name="genome" argument="--genome" type="data" format="fasta" label="Genome File" help="The Genome FASTA file"/>
58 <param name='species' argument ="--species" type="select" label="Which species should be used for identification of TIR candidates">
59 <option value="Others">Others</option>
60 <option value="Rice">Rice</option>
61 <option value="Maize">Maize</option>
62 </param>
63 <param name="te_type" argument="--type" type="select" label="Which type of raw TE candidates do you want?">
64 <option value="all">all</option>
65 <option value="ltr">ltr</option>
66 <option value="tir">tir</option>
67 <option value="helitron">helitron</option>
68 </param>
69 </xml>
70 </macros>