Mercurial > repos > gga > chado_feature_load_gff

comparison feature_load_gff.xml @ 6:5109ff5f4d06 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
author gga
date Mon, 05 Nov 2018 08:11:27 -0500
parents c510dc82df88
children 4451447ae065
comparison
equal deleted inserted replaced
5:c510dc82df88 6:5109ff5f4d06
15 '$organism' 15 '$organism'
16 16
17 #if $landmark_type: 17 #if $landmark_type:
18 --landmark_type '$landmark_type' 18 --landmark_type '$landmark_type'
19 #end if 19 #end if
20 #if $re_protein: 20
21 --re_protein '$re_protein' 21 #if $prot_naming.method == 'regex'
22 #if $re_protein:
23 --re_protein '$re_protein'
24 #end if
25 #if $re_protein_capture:
26 --re_protein_capture '$re_protein_capture'
27 #end if
28 #elif $prot_naming.method == "attr"
29 #if $protein_id_attr:
30 --protein_id_attr '$protein_id_attr'
31 #end if
22 #end if 32 #end if
23 #if $re_protein_capture: 33
24 --re_protein_capture '$re_protein_capture'
25 #end if
26 #if $fasta: 34 #if $fasta:
27 --fasta '$fasta' 35 --fasta '$fasta'
28 #end if 36 #end if
29 37
30 $no_seq_compute 38 $no_seq_compute
47 dynamic_options="list_organisms()" 55 dynamic_options="list_organisms()"
48 label="Organism" /> 56 label="Organism" />
49 57
50 <!-- options --> 58 <!-- options -->
51 <param name="landmark_type" label="Landmark Type" argument="landmark_type" type="text" help="Type of the landmarks (will speed up loading if provided, e.g. contig, should be a term of the Sequence ontology)" /> 59 <param name="landmark_type" label="Landmark Type" argument="landmark_type" type="text" help="Type of the landmarks (will speed up loading if provided, e.g. contig, should be a term of the Sequence ontology)" />
52 <param name="re_protein_capture" label="Regex protein capture" argument="re_protein_capture" type="text" help="Regular expression to capture groups in mRNA name to use in 'Regex protein' (e.g. '^(.*?)-R([A-Z]+)$', default='^(.*?)$' )"> 60 <conditional name="prot_naming">
53 <expand macro="sanitized"/> 61 <param name="method" type="select" label="Protein naming method" help="Will be used to assign uniquename to polypeptide">
54 </param> 62 <option value="auto">Automatic: uses GFF polypeptide features if existing, or derive from mRNA uniquename</option>
55 <param name="re_protein" label="Regex protein" argument="re_protein" type="text" help="Replacement string for the protein name using capturing groups defined in 'Regex protein capture' (e.g. '\1-P\2')"> 63 <option value="regex">Regular expression</option>
56 <expand macro="sanitized"/> 64 <option value="attr">From GFF attribute</option>
57 </param> 65 </param>
66 <when value="auto">
67 </when>
68 <when value="regex">
69 <param name="re_protein_capture" label="Regex protein capture" argument="re_protein_capture" type="text" help="Regular expression to capture groups in mRNA uniquename to use in 'Regex protein'" value="^(.*?)-R([A-Z]+)$">
70 <expand macro="sanitized"/>
71 </param>
72 <param name="re_protein" label="Regex protein" argument="re_protein" type="text" help="Replacement string for the protein name using capturing groups defined in 'Regex protein capture'" value="\1-P\2">
73 <expand macro="sanitized"/>
74 </param>
75 </when>
76 <when value="attr">
77 <param name="protein_id_attr" label="Protein id attribute" argument="protein_id_attr" type="text" help="Attribute containing the protein uniquename. It is searched at the mRNA level, and if not found at CDS level." value="protein_id"/>
78 </when>
79 </conditional>
80
58 <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="A Fasta containing sequences for some features. When creating a feature, if its sequence is in this fasta file it will be loaded. Otherwise for mRNA and polypeptides it will be computed from the genome sequence (if available), otherwise it will be left empty." optional="true" /> 81 <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="A Fasta containing sequences for some features. When creating a feature, if its sequence is in this fasta file it will be loaded. Otherwise for mRNA and polypeptides it will be computed from the genome sequence (if available), otherwise it will be left empty." optional="true" />
59 <param name="no_seq_compute" label="Allow computing missing sequences" argument="no_seq_compute" type="boolean" truevalue="" falsevalue="--no_seq_compute" help="Enable the computation of mRNA and polypeptides sequences based on genome sequence and positions." /> 82 <param name="no_seq_compute" label="Allow computing missing sequences" argument="no_seq_compute" type="boolean" truevalue="" falsevalue="--no_seq_compute" help="Enable the computation of mRNA and polypeptides sequences based on genome sequence and positions." />
60 <param name="add_only" label="Add only" argument="add_only" type="boolean" truevalue="--add_only" falsevalue="" help="Use this flag if you're not updating existing features, but just adding new features to the selected analysis and organism. It will speedup loading, and reduce memory usage, but might produce errors in case of already existing feature." /> 83 <param name="add_only" label="Add only" argument="add_only" type="boolean" truevalue="--add_only" falsevalue="" help="Use this flag if you're not updating existing features, but just adding new features to the selected analysis and organism. It will speedup loading, and reduce memory usage, but might produce errors in case of already existing feature." />
61 84
62 <expand macro="wait_for"/> 85 <expand macro="wait_for"/>