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comparison feature_load_gff.xml @ 8:4451447ae065 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
author gga
date Fri, 23 Nov 2018 11:15:47 -0500
parents 5109ff5f4d06
children 4bd9bbb4dbab
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7:60d7b4054865 8:4451447ae065
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="feature_load_gff" name="Chado load gff" version="@WRAPPER_VERSION@.0"> 2 <tool id="feature_load_gff" name="Chado load gff" version="@WRAPPER_VERSION@.0">
3 <description></description> 3 <description></description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <code file="chado.py"/> 7 <code file="chado.py"/>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 @AUTH@ 10 @AUTH@
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 20
21 #if $prot_naming.method == 'regex' 21 #if $prot_naming.method == 'regex'
22 #if $re_protein: 22 #if $prot_naming.re_protein:
23 --re_protein '$re_protein' 23 --re_protein '$prot_naming.re_protein'
24 #end if 24 #end if
25 #if $re_protein_capture: 25 #if $prot_naming.re_protein_capture:
26 --re_protein_capture '$re_protein_capture' 26 --re_protein_capture '$prot_naming.re_protein_capture'
27 #end if 27 #end if
28 #elif $prot_naming.method == "attr" 28 #elif $prot_naming.method == "attr"
29 #if $protein_id_attr: 29 #if $prot_naming.protein_id_attr:
30 --protein_id_attr '$protein_id_attr' 30 --protein_id_attr '$prot_naming.protein_id_attr'
31 #end if 31 #end if
32 #end if 32 #end if
33 33
34 #if $fasta: 34 #if $fasta:
35 --fasta '$fasta' 35 --fasta '$fasta'
41 41
42 --quiet 42 --quiet
43 43
44 > $results 44 > $results
45 ]]></command> 45 ]]></command>
46 <inputs> 46 <inputs>
47 <!-- arguments --> 47 <!-- arguments -->
48 <param name="gff" label="Gff" argument="gff" type="data" format="gff" help="Path to the Fasta file to load" /> 48 <param name="gff" label="Gff" argument="gff" type="data" format="gff" help="Path to the Fasta file to load" />
49 <param argument="--analysis_id" 49 <param argument="--analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
50 type="select" 50 <param argument="--organism" type="select" dynamic_options="list_organisms()" label="Organism" />
51 dynamic_options="list_analyses()"
52 label="Analysis" />
53 <param argument="--organism"
54 type="select"
55 dynamic_options="list_organisms()"
56 label="Organism" />
57 51
58 <!-- options --> 52 <!-- options -->
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)" /> 53 <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)" />
60 <conditional name="prot_naming"> 54 <conditional name="prot_naming">
61 <param name="method" type="select" label="Protein naming method" help="Will be used to assign uniquename to polypeptide"> 55 <param name="method" type="select" label="Protein naming method" help="Will be used to assign uniquename to polypeptide">
62 <option value="auto">Automatic: uses GFF polypeptide features if existing, or derive from mRNA uniquename</option> 56 <option value="auto">Automatic: uses GFF polypeptide features if existing, or derive from mRNA uniquename</option>
63 <option value="regex">Regular expression</option> 57 <option value="regex">Regular expression</option>
64 <option value="attr">From GFF attribute</option> 58 <option value="attr">From GFF attribute</option>
65 </param> 59 </param>
66 <when value="auto"> 60 <when value="auto">
67 </when> 61 </when>
68 <when value="regex"> 62 <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]+)$"> 63 <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"/> 64 <expand macro="sanitized"/>
71 </param> 65 </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"> 66 <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"/> 67 <expand macro="sanitized"/>
74 </param> 68 </param>
75 </when> 69 </when>
76 <when value="attr"> 70 <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"/> 71 <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> 72 </when>
79 </conditional> 73 </conditional>
80 74
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" /> 75 <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" />
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." /> 76 <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." />
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." /> 77 <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." />
84 78
85 <expand macro="wait_for"/> 79 <expand macro="wait_for"/>
86 </inputs> 80 </inputs>
87 <outputs> 81 <outputs>
88 <data format="txt" name="results"/> 82 <data format="txt" name="results"/>
89 </outputs> 83 </outputs>
90 <help> 84 <help>
91 Load features from a gff file 85 Load features from a gff file
92 86
93 @HELP@ 87 @HELP@
94 </help> 88 </help>
95 </tool> 89 </tool>