Mercurial > repos > tduigou > sculpt_sequences

annotate sculpt_sequences.xml @ 1:a0cd867780ec draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
author tduigou
date Thu, 17 Jul 2025 13:24:49 +0000
parents 0c7f75a2338b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
1 <tool id="sculpt_sequences" name="Sculpt Sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
2 <description>Optimize DNA sequences</description>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
3 <macros>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
4 <token name="@VERSION_SUFFIX@">1</token>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
5 <token name="@TOOL_VERSION@">0.2.0</token>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
6 </macros>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
7 <requirements>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
8 <requirement type="package" version="0.1.11">flametree</requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
9 <requirement type="package" version="1.85"> biopython </requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
10 <requirement type="package" version="0.1.10">proglog</requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
11 <requirement type="package" version="3.2.16">dnachisel</requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
12 <requirement type="package" version="2025.4.15">html2text</requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
13 <requirement type="package" version="2.0.12">dnacauldron</requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
14 <requirement type="package" version="2.2.3">pandas</requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
15 <requirement type="package" version="2.2.5">numpy</requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
16 <requirement type="package" version="0.3.9">pdf-reports</requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
17 <requirement type="package" version="0.1.8">sequenticon</requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
18 <requirement type="package" version="3.1.5">dna_features_viewer</requirement>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
19 </requirements>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
20 <command detect_errors="exit_code"><![CDATA[
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
21 #if str($json_use.use_json_param) == "false":
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
22 #set avoid_list = [line.strip() for line in str($avoid_patterns).strip().split('\n') if line.strip()]
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
23 #set avoid_patterns = ','.join($avoid_list)
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
24
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
25 #set hairpin_lines = [line.strip() for line in str($json_use.hairpin_constraints).strip().split('\n') if line.strip()]
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
26 #set hairpin_constraints = '__cn__'.join($hairpin_lines)
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
27
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
28 #set gc_lines = [line.strip() for line in str($json_use.gc_constraints).strip().split('\n') if line.strip()]
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
29 #set gc_constraints = '__cn__'.join($gc_lines)
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
30
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
31 #set kmer_size = $json_use.kmer_size
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
32
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
33 #else:
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
34 #set avoid_patterns = ''
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
35 #set hairpin_constraints = ''
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
36 #set gc_constraints = ''
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
37 #set kmer_size = ''
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
38 #end if
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
39
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
40 #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
41 #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
42
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
43 mkdir 'outdir_scul' &&
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
44 mkdir 'outdir_unscul' &&
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
45 python '$__tool_directory__/sculpt_sequences.py'
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
46 --use_json_param '$json_use.use_json_param'
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
47 --files_to_sculpt '$genbank_file_paths'
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
48 --file_name_mapping '$file_name_mapping'
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
49 --outdir_scul 'outdir_scul'
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
50 --outdir_unscul 'outdir_unscul'
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
51 --use_file_names_as_id '$use_file_names_as_ids'
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
52 --avoid_patterns '$avoid_patterns'
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
53 --gc_constraints '$gc_constraints'
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
54 --kmer_size '$kmer_size'
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
55 --hairpin_constraints '$hairpin_constraints'
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
56 #if $json_use.use_json_param:
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
57 --json_params '$json_use.json_params'
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
58 #else:
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
59 --json_params ''
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
60 --DnaOptimizationProblemClass '$json_use.DnaOptimizationProblemClass'
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
61 #end if
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
62 ]]></command>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
63 <inputs>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
64 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
65 <conditional name='json_use'>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
66 <param name="use_json_param" type="boolean" checked="false" label="Use parameter from a JSON file" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
67 <when value="false">
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
68 <param name="DnaOptimizationProblemClass" type="select" label="DnaOptimizationProblem Calss" help="select the assambly class">
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
69 <option value="DnaOptimizationProblem" selected="True">DnaOptimizationProblem</option>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
70 <option value="CircularDnaOptimizationProblem">CircularDnaOptimizationProblem</option>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
71 </param>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
72 <param name="avoid_patterns" type="text" area="true" label="Avoid Pattern Constraints" help="Each pattern on a line" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
73 <param name="hairpin_constraints" type="text" area="true" label="Hairpins Constraints" optional="true" help="e.g. (you can add others Hairpins Constraints on a new line): stem_size=20, hairpin_window=200"/>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
74 <param name="gc_constraints" type="text" area="true" label="Enforce GC Content Constraints" optional="true" help="e.g. (you can add others Enforce GC Content Constraints on a new line): mini=0.3, maxi=0.7, window=100"/>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
75 <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
76 </when>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
77 <when value="true">
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
78 <param name="json_params" type="data" format="json" optional="true" label="JSON parameters file" help="Contains tool's parameters" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
79 </when>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
80 </conditional>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
81 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" />
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
82 </inputs>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
83 <outputs>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
84 <collection name="scul" type="list" label="scul group" >
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
85 <discover_datasets pattern="(?P&lt;name&gt;.*).zip" format="zip" directory="outdir_scul" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
86 </collection>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
87 <collection name="unscul" type="list" label="unscul+scul gb" >
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
88 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_unscul" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
89 </collection>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
90 </outputs>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
91 <tests>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
92 <test>
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
93 <!-- test for DnaOptimizationProblem -->
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
94 <param name="genbank_files">
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
95 <collection type="list">
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
96 <element name="p15_PuroR" value="10_emma_genbanks/p15_PuroR.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
97 <element name="p9_PuroR" value="10_emma_genbanks/p9_PuroR.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
98 <element name="p15_Pup9_mTagBFP2roR" value="10_emma_genbanks/p9_mTagBFP2.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
99 <element name="p15_p9_BSDRPuroR" value="10_emma_genbanks/p9_BSDR.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
100 <element name="p8_Linker1" value="10_emma_genbanks/p8_Linker1.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
101 <element name="p7_L7Ae-Weiss" value="10_emma_genbanks/p7_L7Ae-Weiss.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
102 <element name="p6_Nt-IgKLsequence" value="10_emma_genbanks/p6_Nt-IgKLsequence.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
103 <element name="p6_Kozak-ATG" value="10_emma_genbanks/p6_Kozak-ATG.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
104 <element name="p4_Kt-L7Ae-Weiss" value="10_emma_genbanks/p4_Kt-L7Ae-Weiss.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
105 <element name="HC_Amp_ccdB" value="10_emma_genbanks/HC_Amp_ccdB.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
106 </collection>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
107 </param>
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
108 <conditional name="json_use">
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
109 <param name="use_json_param" value="false" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
110 <param name="DnaOptimizationProblemClass" value="DnaOptimizationProblem" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
111 <!-- AvoidPatterns -->
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
112 <param name="avoid_patterns" value="BsaI_site
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
113 NotI_site
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
114 XbaI_site
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
115 ClaI_site
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
116 8x1mer" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
117 <!-- EnforceGCContent -->
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
118 <param name="gc_constraints" value="mini=0.1, maxi=0.9, window=50"/>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
119 </conditional>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
120 <param name="use_file_names_as_ids" value="True" />
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
121 <output_collection name="scul" count="10">
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
122 </output_collection>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
123 <output_collection name="unscul" count="10">
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
124 </output_collection>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
125 </test>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
126 <test>
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
127 <!-- test for CircularDnaOptimizationProblem -->
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
128 <param name="genbank_files">
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
129 <collection type="list">
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
130 <element name="p15_PuroR" value="10_emma_genbanks/p15_PuroR.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
131 <element name="p9_PuroR" value="10_emma_genbanks/p9_PuroR.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
132 <element name="p15_Pup9_mTagBFP2roR" value="10_emma_genbanks/p9_mTagBFP2.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
133 <element name="p15_p9_BSDRPuroR" value="10_emma_genbanks/p9_BSDR.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
134 <element name="p8_Linker1" value="10_emma_genbanks/p8_Linker1.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
135 <element name="p7_L7Ae-Weiss" value="10_emma_genbanks/p7_L7Ae-Weiss.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
136 <element name="p6_Nt-IgKLsequence" value="10_emma_genbanks/p6_Nt-IgKLsequence.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
137 <element name="p6_Kozak-ATG" value="10_emma_genbanks/p6_Kozak-ATG.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
138 <element name="p4_Kt-L7Ae-Weiss" value="10_emma_genbanks/p4_Kt-L7Ae-Weiss.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
139 <element name="HC_Amp_ccdB" value="10_emma_genbanks/HC_Amp_ccdB.gb" />
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
140 </collection>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
141 </param>
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
142 <conditional name="json_use">
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
143 <param name="use_json_param" value="false" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
144 <param name="DnaOptimizationProblemClass" value="CircularDnaOptimizationProblem" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
145 <!-- AvoidPatterns -->
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
146 <param name="avoid_patterns" value="BsaI_site
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
147 NotI_site
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
148 XbaI_site
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
149 ClaI_site
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
150 8x1mer" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
151 <!-- EnforceGCContent -->
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
152 <param name="gc_constraints" value="mini=0.1, maxi=0.9
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
153 mini=0.3, maxi=0.7, window=50"/>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
154 <param name="hairpin_constraints" value="stem_size=20, hairpin_window=200
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
155 stem_size=10, hairpin_window=100"/>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
156 </conditional>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
157 <param name="use_file_names_as_ids" value="True" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
158 <output_collection name="scul" count="10">
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
159 </output_collection>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
160 <output_collection name="unscul" count="10">
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
161 </output_collection>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
162 </test>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
163 <test>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
164 <!-- test json params -->
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
165 <param name="genbank_files">
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
166 <collection type="list">
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
167 <element name="p15_PuroR" value="10_emma_genbanks/p15_PuroR.gb" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
168 <element name="p9_PuroR" value="10_emma_genbanks/p9_PuroR.gb" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
169 <element name="p15_Pup9_mTagBFP2roR" value="10_emma_genbanks/p9_mTagBFP2.gb" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
170 <element name="p15_p9_BSDRPuroR" value="10_emma_genbanks/p9_BSDR.gb" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
171 <element name="p8_Linker1" value="10_emma_genbanks/p8_Linker1.gb" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
172 <element name="p7_L7Ae-Weiss" value="10_emma_genbanks/p7_L7Ae-Weiss.gb" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
173 <element name="p6_Nt-IgKLsequence" value="10_emma_genbanks/p6_Nt-IgKLsequence.gb" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
174 <element name="p6_Kozak-ATG" value="10_emma_genbanks/p6_Kozak-ATG.gb" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
175 <element name="p4_Kt-L7Ae-Weiss" value="10_emma_genbanks/p4_Kt-L7Ae-Weiss.gb" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
176 <element name="HC_Amp_ccdB" value="10_emma_genbanks/HC_Amp_ccdB.gb" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
177 </collection>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
178 </param>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
179 <conditional name="json_use">
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
180 <param name="use_json_param" value="true" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
181 <param name="json_params" value="test_json_workflow2.json" />
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
182 </conditional>
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
183 <param name="use_file_names_as_ids" value="True" />
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
184 <output_collection name="scul" count="10">
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
185 </output_collection>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
186 <output_collection name="unscul" count="10">
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
187 </output_collection>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
188 </test>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
189 </tests>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
190 <help><![CDATA[
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
191 Sculpt Sequences
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
192 =================
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
193
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
194 Sculpt Sequences is a Python library from the EGF Biofoundry for problem detection and sequence optimization using `dnachisel <https://github.com/Edinburgh-Genome-Foundry/DnaChisel/tree/master/dnachisel>`_ (Complete documentation available `here <https://edinburgh-genome-foundry.github.io/DnaChisel/>`_)
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
195
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
196 **Parameters**:
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
197 ---------------
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
198 * **GenBank File(s)**: List of GenBank files to be processed.
1
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
199 * **Use parameter from a JSON file**:
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
200 Yes/No parameter to indicate if user want to set parameter manually or using a json file
a0cd867780ec planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6b6ce806b5d016b3c7f20318180eff2dbe64395a-dirty
tduigou
parents: 0
diff changeset
201 If Yes, user should provide a JSON file contains all parameters
0
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
202 * **DnaOptimizationProblem Class**:
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
203 - "DnaOptimizationProblem": is the class to define and solve an optimization problems. Its methods implement all the solver logics.
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
204 - "CircularDnaOptimizationProblem": is a variant of DnaOptimizationProblem whose optimization algorithm assumes that the sequence is circular.
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
205 * **Avoid Pattern Constraints**: is a sequence design rules that can be used as constraints. It define pattern(s) to avoid during problem optimisation.
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
206 This can include enzyme sites like "BsaI_site", "NotI_site", "XbaI_site"... `enzyme dict <https://github.com/biopython/biopython/blob/master/Bio/Restriction/Restriction_Dictionary.py>`_ . Custom patterns are also supported, such as "5x3mer" means "any 5 consecutive 3-nucleotide sequences — typically 5 unique 3-mers in a row.
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
207 * **Enforce GC Content Constraints**:
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
208 Define acceptable GC content ranges. For example min: 0.4, max: 0.6, window: 50 represents a 40–60% GC content requirement within a 50-base window.
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
209 (Parameters: `EnforceGCContent_params <https://edinburgh-genome-foundry.github.io/DnaChisel/ref/builtin_specifications#enforcegccontent>`_ )
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
210 * **Avoid Hairpins**: Avoid Hairpin patterns as defined by the IDT guidelines.
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
211 A hairpin is defined by a sequence segment which has a reverse complement “nearby” in a given window.
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
212 (Parameters: `AvoidHairpins_params <https://edinburgh-genome-foundry.github.io/DnaChisel/ref/builtin_specifications#avoidhairpins>`_ ).
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
213 * **K-mer Uniqueness Size**: Avoid sub-sequence of length k with homologies elsewhere.
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
214 * **Use File Names As Sequence IDs**: Recommended if the GenBank file names represent the fragment names.
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
215 ]]></help>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
216 <citations>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
217 <citation type="bibtex">
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
218 @unpublished{sculpt_sequences
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
219 author = {Ramiz Khaled},
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
220 title = {{sculpt_sequences}},
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
221 url = {https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb},
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
222 }
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
223 </citation>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
224 </citations>
0c7f75a2338b planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
tduigou
parents:
diff changeset
225 </tool>