Mercurial > repos > tduigou > cloning_simulation
annotate cloning_similation.xml @ 8:07e902da89ad draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 26 May 2025 09:23:51 +0000 |
| parents | 296e5145a862 |
| children | 7d1778f5e164 |
| rev | line source |
|---|---|
|
0
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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1 <tool id="cloning_simulation" name="Cloning Simulation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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2 <description>A cloning simulator for synthetic biology</description> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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3 <macros> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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4 <token name="@VERSION_SUFFIX@">0</token> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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5 <token name="@TOOL_VERSION@">0.1.0</token> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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6 </macros> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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7 <requirements> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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8 <requirement type="package" version="0.1.11">flametree</requirement> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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9 <requirement type="package" version="1.85"> biopython </requirement> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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10 <requirement type="package" version="0.1.10">proglog</requirement> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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11 <requirement type="package" version="2.2.3">pandas</requirement> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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12 <requirement type="package" version="2.0.12">dnacauldron</requirement> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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13 <requirement type="package" version="0.3.9">pdf-reports</requirement> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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14 <requirement type="package" version="0.1.8">sequenticon</requirement> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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15 <requirement type="package" version="3.1.5">dna_features_viewer</requirement> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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16 </requirements> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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17 <command detect_errors="exit_code"><![CDATA[ |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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18 #set genbank_file_paths = ','.join([str(f) for f in $genbank_files]) |
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6
e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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diff
changeset
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19 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files]) |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
5
diff
changeset
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20 #set domesticated_input_paths = ','.join([str(f) for f in $domesticated_input]) |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
5
diff
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21 #set file_name_mapping_dom = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input]) |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
5
diff
changeset
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22 #if $domesticated_input_paths != '' and $genbank_file_paths == '' |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
5
diff
changeset
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23 #set genbank_file_paths = ','.join([str(f) for f in $domesticated_input]) |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
5
diff
changeset
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24 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input]) |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
5
diff
changeset
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25 #set domesticated_input_paths = '' |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
5
diff
changeset
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26 #set file_name_mapping_dom = '' |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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27 #end if |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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28 mkdir 'outdir_zip' && mkdir 'outdir_gb' && |
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b0134502203b
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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29 cp '$assembly_csv' 'assembly_csv.csv' && |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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30 python '$__tool_directory__/cloning_simulation.py' |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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31 --parts_files '$genbank_file_paths' |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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32 --domesticated_seq '$domesticated_input_paths' |
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254d284a5be9
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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33 --assembly_csv 'assembly_csv.csv' |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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34 --assembly_plan_name '$assembly_plan_name' |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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35 --file_name_mapping '$file_name_mapping' |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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36 --file_name_mapping_dom '$file_name_mapping_dom' |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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37 --use_file_names_as_id '$adv.use_file_names_as_ids' |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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38 --outdir_simulation 'outdir_zip' |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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39 --outdir_gb 'outdir_gb' |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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40 --output_simulation 'output_zip.zip' |
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296e5145a862
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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41 --enzyme '$adv.enzyme' |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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42 --topology '$topology' && |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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43 cp 'output_zip.zip' '$output_zip' |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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44 ]]></command> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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45 <inputs> |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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46 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" optional="True"/> |
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296e5145a862
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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47 <param name="assembly_csv" type="data" format="csv" label="Assemby csv"/> |
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e1e985913204
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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48 <param name="domesticated_input" type="data_collection" collection_type="list" format="genbank" label="Domesticated GenBank" optional="True"/> |
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296e5145a862
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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49 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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50 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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51 <option value="GibsonAssembly">Gibson_assembly</option> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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52 <option value="BASICAssembly">BASIC_assembly</option> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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53 <option value="BioBrickStandardAssembly">biobrick_assembly</option> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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54 <option value="LigaseCyclingReactionAssembly">lcr_assembly</option> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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55 </param> |
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296e5145a862
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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56 <param name="topology" type="select" label="Assambly Topology" help="select circular or linear topology"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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57 <option value="linear" selected="True">linear</option> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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58 <option value="circular">circular</option> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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59 </param> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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60 <section name="adv" title="Advanced Options" expanded="false"> |
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296e5145a862
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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61 <param name="enzyme" type="text" label="Enzyme" value="auto" optional="True"/> |
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296e5145a862
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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62 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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63 </section> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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64 </inputs> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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65 <outputs> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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66 <data format="zip" name="output_zip" label="simulation results"/> |
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296e5145a862
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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67 <collection name="construct_gb" type="list" label="All Constract GenBank"> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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68 <discover_datasets pattern="(?P<name>.*).gb" format="genbank" directory="outdir_gb" /> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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69 </collection> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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70 </outputs> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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71 <tests> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
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72 <!--test type2s_assembly class--> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
73 <test> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
74 <param name="genbank_files"> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
75 <collection type="list"> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
76 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
77 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
78 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
79 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
80 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
81 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
82 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
83 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
84 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
85 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
86 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
87 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
88 </collection> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
89 </param> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
90 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
91 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
92 <param name="topology" value="circular"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
93 <param name="adv|use_file_names_as_ids" value="True" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
94 <output name="output_zip" ftype='zip'> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
95 <assert_contents> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
96 <has_archive_member path=".*" n="62"/> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
97 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf"> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
98 <has_size min="5"/> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
99 </has_archive_member> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
100 </assert_contents> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
101 </output> |
|
3
044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
2
diff
changeset
|
102 <output_collection name="construct_gb" type="list" count="4"> |
|
2
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
103 <element name="construct_1"> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
104 <assert_contents> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
105 <has_n_lines min="20" /> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
106 </assert_contents> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
107 </element> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
108 <element name="construct_2"> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
109 <assert_contents> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
110 <has_n_lines min="20" /> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
111 </assert_contents> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
112 </element> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
113 <element name="construct_3"> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
114 <assert_contents> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
115 <has_n_lines min="20" /> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
116 </assert_contents> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
117 </element> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
118 <element name="construct_4"> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
119 <assert_contents> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
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120 <has_n_lines min="20" /> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
121 </assert_contents> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
122 </element> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
123 </output_collection> |
|
0
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
124 </test> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
125 <!--test gibson_assembly class--> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
126 <test> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
127 <param name="genbank_files"> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
128 <collection type="list"> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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129 <element name="gibson_sequences" value="Gibson_assembly_dataset/gibson_sequences.fa" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
130 </collection> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
131 </param> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
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132 <param name="assembly_csv" value="Gibson_assembly_dataset/gibson_assembly.csv" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
133 <param name='assembly_plan_name' value='GibsonAssembly' /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
134 <param name="topology" value="circular"/> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
135 <param name="adv|use_file_names_as_ids" value="True" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
136 <output name="output_zip" ftype='zip'> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
137 <assert_contents> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
138 <has_archive_member path=".*" n="78"/> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
139 <has_archive_member path="assambly_simulation/Report.pdf"> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
140 <has_size min="5"/> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
141 </has_archive_member> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
142 </assert_contents> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
diff
changeset
|
143 </output> |
|
3
044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
2
diff
changeset
|
144 <output_collection name="construct_gb" type="list" count="3"> |
|
2
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
145 <element name="construct_1"> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
|
146 <assert_contents> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
changeset
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147 <has_n_lines min="20" /> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
1
diff
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148 </assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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149 </element> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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150 <element name="construct_2"> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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151 <assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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152 <has_n_lines min="20" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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153 </assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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154 </element> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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155 <element name="construct_3"> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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156 <assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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157 <has_n_lines min="20" /> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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158 </assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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159 </element> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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160 </output_collection> |
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0
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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161 </test> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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162 <!--test lcr_assembly class--> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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163 <test> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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164 <param name="genbank_files"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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165 <collection type="list"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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166 <element name="RFP_GFP_plasmid_BOs" value="lcr_assembly_dataset/RFP_GFP_plasmid_BOs.fa" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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167 <element name="RFP_GFP_plasmid_parts" value="lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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168 </collection> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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169 </param> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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170 <param name="assembly_csv" value="lcr_assembly_dataset/assembly_plan.csv" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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171 <param name='assembly_plan_name' value='LigaseCyclingReactionAssembly' /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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172 <param name="topology" value="circular"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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173 <param name="adv|use_file_names_as_ids" value="True" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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174 <output name="output_zip" ftype='zip'> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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175 <assert_contents> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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176 <has_archive_member path=".*" n="68"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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177 <has_archive_member path="assambly_simulation/Report.pdf"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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178 <has_size min="5"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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179 </has_archive_member> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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180 </assert_contents> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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181 </output> |
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3
044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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182 <output_collection name="construct_gb" type="list" count="0"> |
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2
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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183 </output_collection> |
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0
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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184 </test> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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185 <!--test BASIC_assembly class--> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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186 <test> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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187 <param name="genbank_files"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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188 <collection type="list"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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189 <element name="GFP" value="BASIC_assembly_dataset/GFP.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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190 <element name="p15A_kan" value="BASIC_assembly_dataset/p15A_kan.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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191 <element name="promoter" value="BASIC_assembly_dataset/promoter.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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192 <element name="RFP" value="BASIC_assembly_dataset/RFP.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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193 <element name="oligos" value="BASIC_assembly_dataset/oligos.fa" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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194 </collection> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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195 </param> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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196 <param name="assembly_csv" value="BASIC_assembly_dataset/basic_assembly.csv" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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197 <param name='assembly_plan_name' value='BASICAssembly' /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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198 <param name="topology" value="circular"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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199 <param name="adv|use_file_names_as_ids" value="True" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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200 <output name="output_zip" ftype='zip'> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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201 <assert_contents> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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202 <has_archive_member path=".*" n="47"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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203 <has_archive_member path="assambly_simulation/Report.pdf"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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204 <has_size min="5"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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205 </has_archive_member> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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206 </assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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207 </output> |
|
3
044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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2
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208 <output_collection name="construct_gb" type="list" count="0"> |
|
2
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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209 </output_collection> |
|
0
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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210 </test> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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211 <!--test biobrick_assembly class--> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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212 <test> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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213 <param name="genbank_files"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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214 <collection type="list"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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215 <element name="BBa_E0040_GFP" value="BioBrick_assembly_dataset/BBa_E0040_GFP.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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216 <element name="BBa_J23119_prom" value="BioBrick_assembly_dataset/BBa_J23119_prom.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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217 <element name="BBa_J23119_prom_flawed" value="BioBrick_assembly_dataset/BBa_J23119_prom_flawed.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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218 <element name="BBa_J61048_term" value="BioBrick_assembly_dataset/BBa_J61048_term.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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219 <element name="BBa_K611094_bar" value="BioBrick_assembly_dataset/BBa_K611094_bar.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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220 </collection> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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221 </param> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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222 <param name="assembly_csv" value="BioBrick_assembly_dataset/hierarchical_biobrick.csv" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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223 <param name='assembly_plan_name' value='BioBrickStandardAssembly' /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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224 <param name="topology" value="circular"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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225 <param name="adv|use_file_names_as_ids" value="True" /> |
|
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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226 <output name="output_zip" ftype='zip'> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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227 <assert_contents> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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228 <has_archive_member path=".*" n="47"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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229 <has_archive_member path="assambly_simulation/Report.pdf"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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230 <has_size min="5"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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231 </has_archive_member> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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232 </assert_contents> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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233 </output> |
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3
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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234 <output_collection name="construct_gb" type="list" count="3"> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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235 <element name="C1_prom_barcode"> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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236 <assert_contents> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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237 <has_n_lines min="20" /> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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238 </assert_contents> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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239 </element> |
|
044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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240 <element name="C2_gfp_term"> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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241 <assert_contents> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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242 <has_n_lines min="20" /> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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243 </assert_contents> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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244 </element> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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245 <element name="C3_final"> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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246 <assert_contents> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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247 <has_n_lines min="20" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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248 </assert_contents> |
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044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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249 </element> |
|
2
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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250 </output_collection> |
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0
dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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251 </test> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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252 <!--test type2s_assembly with domesticated files--> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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253 <test> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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254 <param name="genbank_files"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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255 <collection type="list"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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256 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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257 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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258 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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259 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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260 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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261 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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262 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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263 </collection> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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264 </param> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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265 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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266 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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267 <param name="domesticated_input"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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268 <collection type="list"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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269 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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270 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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271 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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272 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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273 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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274 </collection> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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275 </param> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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276 <param name="topology" value="circular"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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277 <param name="adv|use_file_names_as_ids" value="True" /> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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278 <output name="output_zip" ftype='zip'> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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279 <assert_contents> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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280 <has_archive_member path=".*" n="62"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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281 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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282 <has_size min="5"/> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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283 </has_archive_member> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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284 </assert_contents> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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285 </output> |
|
3
044d36066cb3
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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2
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286 <output_collection name="construct_gb" type="list" count="4"> |
|
2
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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1
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287 <element name="construct_1"> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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288 <assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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289 <has_n_lines min="20" /> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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290 </assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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291 </element> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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292 <element name="construct_2"> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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293 <assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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294 <has_n_lines min="20" /> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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295 </assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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296 </element> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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297 <element name="construct_3"> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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298 <assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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299 <has_n_lines min="20" /> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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300 </assert_contents> |
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3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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301 </element> |
|
3171db614963
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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302 <element name="construct_4"> |
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303 <assert_contents> |
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304 <has_n_lines min="20" /> |
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305 </assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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306 </element> |
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307 </output_collection> |
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308 </test> |
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309 <!--test only domestication input--> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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310 <test> |
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311 <param name="domesticated_input"> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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312 <collection type="list"> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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313 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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314 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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315 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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316 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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317 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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318 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" /> |
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319 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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320 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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321 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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322 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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323 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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324 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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325 </collection> |
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326 </param> |
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327 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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328 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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329 <param name="topology" value="circular"/> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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330 <param name="adv|use_file_names_as_ids" value="True" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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331 <output name="output_zip" ftype='zip'> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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332 <assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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333 <has_archive_member path=".*" n="62"/> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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334 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf"> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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335 <has_size min="5"/> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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336 </has_archive_member> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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337 </assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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338 </output> |
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339 <output_collection name="construct_gb" type="list" count="4"> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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340 <element name="construct_1"> |
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341 <assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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342 <has_n_lines min="20" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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343 </assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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344 </element> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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345 <element name="construct_2"> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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346 <assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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347 <has_n_lines min="20" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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348 </assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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349 </element> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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350 <element name="construct_3"> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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351 <assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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352 <has_n_lines min="20" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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353 </assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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354 </element> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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355 <element name="construct_4"> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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356 <assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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357 <has_n_lines min="20" /> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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358 </assert_contents> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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359 </element> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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360 </output_collection> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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361 </test> |
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0
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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362 </tests> |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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363 |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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364 <help><![CDATA[ |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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365 Cloning_Simulation |
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366 ==================== |
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367 |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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368 The Cloning Simulation tool is based on the DnaCauldron package developed by the EGF Biofoundry. It enables rapid and accurate assembly simulation of DNA parts for modular cloning systems, such as Golden Gate Assembly (complete documentation `here <https://edinburgh-genome-foundry.github.io/DnaCauldron/>`_). |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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369 |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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370 **Parameters**: |
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371 --------------- |
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8
07e902da89ad
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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372 * **Assemby csv**: csv file containes the construct names with their parts. (Without Header) |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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373 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s). |
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7
296e5145a862
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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374 * **Domesticated GenBank**: Dimesticated GenBank list (Optional) |
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296e5145a862
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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375 * **Topology**: Can be "circular", "linear". |
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296e5145a862
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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376 * **Enzyme**: It will be selected automatically, or you can set one from this dictionnary : `dict <https://github.com/biopython/biopython/blob/master/Bio/Restriction/Restriction_Dictionary.py>`_ |
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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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377 * **Assembly Class**: |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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378 - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_golden_gate>`_ |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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379 - "gibson_assembly": GibsonAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/gibson_assembly>`_ |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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380 - "BASIC_assembly": BASICAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/BASIC_assembly>`_ |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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381 - "biobrick_assembly": BioBrickStandardAssembly, `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_biobrick>`_ |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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382 - "lcr_assembly": LigaseCyclingReactionAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/lcr_assembly>`_ |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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383 ]]></help> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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384 <citations> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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385 <citation type="bibtex"> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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386 @unpublished{cloning_simulation |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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387 author = {Ramiz Khaled}, |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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388 title = {{cloning_simulation}}, |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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389 url = {https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb}, |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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390 } |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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391 </citation> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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392 </citations> |
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dc450979fcd4
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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393 </tool> |