Mercurial > repos > iuc > checkm_tetra
annotate macros.xml @ 3:0a6606207de1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 5db2d18a153309e00a7db86f8962177e5c11c8bc
| author | iuc |
|---|---|
| date | Tue, 17 Jun 2025 08:40:43 +0000 |
| parents | 7331efc0fedd |
| children | 0eca03954dfb |
| rev | line source |
|---|---|
|
0
10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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1 <?xml version="1.0"?> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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2 <macros> |
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3
0a6606207de1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 5db2d18a153309e00a7db86f8962177e5c11c8bc
iuc
parents:
2
diff
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3 <token name="@TOOL_VERSION@">1.2.4</token> |
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0
10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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4 <token name="@VERSION_SUFFIX@">0</token> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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5 <token name="@PROFILE@">21.01</token> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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6 <xml name="biotools"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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7 <xrefs> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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8 <xref type="bio.tools">checkm</xref> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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9 </xrefs> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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10 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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11 <xml name="requirements"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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12 <requirements> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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13 <requirement type="package" version="@TOOL_VERSION@">checkm-genome</requirement> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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14 <yield/> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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15 </requirements> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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16 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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17 <xml name="bin_inputs"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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18 <conditional name="bins"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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19 <param name="select" type="select" label="Data structure for bins"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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20 <option value="collection">In collection</option> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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21 <option value="individual">In individual datasets</option> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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22 </param> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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23 <when value="collection"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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24 <param name="bins_coll" type="data_collection" collection_type="list" format="fasta" label="Bins"/> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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25 </when> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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26 <when value="individual"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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27 <param name="bins_ind" type="data" format="fasta" multiple="true" label="Bins"/> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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28 </when> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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29 </conditional> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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30 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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31 <token name="@BIN_INPUTS@"><![CDATA[ |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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32 #import re |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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33 mkdir 'bins' && |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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34 #if $bins.select == 'collection' |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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35 #for $b in $bins.bins_coll |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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36 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier)) |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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37 ln -s '$b.file_name' 'bins/${identifier}.fasta' && |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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38 #end for |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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39 #else |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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40 #for $b in $bins.bins_ind |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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41 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier)) |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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42 ln -s '$b.file_name' 'bins/${identifier}.fasta' && |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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43 #end for |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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44 #end if |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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45 ]]></token> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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46 <xml name="ali"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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47 <param argument="--ali" type="boolean" truevalue="--ali" falsevalue="" checked="false" label="Generate HMMER alignment file for each bin?" /> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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48 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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49 <xml name="nt"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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50 <param argument="--nt" type="boolean" truevalue="--nt" falsevalue="" checked="false" label="Generate nucleotide gene sequences for each bin?" /> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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51 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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52 <xml name="genes"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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53 <param argument="--genes" type="boolean" truevalue="--genes" falsevalue="" checked="false" label="Bins contain genes as amino acids instead of nucleotide contigs?" /> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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54 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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55 <xml name="tree_params"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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56 <param argument="--reduced_tree" type="boolean" truevalue="--reduced_tree" falsevalue="" checked="false" label="Use reduced tree for determining lineage of each bin?" help="This option requires less than 16GB of memory"/> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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57 <expand macro="ali" /> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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58 <expand macro="nt" /> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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59 <expand macro="genes" /> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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60 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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61 <xml name="tree_extra_output_options"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
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62 <option value="hmmer_tree_ali">Phylogenetic HMMER alignment file for each bin</option> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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63 <option value="concatenate_pplacer_json">Concatenated pplacer JSON</option> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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64 <option value="genes_fna">Nucleotide gene sequences for each bin (if generate nucleotide gene sequences)</option> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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65 <option value="genes_faa">Protein gene sequences for each bin</option> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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66 <option value="genes_gff">Gene feature files for each bin (if bins do not contain genes as amino acids instead of nucleotide contigs)</option> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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67 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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68 <xml name="analyze_params"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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69 <expand macro="ali" /> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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70 <expand macro="nt" /> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
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71 <expand macro="genes" /> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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72 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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73 <xml name="analyze_extra_output_options"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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74 <option value="hmmer_analyze_ali">Marker HMMER alignment file for each bin</option> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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75 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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76 <xml name="hmm_marker_stats_inputs"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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77 <param name="phylo_hmm_info" type="data" format="zip" label="Phylogenetic HMM model info for each bin" help="Output of the CheckM tree tool"/> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
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78 <param name="bin_stats_tree" type="data" format="tabular" label="Phylogenetic bin stats" help="Output of the CheckM tree tool" /> |
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10941a39b562
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79 <param name="hmmer_tree" type="data_collection" collection_type="list" format="txt" label="Phylogenetic HMM hits to each bin" help="Output of the CheckM tree tool" /> |
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80 </xml> |
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81 <token name="@HMM_MARKER_STATS_INPUTS@"><![CDATA[ |
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82 #import re |
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83 mkdir -p 'inputs/storage/' && |
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84 ln -s '$phylo_hmm_info' 'inputs/storage/phylo_hmm_info.pkl.gz' && |
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85 ln -s '$bin_stats_tree' 'inputs/storage/bin_stats.tree.tsv' && |
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86 #for $i in $hmmer_tree |
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87 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) |
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88 mkdir -p 'inputs/bins/${identifier}' && |
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89 ln -s '$i' 'inputs/bins/${identifier}/hmmer.tree.txt' && |
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90 #end for |
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91 ]]></token> |
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92 <xml name="lineage_set_params"> |
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93 <param argument="--unique" type="integer" min="0" value="10" label="Minimum number of unique phylogenetic markers required to use lineage-specific marker set" /> |
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94 <param argument="--multi" type="integer" min="0" value="10" label="Maximum number of multi-copy phylogenetic markers before defaulting to domain-level marker set " /> |
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95 <param argument="--force_domain" type="boolean" truevalue="--force_domain" falsevalue="" checked="false" label="Use domain-level sets for all bins?" /> |
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96 <param argument="--no_refinement" type="boolean" truevalue="--no_refinement" falsevalue="" checked="false" label="Do not perform lineage-specific marker set refinement?" /> |
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97 </xml> |
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98 <xml name="marker_file"> |
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99 <param name="marker_file" type="data" format="tabular" label="Marker for assessing bins" help="Each marker to exclude should be listed on a separate line of the file. Output of the CheckM lineage_set or taxon_set tools"/> |
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100 </xml> |
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101 <xml name="marker_output"> |
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102 <data name="marker" format="tabular" label="${tool.name} on ${on_string}: Marker genes"/> |
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103 </xml> |
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104 <xml name="qa_params"> |
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105 <param argument="--individual_markers" type="boolean" truevalue="--individual_markers" falsevalue="" checked="false" label="Treat marker as independent?" help="It will ignore co-located set structure"/> |
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10941a39b562
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106 <param argument="--skip_adj_correction" type="boolean" truevalue="--skip_adj_correction" falsevalue="" checked="false" label="Do not exclude adjacent marker genes when estimating contamination?"/> |
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107 <param argument="--skip_pseudogene_correction" type="boolean" truevalue="--skip_pseudogene_correction" falsevalue="" checked="false" label="Skip identification and filtering of pseudogenes?"/> |
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10941a39b562
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108 <param argument="--aai_strain" type="float" min="0" max="1" value="0.9" label="AAI threshold used to identify strain heterogeneity"/> |
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109 <param argument="--ignore_thresholds" type="boolean" truevalue="--ignore_thresholds" falsevalue="" checked="false" label="Ignore model-specific score thresholds?"/> |
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10941a39b562
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110 <param argument="--e_value" type="float" min="0" max="1" value="1e-10" label="E-value cut off"/> |
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111 <param argument="--length" type="float" min="0" max="1" value="0.7" label="Percent overlap between target and query"/> |
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112 </xml> |
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113 <xml name="qa_extra_output_options"> |
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114 <!--<option value="alignment_file">Alignment of multi-copy genes and their AAI identity</option>--> |
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115 <option value="marker_gene_stats">Marker gene stats</option> |
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116 </xml> |
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117 <xml name="qa_extra_outputs"> |
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118 <!--<data name="alignment_file" format="tabular" label="${tool.name} on ${on_string}: Alignment of multi-copy genes and their AAI identity" > |
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119 <filter>'alignment_file' in extra_outputs</filter> |
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120 </data>--> |
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121 <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv" label="${tool.name} on ${on_string}: Marker gene statistics"> |
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1
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122 <filter>extra_outputs and 'marker_gene_stats' in extra_outputs</filter> |
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0
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123 </data> |
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124 </xml> |
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125 <xml name="rank_taxon"> |
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126 <conditional name="rank_taxon"> |
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127 <param argument="--rank" type="select" label="Taxonomic rank"> |
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128 <option value="life">Life</option> |
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129 <option value="domain">Domain</option> |
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130 <option value="phylum">Phylum</option> |
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131 <option value="order">Order</option> |
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132 <option value="family">Family</option> |
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133 <option value="genus">Genus</option> |
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134 <option value="species">Species</option> |
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135 </param> |
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136 <when value="life"> |
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137 <param name="taxon" type="select" label="Taxon of interest" > |
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138 <options from_data_table="life_taxons"> |
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139 <validator message="No taxon database is available" type="no_options" /> |
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140 </options> |
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141 </param> |
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142 </when> |
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143 <when value="domain"> |
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144 <param name="taxon" type="select" label="Taxon of interest" > |
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145 <options from_data_table="domain_taxons"> |
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146 <validator message="No taxon database is available" type="no_options" /> |
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147 </options> |
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148 </param> |
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149 </when> |
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150 <when value="phylum"> |
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151 <param name="taxon" type="select" label="Taxon of interest" > |
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152 <options from_data_table="phylum_taxons"> |
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153 <validator message="No taxon database is available" type="no_options" /> |
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154 </options> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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155 </param> |
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156 </when> |
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10941a39b562
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157 <when value="order"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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158 <param name="taxon" type="select" label="Taxon of interest" > |
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10941a39b562
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159 <options from_data_table="order_taxons"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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160 <validator message="No taxon database is available" type="no_options" /> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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161 </options> |
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10941a39b562
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162 </param> |
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163 </when> |
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10941a39b562
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164 <when value="family"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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165 <param name="taxon" type="select" label="Taxon of interest" > |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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166 <options from_data_table="family_taxons"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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167 <validator message="No taxon database is available" type="no_options" /> |
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10941a39b562
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168 </options> |
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10941a39b562
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169 </param> |
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10941a39b562
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170 </when> |
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10941a39b562
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171 <when value="genus"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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172 <param name="taxon" type="select" label="Taxon of interest" > |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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173 <options from_data_table="genus_taxons"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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174 <validator message="No taxon database is available" type="no_options" /> |
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10941a39b562
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175 </options> |
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176 </param> |
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10941a39b562
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177 </when> |
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178 <when value="species"> |
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10941a39b562
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179 <param name="taxon" type="select" label="Taxon of interest" > |
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10941a39b562
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180 <options from_data_table="species_taxons"> |
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10941a39b562
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181 <validator message="No taxon database is available" type="no_options" /> |
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10941a39b562
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182 </options> |
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183 </param> |
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184 </when> |
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185 </conditional> |
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10941a39b562
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186 </xml> |
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187 <xml name="version"> |
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10941a39b562
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188 <version_command>checkm</version_command> |
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189 </xml> |
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10941a39b562
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190 <token name="@HELP_HEADER@"><![CDATA[ |
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191 What it does |
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192 ============ |
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193 |
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194 CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree. |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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195 ]]></token> |
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10941a39b562
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196 <token name="@HELP_BINS@"><![CDATA[ |
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10941a39b562
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197 - Bins |
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198 ]]></token> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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199 <token name="@HELP_TREE_DEFAULT_OUTPUTS@"><![CDATA[ |
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200 - Phylogenetic HMM model info for each bin |
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201 - Phylogenetic bin stats |
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202 - Phylogenetic HMM hits to each bin |
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10941a39b562
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203 - Concatenated masked sequences |
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204 - Concatenated tree |
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205 ]]></token> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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206 <token name="@HELP_TREE_EXTRA_OUTPUTS@"><![CDATA[ |
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207 |
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208 |
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209 <collection name="hmmer_tree_ali" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMMER alignment file for each bin"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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210 <filter>ali and 'hmmer_tree_ali' in extra_outputs</filter> |
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10941a39b562
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211 <discover_datasets pattern="(?P<designation>.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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212 </collection> |
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10941a39b562
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213 <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${tool.name} on ${on_string}: Concatenated pplacer JSON"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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214 <filter>'concatenate_pplacer_json' in extra_outputs</filter> |
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10941a39b562
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215 </data> |
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216 <collection name="genes_fna" type="list" label="${tool.name} on ${on_string}: Protein gene sequences for each bin"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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217 <filter>not genes and nt and 'genes_fna' in extra_outputs</filter> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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218 <discover_datasets pattern="(?P<designation>.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> |
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10941a39b562
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219 </collection> |
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10941a39b562
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220 <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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221 <filter>'genes_faa' in extra_outputs</filter> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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222 <discover_datasets pattern="(?P<designation>.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> |
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10941a39b562
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223 </collection> |
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10941a39b562
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224 <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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225 <filter>not genes and 'genes_gff' in extra_outputs</filter> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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226 <discover_datasets pattern="(?P<designation>.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/> |
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227 </collection> |
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10941a39b562
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228 ]]></token> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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229 <xml name="citations"> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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230 <citations> |
|
10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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231 <citation type="doi">10.1101/gr.186072.114</citation> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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232 </citations> |
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10941a39b562
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iuc
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233 </xml> |
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10941a39b562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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234 </macros> |