Mercurial > repos > iuc > checkm_analyze
annotate macros.xml @ 0:7ccea589e8b7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
| author | iuc |
|---|---|
| date | Fri, 29 Jul 2022 20:31:27 +0000 |
| parents | |
| children | 5ee29434330f |
| rev | line source |
|---|---|
|
0
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
2 <macros> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
3 <token name="@TOOL_VERSION@">1.2.0</token> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
4 <token name="@VERSION_SUFFIX@">0</token> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
5 <token name="@PROFILE@">21.01</token> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
6 <xml name="biotools"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
7 <xrefs> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
8 <xref type="bio.tools">checkm</xref> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
9 </xrefs> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
10 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
11 <xml name="requirements"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
12 <requirements> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
13 <requirement type="package" version="@TOOL_VERSION@">checkm-genome</requirement> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
14 <yield/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
15 </requirements> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
16 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
17 <xml name="bin_inputs"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
18 <conditional name="bins"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
19 <param name="select" type="select" label="Data structure for bins"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
20 <option value="collection">In collection</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
21 <option value="individual">In individual datasets</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
22 </param> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
23 <when value="collection"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
24 <param name="bins_coll" type="data_collection" collection_type="list" format="fasta" label="Bins"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
25 </when> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
26 <when value="individual"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
27 <param name="bins_ind" type="data" format="fasta" multiple="true" label="Bins"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
28 </when> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
29 </conditional> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
30 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
31 <token name="@BIN_INPUTS@"><![CDATA[ |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
32 #import re |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
33 mkdir 'bins' && |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
34 #if $bins.select == 'collection' |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
35 #for $b in $bins.bins_coll |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
36 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier)) |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
37 ln -s '$b.file_name' 'bins/${identifier}.fasta' && |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
38 #end for |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
39 #else |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
40 #for $b in $bins.bins_ind |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
41 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier)) |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
42 ln -s '$b.file_name' 'bins/${identifier}.fasta' && |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
43 #end for |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
44 #end if |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
45 ]]></token> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
46 <xml name="ali"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
47 <param argument="--ali" type="boolean" truevalue="--ali" falsevalue="" checked="false" label="Generate HMMER alignment file for each bin?" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
48 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
49 <xml name="nt"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
50 <param argument="--nt" type="boolean" truevalue="--nt" falsevalue="" checked="false" label="Generate nucleotide gene sequences for each bin?" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
51 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
52 <xml name="genes"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
53 <param argument="--genes" type="boolean" truevalue="--genes" falsevalue="" checked="false" label="Bins contain genes as amino acids instead of nucleotide contigs?" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
54 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
55 <xml name="tree_params"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
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"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
57 <expand macro="ali" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
58 <expand macro="nt" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
59 <expand macro="genes" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
60 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
61 <xml name="tree_extra_output_options"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
62 <option value="hmmer_tree_ali">Phylogenetic HMMER alignment file for each bin</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
63 <option value="concatenate_pplacer_json">Concatenated pplacer JSON</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
64 <option value="genes_fna">Nucleotide gene sequences for each bin (if generate nucleotide gene sequences)</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
65 <option value="genes_faa">Protein gene sequences for each bin</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
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> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
67 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
68 <xml name="analyze_params"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
69 <expand macro="ali" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
70 <expand macro="nt" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
71 <expand macro="genes" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
72 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
73 <xml name="analyze_extra_output_options"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
74 <option value="hmmer_analyze_ali">Marker HMMER alignment file for each bin</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
75 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
76 <xml name="hmm_marker_stats_inputs"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
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"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
78 <param name="bin_stats_tree" type="data" format="tabular" label="Phylogenetic bin stats" help="Output of the CheckM tree tool" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
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" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
80 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
81 <token name="@HMM_MARKER_STATS_INPUTS@"><![CDATA[ |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
82 #import re |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
83 mkdir -p 'inputs/storage/' && |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
84 ln -s '$phylo_hmm_info' 'inputs/storage/phylo_hmm_info.pkl.gz' && |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
85 ln -s '$bin_stats_tree' 'inputs/storage/bin_stats.tree.tsv' && |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
86 #for $i in $hmmer_tree |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
87 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
88 mkdir -p 'inputs/bins/${identifier}' && |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
89 ln -s '$i' 'inputs/bins/${identifier}/hmmer.tree.txt' && |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
90 #end for |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
91 ]]></token> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
92 <xml name="lineage_set_params"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
93 <param argument="--unique" type="integer" min="0" value="10" label="Minimum number of unique phylogenetic markers required to use lineage-specific marker set" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
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 " /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
95 <param argument="--force_domain" type="boolean" truevalue="--force_domain" falsevalue="" checked="false" label="Use domain-level sets for all bins?" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
96 <param argument="--no_refinement" type="boolean" truevalue="--no_refinement" falsevalue="" checked="false" label="Do not perform lineage-specific marker set refinement?" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
97 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
98 <xml name="marker_file"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
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"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
100 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
101 <xml name="marker_output"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
102 <data name="marker" format="tabular" label="${tool.name} on ${on_string}: Marker genes"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
103 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
104 <xml name="qa_params"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
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"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
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?"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
107 <param argument="--skip_pseudogene_correction" type="boolean" truevalue="--skip_pseudogene_correction" falsevalue="" checked="false" label="Skip identification and filtering of pseudogenes?"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
108 <param argument="--aai_strain" type="float" min="0" max="1" value="0.9" label="AAI threshold used to identify strain heterogeneity"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
109 <param argument="--ignore_thresholds" type="boolean" truevalue="--ignore_thresholds" falsevalue="" checked="false" label="Ignore model-specific score thresholds?"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
110 <param argument="--e_value" type="float" min="0" max="1" value="1e-10" label="E-value cut off"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
111 <param argument="--length" type="float" min="0" max="1" value="0.7" label="Percent overlap between target and query"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
112 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
113 <xml name="qa_extra_output_options"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
114 <!--<option value="alignment_file">Alignment of multi-copy genes and their AAI identity</option>--> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
115 <option value="marker_gene_stats">Marker gene stats</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
116 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
117 <xml name="qa_extra_outputs"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
118 <!--<data name="alignment_file" format="tabular" label="${tool.name} on ${on_string}: Alignment of multi-copy genes and their AAI identity" > |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
119 <filter>'alignment_file' in extra_outputs</filter> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
120 </data>--> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
121 <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv" label="${tool.name} on ${on_string}: Marker gene statistics"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
122 <filter>'marker_gene_stats' in extra_outputs</filter> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
123 </data> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
124 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
125 <xml name="rank_taxon"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
126 <conditional name="rank_taxon"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
127 <param argument="--rank" type="select" label="Taxonomic rank"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
128 <option value="life">Life</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
129 <option value="domain">Domain</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
130 <option value="phylum">Phylum</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
131 <option value="order">Order</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
132 <option value="family">Family</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
133 <option value="genus">Genus</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
134 <option value="species">Species</option> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
135 </param> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
136 <when value="life"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
137 <param name="taxon" type="select" label="Taxon of interest" > |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
138 <options from_data_table="life_taxons"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
139 <validator message="No taxon database is available" type="no_options" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
140 </options> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
141 </param> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
142 </when> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
143 <when value="domain"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
144 <param name="taxon" type="select" label="Taxon of interest" > |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
145 <options from_data_table="domain_taxons"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
146 <validator message="No taxon database is available" type="no_options" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
147 </options> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
148 </param> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
149 </when> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
150 <when value="phylum"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
151 <param name="taxon" type="select" label="Taxon of interest" > |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
152 <options from_data_table="phylum_taxons"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
153 <validator message="No taxon database is available" type="no_options" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
154 </options> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
155 </param> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
156 </when> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
157 <when value="order"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
158 <param name="taxon" type="select" label="Taxon of interest" > |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
159 <options from_data_table="order_taxons"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
160 <validator message="No taxon database is available" type="no_options" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
161 </options> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
162 </param> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
163 </when> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
164 <when value="family"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
165 <param name="taxon" type="select" label="Taxon of interest" > |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
166 <options from_data_table="family_taxons"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
167 <validator message="No taxon database is available" type="no_options" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
168 </options> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
169 </param> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
170 </when> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
171 <when value="genus"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
172 <param name="taxon" type="select" label="Taxon of interest" > |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
173 <options from_data_table="genus_taxons"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
174 <validator message="No taxon database is available" type="no_options" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
175 </options> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
176 </param> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
177 </when> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
178 <when value="species"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
179 <param name="taxon" type="select" label="Taxon of interest" > |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
180 <options from_data_table="species_taxons"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
181 <validator message="No taxon database is available" type="no_options" /> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
182 </options> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
183 </param> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
184 </when> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
185 </conditional> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
186 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
187 <xml name="version"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
188 <version_command>checkm</version_command> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
189 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
190 <token name="@HELP_HEADER@"><![CDATA[ |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
191 What it does |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
192 ============ |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
193 |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
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. |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
195 ]]></token> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
196 <token name="@HELP_BINS@"><![CDATA[ |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
197 - Bins |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
198 ]]></token> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
199 <token name="@HELP_TREE_DEFAULT_OUTPUTS@"><![CDATA[ |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
200 - Phylogenetic HMM model info for each bin |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
201 - Phylogenetic bin stats |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
202 - Phylogenetic HMM hits to each bin |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
203 - Concatenated masked sequences |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
204 - Concatenated tree |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
205 ]]></token> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
206 <token name="@HELP_TREE_EXTRA_OUTPUTS@"><![CDATA[ |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
207 |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
208 |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
209 <collection name="hmmer_tree_ali" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMMER alignment file for each bin"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
210 <filter>ali and 'hmmer_tree_ali' in extra_outputs</filter> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
211 <discover_datasets pattern="(?P<designation>.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
212 </collection> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
213 <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${tool.name} on ${on_string}: Concatenated pplacer JSON"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
214 <filter>'concatenate_pplacer_json' in extra_outputs</filter> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
215 </data> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
216 <collection name="genes_fna" type="list" label="${tool.name} on ${on_string}: Protein gene sequences for each bin"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
217 <filter>not genes and nt and 'genes_fna' in extra_outputs</filter> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
218 <discover_datasets pattern="(?P<designation>.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
219 </collection> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
220 <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
221 <filter>'genes_faa' in extra_outputs</filter> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
222 <discover_datasets pattern="(?P<designation>.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
223 </collection> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
224 <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
225 <filter>not genes and 'genes_gff' in extra_outputs</filter> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
226 <discover_datasets pattern="(?P<designation>.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
227 </collection> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
228 ]]></token> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
229 <xml name="citations"> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
230 <citations> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
231 <citation type="doi">10.1101/gr.186072.114</citation> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
232 </citations> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
233 </xml> |
|
7ccea589e8b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff
changeset
|
234 </macros> |