Mercurial > repos > iuc > dram_merge_annotations
annotate dram_merge_annotations.xml @ 2:866be6c60810 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit a5e28ac40a63a269100ddec5629aee5256ce00ef
author | iuc |
---|---|
date | Fri, 09 Feb 2024 21:36:08 +0000 |
parents | 96c0067106ec |
children | ca2c752a22e4 |
rev | line source |
---|---|
1
96c0067106ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
parents:
0
diff
changeset
|
1 <tool id="dram_merge_annotations" name="DRAM merge multiple annotations" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
0
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
2 <description>into a single set</description> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
3 <macros> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
5 </macros> |
2
866be6c60810
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit a5e28ac40a63a269100ddec5629aee5256ce00ef
iuc
parents:
1
diff
changeset
|
6 <expand macro="bio_tools"/> |
0
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
7 <expand macro="requirements"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
8 <command detect_errors="exit_code"><![CDATA[ |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
9 ## DRAM expects a specific file name for each file in the set. |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
10 #set annotations_file_name = 'annotations.tsv' |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
11 #set genbank_file_name = 'genbank' |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
12 #set trnas_file_name = 'trnas.tsv' |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
13 #set rrnas_file_name = 'rrnas.tsv' |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
14 #set scaffolds_file_name = 'scaffolds.fna' |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
15 #set genes_gff_file_name = 'genes.gff' |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
16 #set genes_fna_file_name = 'genes.fna' |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
17 #set genes_faa_file_name = 'genes.faa' |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
18 |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
19 ## DRAM expects each annotation set to be in a different directory. |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
20 #set input_dirs = list() |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
21 #for $index, $item in enumerate($annotations_collection): |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
22 #set dir_name = 'input_dir_' + str($index) |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
23 mkdir '$dir_name' && |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
24 ln -s '$item' '$dir_name/$annotations_file_name' && |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
25 ln -s '$genbank_collection[$index]' '$dir_name/$genbank_file_name' && |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
26 #if $trnas_collection: |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
27 ln -s '$trnas_collection[$index]' '$dir_name/$trnas_file_name' && |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
28 #end if |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
29 #if $rrnas_collection |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
30 ln -s '$rrnas_collection[$index]' '$dir_name/$rrnas_file_name' && |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
31 #end if |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
32 ln -s '$scaffolds_collection[$index]' '$dir_name/$scaffolds_file_name' && |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
33 ln -s '$genes_gff_collection[$index]' '$dir_name/$genes_gff_file_name' && |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
34 ln -s '$genes_fna_collection[$index]' '$dir_name/$genes_fna_file_name' && |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
35 ln -s '$genes_faa_collection[$index]' '$dir_name/$genes_faa_file_name' && |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
36 $input_dirs.append($dir_name) |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
37 #end for |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
38 |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
39 DRAM.py merge_annotations |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
40 --input_dirs 'input_dir*' |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
41 --output_dir 'output_dir' |
1
96c0067106ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
parents:
0
diff
changeset
|
42 && (test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced') |
96c0067106ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
parents:
0
diff
changeset
|
43 && (test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced') |
96c0067106ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
parents:
0
diff
changeset
|
44 && (test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced') |
96c0067106ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
parents:
0
diff
changeset
|
45 && (test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced') |
0
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
46 #if $rrnas_collection: |
1
96c0067106ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
parents:
0
diff
changeset
|
47 && (test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced') |
0
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
48 #end if |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
49 #if $trnas_collection: |
1
96c0067106ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
parents:
0
diff
changeset
|
50 && (test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced') |
0
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
51 #end if |
1
96c0067106ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
iuc
parents:
0
diff
changeset
|
52 && (test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced') |
0
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
53 ]]></command> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
54 <inputs> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
55 <param name="annotations_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of annotation files"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
56 <param name="genbank_collection" type="data_collection" format="genbank" collection_type="list" label="Collection of genbank files"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
57 <param name="trnas_collection" type="data_collection" format="tabular" collection_type="list" optional="true" label="Collection of trna files"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
58 <param name="rrnas_collection" type="data_collection" format="tabular" collection_type="list" optional="true" label="Collection of rrna files"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
59 <param name="scaffolds_collection" type="data_collection" format="fasta" collection_type="list" label="Collection of scaffolds files"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
60 <param name="genes_gff_collection" type="data_collection" format="gff3" collection_type="list" label="Collection of genes.gff files"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
61 <param name="genes_fna_collection" type="data_collection" format="fasta" collection_type="list" label="Collection of genes.fna files"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
62 <param name="genes_faa_collection" type="data_collection" format="fasta" collection_type="list" label="Collection of genes.faa files"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
63 </inputs> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
64 <outputs> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
65 <data name="output_genes_faa" format="fasta" label="${tool.name} on ${on_string}: genes.faa"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
66 <data name="output_genes_fna" format="fasta" label="${tool.name} on ${on_string}: genes.fna"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
67 <data name="output_genes_gff" format="gff3" label="${tool.name} on ${on_string}: genes.gff"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
68 <data name="output_scaffolds_fna" format="fasta" label="${tool.name} on ${on_string}: scaffolds"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
69 <data name="output_rrnas" format="tabular" label="${tool.name} on ${on_string}: rrnas"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
70 <filter>rrnas_collection</filter> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
71 </data> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
72 <data name="output_trnas" format="tabular" label="${tool.name} on ${on_string}: trnas"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
73 <filter>trnas_collection</filter> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
74 </data> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
75 <!-- DRAM just copies the genbank files to a directory --> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
76 <collection name="output_genbank" type="list" label="${tool.name} on ${on_string}: genbank"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
77 <discover_datasets pattern="__name__" ext="genbank" directory="output_dir/genbank"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
78 </collection> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
79 <data name="output_annotations" format="tabular" label="${tool.name} on ${on_string}: annotations"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
80 </outputs> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
81 <tests> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
82 <!-- |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
83 These tests succeed, but the outputs are empty because the DRAM |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
84 database is not available in the test environment. |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
85 --> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
86 <test expect_num_outputs="8"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
87 <param name="annotations_collection"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
88 <collection type="list"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
89 <element name="annotated1" value="annotated1.tabular"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
90 <element name="annotated2" value="annotated2.tabular"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
91 </collection> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
92 </param> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
93 <param name="genbank_collection"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
94 <collection type="list"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
95 <element name="annotated1" value="annotated1.genbank"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
96 <element name="annotated2" value="annotated2.genbank"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
97 </collection> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
98 </param> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
99 <param name="trnas_collection"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
100 <collection type="list"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
101 <element name="annotated1" value="annotated1_trnas.tabular"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
102 <element name="annotated2" value="annotated2_trnas.tabular"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
103 </collection> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
104 </param> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
105 <param name="rrnas_collection"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
106 <collection type="list"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
107 <element name="annotated1" value="annotated1_rrnas.tabular"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
108 <element name="annotated2" value="annotated2_rrnas.tabular"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
109 </collection> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
110 </param> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
111 <param name="scaffolds_collection"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
112 <collection type="list"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
113 <element name="annotated1" value="annotated1_scaffold.fasta"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
114 <element name="annotated2" value="annotated2_scaffold.fasta"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
115 </collection> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
116 </param> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
117 <param name="genes_gff_collection"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
118 <collection type="list"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
119 <element name="annotated1" value="annotated1.gff"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
120 <element name="annotated2" value="annotated2.gff"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
121 </collection> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
122 </param> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
123 <param name="genes_fna_collection"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
124 <collection type="list"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
125 <element name="annotated1" value="annotated1_genes_fna.fasta"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
126 <element name="annotated2" value="annotated2_genes_fna.fasta"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
127 </collection> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
128 </param> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
129 <param name="genes_faa_collection"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
130 <collection type="list"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
131 <element name="annotated1" value="annotated1_genes_faa.fasta"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
132 <element name="annotated2" value="annotated2_genes_faa.fasta"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
133 </collection> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
134 </param> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
135 <output name="output_annotations"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
136 <assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
137 <has_n_lines n="530" delta="1"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
138 </assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
139 </output> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
140 <output_collection name="output_genbank" type="list" count="2"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
141 <element name="annotation_0.gbk" ftype="genbank"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
142 <assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
143 <has_text text="LOCUS"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
144 </assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
145 </element> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
146 <element name="annotation_1.gbk" ftype="genbank"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
147 <assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
148 <has_text text="LOCUS"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
149 </assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
150 </element> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
151 </output_collection> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
152 <output name="output_trnas"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
153 <assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
154 <has_n_lines n="8" delta="1"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
155 </assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
156 </output> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
157 <output name="output_rrnas"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
158 <assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
159 <has_n_lines n="3" delta="1"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
160 </assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
161 </output> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
162 <output name="output_scaffolds_fna"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
163 <assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
164 <has_n_lines n="4" delta="1"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
165 </assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
166 </output> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
167 <output name="output_genes_gff"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
168 <assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
169 <has_n_lines n="23" delta="1"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
170 </assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
171 </output> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
172 <output name="output_genes_fna"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
173 <assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
174 <has_n_lines n="26" delta="1"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
175 </assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
176 </output> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
177 <output name="output_genes_faa"> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
178 <assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
179 <has_n_lines n="26" delta="1"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
180 </assert_contents> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
181 </output> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
182 </test> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
183 </tests> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
184 <help> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
185 **What it does** |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
186 |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
187 @WHATITDOESHEADER@ |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
188 |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
189 This tool accepts collections of the components of a DRAM annotations (i.e., annotations, genbank files, GFF files, tRNAs, |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
190 rRNas, etc) and, except for the genbank files which remain a collection, merges the set of files for each component into |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
191 a single file. |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
192 |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
193 @WHATITDOESFOOTER@ |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
194 </help> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
195 <expand macro="citations"/> |
2675f8d7b2a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
iuc
parents:
diff
changeset
|
196 </tool> |