Mercurial > repos > iuc > cami_amber

annotate cami_amber.xml @ 5:e30bc6da7a36 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 04a067550f7d61ca8ff489e3de64efd0da3abcf1
author iuc
date Sun, 08 Sep 2024 14:37:28 +0000
parents 6c71acde9d52
children 2e7b727a0e05
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
1 <tool id="cami_amber" name="CAMI AMBER" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
2 <description>Evaluation package for MAGs</description>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
3 <macros>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
4 <import>macros.xml</import>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
5 </macros>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
6 <expand macro="requirements" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
7 <command detect_errors="exit_code">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
8 <![CDATA[
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
9
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
10 #set $path_to_html = $html.files_path
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
11 #set $max = []
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
12 #set $min = []
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
13 #set $label = []
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
14
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
15 mkdir -p output inputs '$path_to_html' &&
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
16
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
17 #if $tox.ncbi.is_select == 'yes':
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
18 #if $tox.input.is_select == 'manually':
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
19 mkdir -p ncbi &&
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
20 #for $file in $tox.ncbi_dir:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
21 ln -s '$file' './ncbi/$file.element_identifier' &&
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
22 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
23 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
24 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
25
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
26 #for $i, $file in enumerate($input_files):
5
e30bc6da7a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 04a067550f7d61ca8ff489e3de64efd0da3abcf1
iuc
parents: 0
diff changeset
27 ln -s '$file.binning_files' './inputs/${i}.tsv' &&
0
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
28 #if $file.labels:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
29 $label.append($file.labels)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
30 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
31 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
32
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
33 #if $genome.thresholds:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
34 #for $i, $arg in enumerate($genome.thresholds):
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
35 #if $arg.min_completeness:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
36 $min.append($arg.min_completeness)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
37 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
38 #if $arg.max_contamination:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
39 $max.append($arg.max_contamination)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
40 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
41 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
42 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
43
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
44 amber.py
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
45 -g '${gold_standard_file}'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
46 #if $label:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
47 #set $sep = ''
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
48 -l
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
49 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
50 #for $lab in $label:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
51 $sep$lab
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
52 #set $sep = ','
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
53 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
54 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
55 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
56 -p ${filter}
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
57 #if $min_length:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
58 -n $min_length
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
59 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
60 #if $desc:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
61 -d '${desc}'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
62 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
63 #if $min:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
64 #set $sep = ''
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
65 --min_completeness
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
66 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
67 #for $i in $min:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
68 $sep$i
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
69 #set $sep = ','
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
70 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
71 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
72 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
73 #if $max:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
74 #set $sep = ''
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
75 --max_contamination
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
76 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
77 #for $i in $max:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
78 $sep$i
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
79 #set$sep = ','
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
80 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
81 '
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
82 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
83 #if $genome.remove_genomes:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
84 -r '$genome.remove_genomes'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
85 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
86 #if $genome.remove.is_select == 'yes':
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
87 -k '$genome.keyword'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
88 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
89 #if $genome.genome_coverage:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
90 --genome_coverage '$genome.genome_coverage'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
91 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
92 #if $tox.ncbi.is_select == 'yes':
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
93 #if $tox.input.is_select == 'manually':
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
94 --ncbi_dir ncbi
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
95 #else:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
96 --ncbi_dir '$tox.ncbi_dir.fields.path'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
97 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
98 #end if
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
99 -o output
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
100 #for $i, $bin in enumerate($input_files):
5
e30bc6da7a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 04a067550f7d61ca8ff489e3de64efd0da3abcf1
iuc
parents: 0
diff changeset
101 'inputs/${i}.tsv'
0
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
102 #end for
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
103
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
104 &&
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
105
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
106 mv 'output/heatmap_bar.png' '$path_to_html'
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
107
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
108 ]]>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
109 </command>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
110 <inputs>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
111 <param argument="--gold_standard_file" format="tabular" type="data"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
112 label="Mapping of contigs or reads"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
113 help="Input the gold standard file here so amber know the correct IDs for each contig/read" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
114 <repeat name="input_files" title="Binning files and names "
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
115 help="Enter multiple binning files and names (names are optional). IMPORTANT: for each binning file you use in the program you need to state one label, this mean for example for 3 binning files you need 3 labels (3 slots) not more or less!">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
116 <param name="binning_files" format="tabular" type="data"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
117 label="Input bin files here" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
118 <param argument="--labels" type="text" value="" optional="true"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
119 label="Name for bin" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
120 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
121 <param argument="--filter" type="integer" value="0" min="0"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
122 label="Filter out the n smallest genome bins"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
123 help="Optional filter for filter out the n smallest genome bins" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
124 <param argument="--min_length" type="integer" value="" optional="true"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
125 label="Minimum length of sequences"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
126 help="Input how long the sequences has to be" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
127 <param argument="--desc" type="text" value=""
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
128 label="HTML description"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
129 help="Enter the HTML page description here" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
130 <section name="genome" title="Genome binning-specific options" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
131 <repeat name="thresholds" title="Min. completeness and max. contamination thresholds"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
132 help="Enter certain thresholds for min. completeness (Default %: 50,70,90) and certain thresholds for max. contamination (Default %: 5, 10), the program itself will transform it to %!" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
133 <param argument="--min_completeness" type="integer" value="" min="0" max="100" optional="true"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
134 label="Min. completeness threshold" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
135 <param argument="--max_contamination" type="integer" value="" min="0" max="100" optional="true"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
136 label="Max. contamination threshold" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
137 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
138 <param argument="--remove_genomes" type="data" format="tabular" optional="true"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
139 label="tsv file for genomes to remove"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
140 help="Input a tsv file with binid and type in each line. In the help section is an example. WARNING: IF THE LIST CONTAIN ALL GENOME THE PROGRAM WILL FAIL!" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
141 <conditional name="remove">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
142 <param name="is_select" type="select" label="Remove one or all genomes which are in the list?"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
143 help="Select yes and enter a keyword to remove certain type of genomes which are in the list. When all genomes in the list should remove also select yes and do not enter a keyword!">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
144 <option value="yes" selected="false">Yes</option>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
145 <option value="no" selected="true">No</option>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
146 </param>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
147 <when value="yes">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
148 <param argument="--keyword" type="text" value=""
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
149 label="Keyword for removing certain genomes"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
150 help="Input a keyword which should be match with binid giving in the file for removing genomes. When no keyword is giving the program remove all genomes which are in the list!" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
151 </when>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
152 <when value="no" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
153 </conditional>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
154 <param argument="--genome_coverage" type="data" format="tabular" optional="true"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
155 label="Genome coverages tsv file"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
156 help="Input a tsv file where the genome coverage is stated. Look at the help section to see how this file should look like!" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
157 </section>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
158 <section name="tox" title="taxonomic binning-specific option">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
159 <conditional name="ncbi">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
160 <param name="is_select" type="select" label="Want to use the NCBI database?"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
161 help="Select yes if you want to use the NCBI database to evaluate taxonomic binning">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
162 <option value="yes" selected="false">Yes</option>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
163 <option value="no" selected="true">No</option>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
164 </param>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
165 <when value="yes">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
166 <conditional name="input">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
167 <param name="is_select" type="select" label="Select how you want to use NCBI database"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
168 help="Either select manually input or data manager. For more help read the help of the type of the input you selected." >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
169 <option value="manually">Manually</option>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
170 <option value="data">Data manager</option>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
171 </param>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
172 <when value="manually">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
173 <param argument="--ncbi_dir" format="tabular" type="data" multiple="true"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
174 label="Input .dmp files"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
175 help="To use the NCBI database we need to provide followed .dmp files: nodes.dmp, names.dmp and merged.dmp. You can get the via download of this file **ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz** and unzip it!" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
176 </when>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
177 <when value="data" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
178 <param argument="--ncbi_dir" type="select"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
179 label="Assessing taxonomic binning"
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
180 help="Include the NCBI taxonomy database. For this you can use the data manager data_manager_fetch_ncbi_taxonomy which can be install via galaxy. For more help look at the help section at the bottom!" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
181 <options from_data_table="ncbi_taxonomy">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
182 <validator message="No NCBI database is available" type="no_options"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
183 </options>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
184 </param>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
185 </when>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
186 </conditional>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
187 </when>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
188 <when value="no"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
189 </conditional>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
190 </section>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
191 </inputs>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
192 <outputs>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
193 <data name="html" format="html" from_work_dir="output/index.html" label="${tool.name}: HTML" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
194 <data name="result" format="tabular" from_work_dir="output/results.tsv" label="${tool.name}: Results" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
195 <data name="metrics_genome" format="tabular" from_work_dir="output/genome_metrics_cami1.tsv" label="${tool.name}: Genome metrics" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
196 <data name="metrics_bin" format="tabular" from_work_dir="output/bin_metrics.tsv" label="${tool.name}: Bin metrics" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
197 </outputs>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
198 <tests>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
199 <test expect_num_outputs="4">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
200 <param name="gold_standard_file" value="gsa_mapping.binning" ftype="tabular" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
201 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
202 <param name="binning_files" value="elated_franklin_0" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
203 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
204 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
205 <param name="binning_files" value="goofy_hypatia_2" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
206 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
207 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
208 <param name="binning_files" value="naughty_carson_2" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
209 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
210 <output name="metrics_bin">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
211 <assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
212 <has_text text="genome_id" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
213 <has_text text="sample_id" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
214 </assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
215 </output>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
216 <output name="metrics_genome">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
217 <assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
218 <has_text text="precision_seq" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
219 <has_text text="total_length" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
220 </assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
221 </output>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
222 </test>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
223 <test expect_num_outputs="4">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
224 <param name="gold_standard_file" value="gsa_mapping.binning" ftype="tabular" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
225 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
226 <param name="binning_files" value="elated_franklin_0" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
227 <param name="labels" value="test1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
228 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
229 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
230 <param name="binning_files" value="goofy_hypatia_2" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
231 <param name="labels" value="test2" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
232 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
233 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
234 <param name="binning_files" value="naughty_carson_2" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
235 <param name="labels" value="test3" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
236 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
237 <param name="filter" value="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
238 <param name="min_length" value="200" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
239 <section name="genome" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
240 <repeat name="thresholds" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
241 <param name="max_contamination" value="2" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
242 <param name="min_completeness" value="50" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
243 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
244 <repeat name="thresholds" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
245 <param name="min_completeness" value="70" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
246 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
247 <repeat name="thresholds" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
248 <param name="min_completeness" value="90" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
249 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
250 <param name="genome_coverage" value="cami2_mouse_gut_average_genome_coverage.tsv" ftype="tabular" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
251 <param name="remove_genomes" value="unique_common.tsv" ftype="tabular" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
252 <conditional name="remove" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
253 <param name="is_select" value="yes" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
254 <param name="keyword" value="circular element" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
255 </conditional>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
256 </section>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
257 <section name="tox">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
258 <conditional name="ncbi">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
259 <param name="is_select" value="yes" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
260 <conditional name="input" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
261 <param name="is_select" value="manually" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
262 <param name="ncbi_dir" value="test-db/nodes.dmp,test-db/merged.dmp,test-db/names.dmp" ftype="tabular" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
263 </conditional>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
264 </conditional>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
265 </section>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
266 <output name="result">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
267 <assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
268 <has_text text="test1" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
269 <has_text text="test2" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
270 <has_text text="test3" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
271 </assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
272 </output>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
273 </test>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
274 <test expect_num_outputs="4">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
275 <param name="gold_standard_file" value="gsa_mapping.binning" ftype="tabular" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
276 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
277 <param name="binning_files" value="elated_franklin_0" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
278 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
279 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
280 <param name="binning_files" value="goofy_hypatia_2" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
281 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
282 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
283 <param name="binning_files" value="naughty_carson_2" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
284 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
285 <param name="desc" value="TEST FOR GALAXY" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
286 <section name="tox">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
287 <conditional name="ncbi">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
288 <param name="is_select" value="yes" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
289 <conditional name="input" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
290 <param name="is_select" value="data" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
291 <param name="ncbi_dir" value="test-db-tox" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
292 </conditional>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
293 </conditional>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
294 </section>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
295 <output name="html">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
296 <assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
297 <has_text text="TEST FOR GALAXY" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
298 </assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
299 </output>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
300 </test><test expect_num_outputs="4">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
301 <param name="gold_standard_file" value="test_gold.tsv" ftype="tabular" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
302 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
303 <param name="binning_files" value="test_binning.tsv" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
304 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
305 <repeat name="input_files">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
306 <param name="binning_files" value="test_binning2.tsv" ftype="tabular"/>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
307 </repeat>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
308 <section name="tox">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
309 <conditional name="ncbi">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
310 <param name="is_select" value="yes" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
311 <conditional name="input" >
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
312 <param name="is_select" value="data" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
313 <param name="ncbi_dir" value="test-db-tox" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
314 </conditional>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
315 </conditional>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
316 </section>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
317 <output name="metrics_bin">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
318 <assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
319 <has_text text="genome_id" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
320 <has_text text="sample_id" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
321 </assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
322 </output>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
323 <output name="metrics_genome">
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
324 <assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
325 <has_text text="precision_seq" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
326 <has_text text="total_length" n="1" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
327 </assert_contents>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
328 </output>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
329 </test>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
330 </tests>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
331 <help>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
332 <![CDATA[
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
333 .. class:: infomark
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
334
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
335 **What is AMBER**
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
336
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
337 AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets.
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
338
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
339 .. class:: infomark
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
340
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
341 **What it does**
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
342
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
343 AMBER calculate multiple metrics per bin and multiple metrics per sample. Each of them are provided then in results rankings, and comparative visualizations for assessing multiple programs or parameter effects.
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
344
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
345 For more information please visit `AMBER in GitHub <https://github.com/CAMI-challenge/AMBER>`_.
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
346
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
347 **Input**
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
348
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
349 AMBER use only 2 required inputs:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
350
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
351 - The golden standard file (biobox format)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
352
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
353 This file can be created via the add_length tool
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
354
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
355 .. class:: infomark
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
356
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
357 Example(tab separated)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
358
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
359 ::
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
360
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
361 @Version:0.9.1
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
362 @SampleID:CAMI_low
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
363
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
364 @@SEQUENCEID BINID _LENGTH
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
365 RL|S1|C10817 Sample18_57 20518
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
366 RL|S1|C11497 Sample22_57 37672
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
367 RL|S1|C6571 evo_1286_AP.033 69914
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
368 RL|S1|C10560 evo_1286_AP.033 995657
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
369 RL|S1|C13546 evo_1286_AP.033 626775
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
370
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
371 Note: This file looks similar to the binning files but the only different which is also is important is the length column.
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
372
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
373 - Multiple binning files (biobox format)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
374
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
375 Files can be created via the convert_to_biobox tool
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
376
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
377 .. class:: infomark
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
378
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
379 Example(tab separated):
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
380
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
381 ::
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
382
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
383 #CAMI Format for Binning
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
384 @Version:0.9.0
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
385 @SampleID:CAMI_low
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
386 @@SEQUENCEID BINID
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
387 RL|S1|C10 Bin_034
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
388 RL|S1|C100 Bin_023
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
389 RL|S1|C1000 Bin_034
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
390 RL|S1|C10000 Bin_019
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
391 RL|S1|C10002 Bin_035
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
392 RL|S1|C10004 Bin_035
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
393 RL|S1|C10008 Bin_034
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
394 RL|S1|C10011 Bin_035
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
395 RL|S1|C10012 Bin_013
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
396 RL|S1|C10014 Bin_035
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
397
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
398 There are also additional inputs which can be used:
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
399
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
400 - A genome list which should be removed(tabular format)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
401
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
402 .. class:: infomark
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
403
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
404 Example(tab separated):
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
405
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
406 ::
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
407
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
408 evo_1035930.029 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
409 1035930 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
410 evo_1035930.032 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
411 evo_1035930.011 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
412 evo_1286_AP.033 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
413 1286_AP common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
414 evo_1286_AP.026 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
415 evo_1286_AP.037 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
416 evo_1286_AP.008 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
417 1052944 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
418 1053058 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
419 1052947 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
420 evo_1049056.013 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
421 evo_1049056.031 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
422 evo_1049056.011 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
423 1049056 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
424 evo_1049056.039 common strain
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
425
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
426 Note: The first column contain the BINID and the second contain any kind of string. IMPORTANT: The argument where to state a keyword has to match to the anything in the second column to filter these kind of genomes out. If there is no keyword stated it can happen if the remove list contain all genomes which should be used then AMBER will fail since there are no genomes left to use!
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
427
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
428 - Genome coverage file (tabular format)
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
429
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
430 .. class:: infomark
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
431
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
432 Example(tab separated):
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
433
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
434 ::
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
435
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
436 @SampleID:gsa_pooled
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
437 @@GENOMEID COVERAGE
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
438 4378740.0 82.85111527272727
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
439 4378740.1 27.159305090909097
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
440 denovo10559.0 2.1596957142857143
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
441 179927.0 1.6946866666666667
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
442 denovo8373.1 2.07144
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
443 136604.0 9.150489565217391
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
444 denovo8373.0 1.1413460000000002
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
445 269378.0 8.051563333333332
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
446 190114.0 18.253119629629627
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
447 228140.0 3.078681818181818
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
448 135956.0 121.52672015625001
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
449 259846.0 12.298210588235296
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
450 162576.0 9.57867191489362
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
451 184966.0 14.461031521739134
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
452
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
453 There is also an option to include the NCBI database in AMBER. This can be used when including the link which is stated in the data manager: **data_manager_fetch_ncbi_taxonomy**. This data manager download the current version of the database and store all files for you. If there are questions about data manager maybe have a look at this `Tutorial <https://usegalaxy.eu/training-material/topics/admin/tutorials/reference-genomes/tutorial.html>`_.
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
454
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
455 **Output**
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
456
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
457 AMBER will output 3 tsv files where each metrics value is stated. The important output is the HTML file where all data are included and also can be visualized with certain plots!
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
458
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
459 **Additional information**
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
460
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
461 The package **Bokeh** will create warnings which can be ignored since the only tell you that certain functions in the code are swapped with the new functions. AMBER was tested with the stated version of **Bokeh** and with the newest version of it and both generate the same output!
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
462 ]]>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
463 </help>
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
464 <expand macro="citations" />
6c71acde9d52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96
iuc
parents:
diff changeset
465 </tool>