Mercurial > repos > bgruening > gfastats
annotate gfastats.xml @ 7:3ef480892a9f draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
author | bgruening |
---|---|
date | Fri, 23 Dec 2022 20:00:51 +0000 |
parents | 690c2caa367e |
children |
rev | line source |
---|---|
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
1 <tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
2 <description>the swiss army knife for genome assembly</description> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
3 <macros> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
4 <import>macros.xml</import> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
5 </macros> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
6 <expand macro="requirements" /> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
7 <expand macro="biotools"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
8 <version_command>gfastats --version</version_command> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
9 <command detect_errors="exit_code"><![CDATA[ |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
10 gfastats |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
11 '$input_file' |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
12 #if $mode_condition.selector == 'statistics' |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
13 #if $mode_condition.statistics_condition.selector == 'assembly' |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
14 $mode_condition.statistics_condition.expected_genomesize |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
15 #end if |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
16 #end if |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
17 #if $target_condition.target_option == 'true' |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
18 $target_condition.target_sequence |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
19 #if $target_condition.include_bed |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
20 --include-bed $target_condition.include_bed |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
21 #end if |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
22 #if $target_condition.exclude_bed |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
23 --exclude-bed $target_condition.exclude_bed |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
24 #end if |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
25 #end if |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
26 #if $mode_condition.selector == 'manipulation' |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
27 #if $mode_condition.swiss_army_knife |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
28 -k $mode_condition.swiss_army_knife |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
29 #end if |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
30 #if $mode_condition.sort |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
31 --sort $mode_condition.sort |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
32 #end if |
1
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
33 #if $mode_condition.homopolymer_compress |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
34 --homopolymer-compress $mode_condition.homopolymer_compress |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
35 #end if |
6
690c2caa367e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
4
diff
changeset
|
36 $mode_condition.discover_paths |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
37 -o dataset.$mode_condition.output_condition.out_format |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
38 #if $mode_condition.output_condition.out_format in ['fasta','fasta.gz'] |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
39 #if $mode_condition.output_condition.line_length |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
40 --line-length $mode_condition.output_condition.line_length |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
41 #end if |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
42 #end if |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
43 #if $mode_condition.output_condition.out_format in ['gfa','gfa.gz'] |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
44 #if $mode_condition.output_condition.terminal_overlaps_condition.terminal_overlaps_select == 'yes': |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
45 --discover-terminal-overlaps $mode_condition.output_condition.terminal_overlaps_condition.terminal_overlaps_length |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
46 #end if |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
47 #end if |
1
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
48 #else if $mode_condition.selector == "statistics" |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
49 #if $mode_condition.statistics_condition.selector == 'size' |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
50 --out-size $mode_condition.statistics_condition.out_size |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
51 #else if $mode_condition.statistics_condition.selector == 'coordinates' |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
52 --out-coord $mode_condition.statistics_condition.out_coord |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
53 #else if $mode_condition.statistics_condition.selector == 'assembly' |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
54 --nstar-report |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
55 #else |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
56 --seq-report |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
57 $mode_condition.statistics_condition.out_sequence |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
58 #end if |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
59 $mode_condition.locale |
3
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
60 $mode_condition.discover_paths |
1
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
61 $mode_condition.tabular > '$stats' |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
62 #else |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
63 --agp-to-path $mode_condition.agp_to_path |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
64 $mode_condition.discover_paths |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
65 -o dataset.gfa |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
66 #end if |
3
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
67 --threads \${GALAXY_SLOTS:-8} |
1
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
68 #if $mode_condition.selector == 'manipulation' or $mode_condition.selector == 'scaffolding' |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
69 && mv dataset* output_dataset |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
70 #end if |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
71 ]]></command> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
72 <inputs> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
73 <param name="input_file" argument="--fasta" type="data" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
74 format="fasta,fastq,fastqsanger,gfa1,fasta.gz,fastq.gz,fastqsanger.gz,gfa1.gz" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
75 label="Input file"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
76 <conditional name="target_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
77 <param name="target_option" type="select" label="Specify target sequences"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
78 <option value="false">Disabled</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
79 <option value="true">Enabled</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
80 </param> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
81 <when value="false"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
82 <when value="true"> |
2
ad1149b4f795
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents:
1
diff
changeset
|
83 <param name="target_sequence" type="text" value="" label="Target sequence" optional="true" help="Target specific sequence by header, optionally with coordinates: header[:start-end]"> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
84 <sanitizer invalid_char=""> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
85 <valid initial="string.digits,string.letters"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
86 <add value=":"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
87 <add value="-"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
88 <add value="_"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
89 <add value="|"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
90 <add value=" "/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
91 </valid> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
92 </sanitizer> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
93 <validator type="regex">[0-9A-Za-z:-_| ]+</validator> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
94 </param> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
95 <param argument="--include-bed" type="data" optional="true" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
96 format="bed" label="Include specific intervals" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
97 help="Generates output on a subset list of headers or coordinates |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
98 in 0-based bed format. It can be combined with --exclude-bed. Optional."/> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
99 <param argument="--exclude-bed" type="data" format="bed" optional="true" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
100 label="Exclude specific intervals" |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
101 help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed. Optional."/> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
102 </when> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
103 <when value="false"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
104 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
105 <conditional name="mode_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
106 <param name="selector" type="select" label="Tool mode"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
107 <option value="statistics">Summary statistics generation</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
108 <option value="manipulation">Genome assembly manipulation</option> |
1
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
109 <option value="scaffolding">Scaffolding</option> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
110 </param> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
111 <when value="manipulation"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
112 <param argument="--swiss-army-knife" type="data" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
113 format="text" label="SAK input file" optional="true" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
114 help="Set of instructions provided as an ordered list"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
115 <conditional name="output_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
116 <param argument="--out-format" type="select" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
117 label="Output format" help="Outputs selected sequences."> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
118 <option value="fasta">FASTA</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
119 <option value="fasta.gz">FASTA.gz</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
120 <option value="fastq">FASTQ</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
121 <option value="fastq.gz" selected="true">FASTQ.gz</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
122 <option value="gfa">GFA</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
123 <option value="gfa.gz">GFA.gz</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
124 </param> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
125 <when value="fasta"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
126 <expand macro="length_macro"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
127 </when> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
128 <when value="fasta.gz"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
129 <expand macro="length_macro"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
130 </when> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
131 <when value="fastq"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
132 <when value="fastq.gz"/> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
133 <when value="gfa"> |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
134 <expand macro="terminal_overlaps_macro"/> |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
135 </when> |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
136 <when value="gfa.gz"> |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
137 <expand macro="terminal_overlaps_macro"/> |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
138 </when> |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
139 </conditional> |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
140 <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space, an assembly |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
141 is a collection of segments and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence." /> |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
142 <param argument="--sort" type="select" label="Sort sequences" help="Specify how to sort the sequences. Ascending/descending uses the sequence/path header."> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
143 <option value="" selected="true">Disabled</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
144 <option value="ascending">Ascending</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
145 <option value="descending">Descending</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
146 <option value="largest">Largest</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
147 <option value="smallest">Smallest</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
148 </param> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
149 <param argument="--homopolymer-compress" type="integer" min="0" value="" optional="true" label="Homopolymer compression" help="Compress all the homopolymers in the input above the given threshold." /> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
150 </when> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
151 <when value="statistics"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
152 <conditional name="statistics_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
153 <param name="selector" type="select" label="Report mode"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
154 <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
155 <option value="size">Scaffold, contig or gap sizes (--out-size)</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
156 <option value="coordinates">AGP, contig or gap coordinates (--out-coord)</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
157 <option value="sequence">Sequence statistics (--seq-report)</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
158 </param> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
159 <when value="size"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
160 <param argument="--out-size" type="select" label="Feature for reporting sizes" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
161 help="Generate a tabular file with the sequence sizes"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
162 <option value="s">Scaffolds</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
163 <option value="c">Contigs</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
164 <option value="g">Gaps</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
165 </param> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
166 </when> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
167 <when value="coordinates"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
168 <param argument="--out-coord" type="select" label="BED coordinares feature" |
3
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
169 help="Generates bed coordinates of given feature. Default: AGP"> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
170 <option value="a">AGP</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
171 <option value="c">Contigs</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
172 <option value="g">Gaps</option> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
173 </param> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
174 </when> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
175 <when value="assembly"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
176 <param name="expected_genomesize" type="integer" min="0" optional="true" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
177 label="Expected genome size" help="Estimated genome size. This parameter is optional, but required for NG* statistics."/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
178 </when> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
179 <when value="sequence"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
180 <param argument="--out-sequence" type="boolean" truevalue="--out-sequence" falsevalue="" checked="false" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
181 label="Report actual sequence" help="It reports also the actual sequence"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
182 </when> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
183 </conditional> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
184 <param argument="--locale" type="boolean" truevalue="--locale en_US.UTF-8" falsevalue="" checked="true" |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
185 label="Thousands separator in output" help="Use commas for thousands separator in output?"/> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
186 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true" |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
187 label="Tabular-format output" help="Generate output in tabular format"/> |
3
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
188 <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
189 is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" /> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
190 </when> |
1
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
191 <when value="scaffolding"> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
192 <param argument="--agp-to-path" type="data" format="agp" label="Input AGP file" help="Integrate the AGP information into the assembly graph as paths. The scaffolding information is converted into paths through the graph" /> |
3
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
193 <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly |
1
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
194 is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" /> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
195 </when> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
196 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
197 </inputs> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
198 <outputs> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
199 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
200 <filter>mode_condition['selector'] == 'statistics'</filter> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
201 <change_format> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
202 <when input="tabular" value="false" format="text"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
203 </change_format> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
204 </data> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
205 <data name="output" format="fastq" from_work_dir="output_dataset" label="${tool.name} on ${on_string}: edited sequences"> |
1
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
206 <filter>mode_condition['selector'] == 'manipulation' or mode_condition['selector'] == 'scaffolding'</filter> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
207 <change_format> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
208 <when input="mode_condition.output_condition.out_format" value="fasta" format="fasta"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
209 <when input="mode_condition.output_condition.out_format" value="fasta.gz" format="fasta.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
210 <when input="mode_condition.output_condition.out_format" value="fastq" format="fastq"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
211 <when input="mode_condition.output_condition.out_format" value="fastq.gz" format="fastq.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
212 <when input="mode_condition.output_condition.out_format" value="gfa" format="gfa1"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
213 <when input="mode_condition.output_condition.out_format" value="gfa.gz" format="gfa1.gz"/> |
1
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
214 <when input="mode_condition.selector" value="scaffolding" format="gfa1"/> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
215 </change_format> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
216 </data> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
217 </outputs> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
218 <tests> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
219 <!--Test 01 --> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
220 <test expect_num_outputs="1"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
221 <param name="input_file" value="dataset_01.fastq.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
222 <conditional name="mode_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
223 <param name="selector" value="manipulation"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
224 <param name="swiss_army_knife" value="swiss_army.sak"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
225 <conditional name="output_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
226 <param name="out_format" value="fasta.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
227 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
228 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
229 <output name="output" value="test_01.fasta.gz" ftype="fasta.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
230 </test> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
231 <!--Test 02 --> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
232 <test expect_num_outputs="1"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
233 <param name="input_file" value="dataset_01.fastq.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
234 <conditional name="target_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
235 <param name="target_condition" value="true"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
236 <param name="target_sequence" value="S1_1"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
237 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
238 <conditional name="mode_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
239 <param name="selector" value="statistics"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
240 <conditional name="statistics_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
241 <param name="selector" value="size"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
242 <param name="out_size" value="c"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
243 </conditional> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
244 <param name="locale" value="false"/> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
245 </conditional> |
4
3fba9c77550a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents:
3
diff
changeset
|
246 <output name="stats" ftype="tabular"> |
3fba9c77550a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents:
3
diff
changeset
|
247 <assert_contents> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
248 <has_text text="S1_1.1	8550" /> |
4
3fba9c77550a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents:
3
diff
changeset
|
249 </assert_contents> |
3fba9c77550a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents:
3
diff
changeset
|
250 </output> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
251 </test> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
252 <!--Test 03 --> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
253 <test expect_num_outputs="1"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
254 <param name="input_file" value="dataset_02.fasta.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
255 <conditional name="mode_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
256 <param name="selector" value="statistics"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
257 <conditional name="statistics_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
258 <param name="selector" value="sequence"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
259 </conditional> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
260 <param name="locale" value="false"/> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
261 </conditional> |
4
3fba9c77550a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents:
3
diff
changeset
|
262 <output name="stats" ftype="tabular"> |
3fba9c77550a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents:
3
diff
changeset
|
263 <assert_contents> |
3fba9c77550a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents:
3
diff
changeset
|
264 <has_text text="23029444-6c7d-4f19-ac8e-4c0a478589d0.1		476	198	68	93	117	33.82	0" /> |
3fba9c77550a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents:
3
diff
changeset
|
265 </assert_contents> |
3fba9c77550a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents:
3
diff
changeset
|
266 </output> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
267 </test> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
268 <!--Test 04 --> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
269 <test expect_num_outputs="1"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
270 <param name="input_file" value="dataset_03.fasta"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
271 <conditional name="mode_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
272 <param name="selector" value="statistics"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
273 <conditional name="statistics_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
274 <param name="selector" value="assembly"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
275 <param name="expected_genomesize" value="600000"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
276 </conditional> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
277 <param name="locale" value="false"/> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
278 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
279 <output name="stats" value="test_04_stats.tabular" ftype="tabular"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
280 </test> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
281 <!--Test 05 --> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
282 <test expect_num_outputs="1"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
283 <param name="input_file" value="dataset_04.gfa"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
284 <conditional name="mode_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
285 <param name="selector" value="statistics"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
286 <conditional name="statistics_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
287 <param name="selector" value="coordinates"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
288 <param name="out_coord" value="a"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
289 </conditional> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
290 <param name="locale" value="false"/> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
291 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
292 <output name="stats" value="test_05_stats.tabular" ftype="tabular"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
293 </test> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
294 <!--Test 06 --> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
295 <test expect_num_outputs="1"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
296 <param name="input_file" value="dataset_04.gfa"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
297 <conditional name="mode_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
298 <param name="selector" value="manipulation"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
299 <conditional name="output_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
300 <param name="out_format" value="fasta.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
301 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
302 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
303 <output name="output" value="test_06.fasta.gz" ftype="fasta.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
304 </test> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
305 <!--Test 07 --> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
306 <test expect_num_outputs="1"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
307 <param name="input_file" value="dataset_03.fasta"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
308 <conditional name="mode_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
309 <param name="selector" value="statistics"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
310 <conditional name="statistics_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
311 <param name="selector" value="assembly"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
312 </conditional> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
313 <param name="locale" value="false"/> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
314 <param name="tabular" value="false"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
315 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
316 <output name="stats" value="test_07_stats.tabular" ftype="tabular"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
317 </test> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
318 <!--Test 08 --> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
319 <test expect_num_outputs="1"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
320 <param name="input_file" value="dataset_01.fastq.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
321 <conditional name="mode_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
322 <param name="selector" value="manipulation"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
323 <conditional name="output_condition"> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
324 <param name="out_format" value="fasta.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
325 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
326 <param name="sort" value="ascending"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
327 </conditional> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
328 <output name="output" value="test_08.fasta.gz" ftype="fasta.gz"/> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
329 </test> |
1
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
330 <!--Test 09 --> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
331 <test expect_num_outputs="1"> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
332 <param name="input_file" value="dataset_03.fasta"/> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
333 <conditional name="mode_condition"> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
334 <param name="selector" value="manipulation"/> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
335 <conditional name="output_condition"> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
336 <param name="out_format" value="fasta.gz"/> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
337 </conditional> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
338 <param name="homopolymer_compress" value="10"/> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
339 </conditional> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
340 <output name="output" value="test_09.fasta.gz" ftype="fasta.gz"/> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
341 </test> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
342 <!--Test 10 --> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
343 <test expect_num_outputs="1"> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
344 <param name="input_file" value="dataset_04.gfa"/> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
345 <conditional name="mode_condition"> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
346 <param name="selector" value="scaffolding"/> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
347 <param name="agp_to_path" value="dataset_05.agp"/> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
348 <param name="discover_paths" value="true"/> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
349 </conditional> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
350 <output name="output" value="test_10.gfa" ftype="gfa1"/> |
2b8b4cacb83d
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents:
0
diff
changeset
|
351 </test> |
2
ad1149b4f795
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents:
1
diff
changeset
|
352 <!--Test 11 --> |
ad1149b4f795
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents:
1
diff
changeset
|
353 <test expect_num_outputs="1"> |
ad1149b4f795
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents:
1
diff
changeset
|
354 <param name="input_file" value="dataset_03.fasta"/> |
ad1149b4f795
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents:
1
diff
changeset
|
355 <conditional name="target_condition"> |
ad1149b4f795
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents:
1
diff
changeset
|
356 <param name="target_option" value="true"/> |
ad1149b4f795
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents:
1
diff
changeset
|
357 <param name="include_bed" value="regions.bed"/> |
ad1149b4f795
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents:
1
diff
changeset
|
358 </conditional> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
359 <conditional name="mode_condition"> |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
360 <param name="locale" value="false"/> |
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
361 </conditional> |
2
ad1149b4f795
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents:
1
diff
changeset
|
362 <output name="stats" value="test_11_stats.tabular" ftype="tabular"/> |
ad1149b4f795
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents:
1
diff
changeset
|
363 </test> |
3
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
364 <!--Test 12 --> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
365 <test expect_num_outputs="1"> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
366 <param name="input_file" value="dataset_04.gfa"/> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
367 <conditional name="mode_condition"> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
368 <param name="selector" value="statistics"/> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
369 <conditional name="statistics_condition"> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
370 <param name="selector" value="assembly"/> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
371 </conditional> |
7
3ef480892a9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
bgruening
parents:
6
diff
changeset
|
372 <param name="locale" value="false"/> |
3
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
373 <param name="tabular" value="false"/> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
374 <param name="discover_paths" value="true"/> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
375 </conditional> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
376 <output name="stats" value="test_12_stats.tabular" ftype="tabular"/> |
8ccbf07a5433
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents:
2
diff
changeset
|
377 </test> |
0
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
378 </tests> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
379 <help><![CDATA[ |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
380 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
381 .. class:: infomark |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
382 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
383 **Purpose** |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
384 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
385 gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless format conversion. |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
386 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
387 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
388 .. class:: infomark |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
389 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
390 **Metrics details** |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
391 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
392 Typical fast* metrics include: |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
393 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
394 - Scaffold, contig and gap size |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
395 - Number of scaffolds, contigs and gaps |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
396 - Total length of scaffolds, contigs and gaps |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
397 - Scaffold, contig, gap N50 and statistics (full N*/NG* statistics with the --nstar-report flag) |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
398 - Area under the curve (AuN/AuNG) values for scaffolds, contigs and gaps |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
399 - Average scaffold, contig, gap size |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
400 - Largest scaffold, contig and gap |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
401 - Base composition and GC content |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
402 - Soft-masked base counts (lower case bases) |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
403 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
404 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
405 Typical gfa metrics include: |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
406 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
407 - Number of nodes and edges |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
408 - Average degree |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
409 - Number of connected components, and length of the largets connected component |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
410 - Number of dead ends |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
411 - Number of disconnected components, and their total length |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
412 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
413 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
414 .. class:: infomark |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
415 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
416 **Assembly manipulation** |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
417 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
418 gfastats allows extensive assembly manipulation at the sequence level. Manipulation is achieved using a set of instructions provided as an ordered list in a file to the option **swiss army knife**. See the `instruction wiki <https://github.com/vgl-hub/gfastats/tree/main/instructions>`_ for a full list of instructions. |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
419 |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
420 ]]></help> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
421 <expand macro="citations" /> |
5799092ffdff
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff
changeset
|
422 </tool> |