Mercurial > repos > bgruening > gfastats

annotate gfastats.xml @ 1:2b8b4cacb83d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
author bgruening
date Mon, 25 Apr 2022 09:38:18 +0000
parents 5799092ffdff
children ad1149b4f795
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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 $mode_condition.homopolymer_compress
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
35 #end if
0
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
36 -o dataset.$mode_condition.output_condition.out_format
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
37 #if $mode_condition.output_condition.out_format == 'fasta'
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
38 #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
39 --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
40 #end if
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
41 #else if $mode_condition.output_condition.out_format == 'fasta.gz'
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
42 #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
43 --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
44 #end if
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
45 #end if
1
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
46 #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
47 #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
48 --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
49 #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
50 --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
51 #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
52 --nstar-report
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
53 #else
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
54 --seq-report
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
55 $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
56 #end if
1
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
57 $mode_condition.tabular > '$stats'
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
58 #else
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
59 --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
60 $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
61 -o dataset.gfa
0
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
62 #end if
1
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
63 #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
64 && mv dataset* output_dataset
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
65 #end if
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
66 ]]></command>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
67 <inputs>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
68 <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
69 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
70 label="Input file"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
71 <conditional name="target_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
72 <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
73 <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
74 <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
75 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
76 <when value="false"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
77 <when value="true">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
78 <param name="target_sequence" type="text" value="" label="Target sequence" help="Target specific sequence by header, optionally with coordinates: header[:start-end]">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
79 <sanitizer invalid_char="">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
80 <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
81 <add value=":"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
82 <add value="-"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
83 <add value="_"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
84 <add value="|"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
85 <add value=" "/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
86 </valid>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
87 </sanitizer>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
88 <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
89 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
90 <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
91 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
92 help="Generates output on a subset list of headers or coordinates
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
93 in 0-based bed format. It can be combined with --exclude-bed. Optional"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
94 <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
95 label="Exclude specific intervals"
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
96 help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed Optional"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
97 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
98 <when value="false"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
99 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
100 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
101 <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
102 <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
103 <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
104 <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
105 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
106 <when value="manipulation">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
107 <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
108 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
109 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
110 <conditional name="output_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
111 <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
112 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
113 <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
114 <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
115 <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
116 <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
117 <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
118 <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
119 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
120 <when value="fasta">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
121 <expand macro="length_macro"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
122 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
123 <when value="fasta.gz">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
124 <expand macro="length_macro"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
125 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
126 <when value="fastq"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
127 <when value="fastq.gz"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
128 <when value="gfa"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
129 <when value="gfa.gz"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
130 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
131 <param argument="--sort" type="select" label="Sort sequences" help="Specify how to sort the sequences. Ascending/descending used the sequence/path header.">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
132 <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
133 <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
134 <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
135 <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
136 <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
137 </param>
1
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
138 <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 threshhold" />
0
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
139 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
140 <when value="statistics">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
141 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
142 <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
143 <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
144 <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
145 <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
146 <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
147 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
148 <when value="size">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
149 <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
150 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
151 <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
152 <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
153 <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
154 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
155 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
156 <when value="coordinates">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
157 <param argument="--out-coord" type="select" label="BED coordinares feature"
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
158 help="Generates bed coordinates of given feature. Default: agp">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
159 <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
160 <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
161 <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
162 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
163 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
164 <when value="assembly">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
165 <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
166 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
167 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
168 <when value="sequence">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
169 <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
170 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
171 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
172 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
173 <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
174 label="Tabular-format output" help="Generate output in tabular format"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
175 </when>
1
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
176 <when value="scaffolding">
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
177 <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" />
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
178 <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
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
179 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
180 </when>
0
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
181 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
182 </inputs>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
183 <outputs>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
184 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
185 <filter>mode_condition['selector'] == 'statistics'</filter>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
186 <change_format>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
187 <when input="tabular" value="false" format="text"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
188 </change_format>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
189 </data>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
190 <data name="output" format="fastq" from_work_dir="output_dataset" label="${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
191 <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
192 <change_format>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
193 <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
194 <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
195 <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
196 <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
197 <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
198 <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
199 <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
200 </change_format>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
201 </data>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
202 </outputs>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
203 <tests>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
204 <!--Test 01 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
205 <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
206 <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
207 <conditional name="target_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
208 <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
209 <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
210 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
211 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
212 <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
213 <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
214 <conditional name="output_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
215 <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
216 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
217 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
218 <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
219 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
220 <!--Test 02 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
221 <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
222 <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
223 <conditional name="target_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
224 <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
225 <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
226 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
227 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
228 <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
229 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
230 <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
231 <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
232 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
233 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
234 <output name="stats" value="test_02_stats.tabular" ftype="tabular"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
235 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
236 <!--Test 03 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
237 <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
238 <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
239 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
240 <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
241 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
242 <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
243 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
244 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
245 <output name="stats" value="test_03_stats.tabular" ftype="tabular"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
246 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
247 <!--Test 04 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
248 <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
249 <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
250 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
251 <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
252 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
253 <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
254 <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
255 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
256 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
257 <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
258 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
259 <!--Test 05 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
260 <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
261 <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
262 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
263 <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
264 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
265 <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
266 <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
267 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
268 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
269 <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
270 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
271 <!--Test 06 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
272 <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
273 <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
274 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
275 <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
276 <conditional name="output_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
277 <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
278 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
279 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
280 <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
281 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
282 <!--Test 07 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
283 <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
284 <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
285 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
286 <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
287 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
288 <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
289 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
290 <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
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_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
293 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
294 <!--Test 08 -->
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_01.fastq.gz"/>
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 <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
303 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
304 <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
305 </test>
1
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
306 <!--Test 09 -->
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
307 <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
308 <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
309 <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
310 <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
311 <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
312 <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
313 </conditional>
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
314 <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
315 </conditional>
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
316 <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
317 </test>
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
318 <!--Test 10 -->
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
319 <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
320 <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
321 <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
322 <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
323 <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
324 <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
325 </conditional>
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
326 <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
327 </test>
0
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
328 </tests>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
329 <help><![CDATA[
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
330
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
331 .. class:: infomark
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
332
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
333 **Purpose**
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
334
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
335 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
336
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
337
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
338 .. class:: infomark
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
339
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
340 **Metrics details**
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
341
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
342 Typical fast* metrics include:
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
343
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
344 - 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
345 - 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
346 - 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
347 - 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
348 - 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
349 - 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
350 - 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
351 - 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
352 - 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
353
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
354
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
355 Typical gfa metrics include:
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
356
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
357 - 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
358 - Average degree
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
359 - 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
360 - Number of dead ends
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
361 - 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
362
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
363
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
364 .. class:: infomark
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
365
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
366 **Assembly manipulation**
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
367
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
368 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
369
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
370 ]]></help>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
371 <expand macro="citations" />
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
372 </tool>