Mercurial > repos > bgruening > gfastats

annotate gfastats.xml @ 6:690c2caa367e 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 10ccc47885ce71e602d66e157bd475f1facbd042
author bgruening
date Mon, 05 Dec 2022 12:20:31 +0000
parents 3fba9c77550a
children 3ef480892a9f
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
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
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.out_format == 'fasta'
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
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
42 #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
43 #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
44 --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
45 #end if
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
46 #end if
1
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
47 #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
48 #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
49 --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
50 #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
51 --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
52 #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
53 --nstar-report
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
54 #else
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
55 --seq-report
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
56 $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
57 #end if
3
8ccbf07a5433 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents: 2
diff changeset
58 $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
59 $mode_condition.tabular > '$stats'
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
60 #else
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
61 --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
62 $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
63 -o dataset.gfa
0
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
64 #end if
3
8ccbf07a5433 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents: 2
diff changeset
65 --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
66 #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
67 && mv dataset* output_dataset
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
68 #end if
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
69 ]]></command>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
70 <inputs>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
71 <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
72 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
73 label="Input file"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
74 <conditional name="target_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
75 <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
76 <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
77 <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
78 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
79 <when value="false"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
80 <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
81 <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
82 <sanitizer invalid_char="">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
83 <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
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 <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 </valid>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
90 </sanitizer>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
91 <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
92 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
93 <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
94 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
95 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
96 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
97 <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
98 label="Exclude specific intervals"
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
99 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
100 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
101 <when value="false"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
102 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
103 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
104 <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
105 <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
106 <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
107 <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
108 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
109 <when value="manipulation">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
110 <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
111 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
112 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
113 <conditional name="output_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
114 <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
115 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
116 <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
117 <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
118 <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
119 <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
120 <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
121 <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
122 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
123 <when value="fasta">
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="fasta.gz">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
127 <expand macro="length_macro"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
128 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
129 <when value="fastq"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
130 <when value="fastq.gz"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
131 <when value="gfa"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
132 <when value="gfa.gz"/>
6
690c2caa367e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 4
diff changeset
133 </conditional>
690c2caa367e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 4
diff changeset
134 <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
690c2caa367e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 4
diff changeset
135 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
136 <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
137 <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
138 <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
139 <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
140 <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
141 <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
142 </param>
1
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
143 <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
144 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
145 <when value="statistics">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
146 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
147 <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
148 <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
149 <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
150 <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
151 <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
152 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
153 <when value="size">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
154 <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
155 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
156 <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
157 <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
158 <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
159 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
160 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
161 <when value="coordinates">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
162 <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
163 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
164 <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
165 <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
166 <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
167 </param>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
168 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
169 <when value="assembly">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
170 <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
171 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
172 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
173 <when value="sequence">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
174 <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
175 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
176 </when>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
177 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
178 <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
179 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
180 <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
181 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
182 </when>
1
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
183 <when value="scaffolding">
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
184 <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
185 <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
186 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
187 </when>
0
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
188 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
189 </inputs>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
190 <outputs>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
191 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
192 <filter>mode_condition['selector'] == 'statistics'</filter>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
193 <change_format>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
194 <when input="tabular" value="false" format="text"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
195 </change_format>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
196 </data>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
197 <data name="output" format="fastq" from_work_dir="output_dataset" label="${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
198 <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
199 <change_format>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
200 <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
201 <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
202 <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
203 <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
204 <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
205 <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
206 <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
207 </change_format>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
208 </data>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
209 </outputs>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
210 <tests>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
211 <!--Test 01 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
212 <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
213 <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
214 <conditional name="target_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
215 <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
216 <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
217 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
218 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
219 <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
220 <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
221 <conditional name="output_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
222 <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
223 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
224 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
225 <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
226 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
227 <!--Test 02 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
228 <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
229 <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
230 <conditional name="target_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
231 <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
232 <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
233 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
234 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
235 <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
236 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
237 <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
238 <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
239 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
240 </conditional>
4
3fba9c77550a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents: 3
diff changeset
241 <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
242 <assert_contents>
3fba9c77550a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents: 3
diff changeset
243 <has_text text="S1_76.1&#009;9445" />
3fba9c77550a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents: 3
diff changeset
244 </assert_contents>
3fba9c77550a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents: 3
diff changeset
245 </output>
0
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 03 -->
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_02.fasta.gz"/>
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="sequence"/>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
254 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
255 </conditional>
4
3fba9c77550a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents: 3
diff changeset
256 <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
257 <assert_contents>
3fba9c77550a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents: 3
diff changeset
258 <has_text text="23029444-6c7d-4f19-ac8e-4c0a478589d0.1&#009;&#009;476&#009;198&#009;68&#009;93&#009;117&#009;33.82&#009;0" />
3fba9c77550a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents: 3
diff changeset
259 </assert_contents>
3fba9c77550a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit b0a88a5b8e4870f681f572f533a8091b3caee38c
bgruening
parents: 3
diff changeset
260 </output>
0
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
261 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
262 <!--Test 04 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
263 <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
264 <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
265 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
266 <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
267 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
268 <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
269 <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
270 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
271 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
272 <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
273 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
274 <!--Test 05 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
275 <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
276 <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
277 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
278 <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
279 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
280 <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
281 <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
282 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
283 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
284 <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
285 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
286 <!--Test 06 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
287 <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
288 <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
289 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
290 <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
291 <conditional name="output_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
292 <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
293 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
294 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
295 <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
296 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
297 <!--Test 07 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
298 <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
299 <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
300 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
301 <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
302 <conditional name="statistics_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
303 <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
304 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
305 <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
306 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
307 <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
308 </test>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
309 <!--Test 08 -->
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
310 <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
311 <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
312 <conditional name="mode_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
313 <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
314 <conditional name="output_condition">
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
315 <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
316 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
317 <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
318 </conditional>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
319 <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
320 </test>
1
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
321 <!--Test 09 -->
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
322 <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
323 <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
324 <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
325 <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
326 <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
327 <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
328 </conditional>
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
329 <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
330 </conditional>
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
331 <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
332 </test>
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
333 <!--Test 10 -->
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
334 <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
335 <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
336 <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
337 <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
338 <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
339 <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
340 </conditional>
2b8b4cacb83d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
341 <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
342 </test>
2
ad1149b4f795 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents: 1
diff changeset
343 <!--Test 11 -->
ad1149b4f795 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents: 1
diff changeset
344 <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
345 <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
346 <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
347 <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
348 <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
349 </conditional>
ad1149b4f795 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents: 1
diff changeset
350 <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
351 </test>
3
8ccbf07a5433 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents: 2
diff changeset
352 <!--Test 12 -->
8ccbf07a5433 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents: 2
diff changeset
353 <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
354 <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
355 <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
356 <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
357 <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
358 <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
359 </conditional>
8ccbf07a5433 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents: 2
diff changeset
360 <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
361 <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
362 </conditional>
8ccbf07a5433 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
parents: 2
diff changeset
363 <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
364 </test>
0
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
365 </tests>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
366 <help><![CDATA[
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 .. class:: infomark
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 **Purpose**
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
371
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
372 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
373
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
374
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
375 .. class:: infomark
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
376
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
377 **Metrics details**
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
378
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
379 Typical fast* metrics include:
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 - 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
382 - 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
383 - 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
384 - 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
385 - 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
386 - 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
387 - 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
388 - 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
389 - 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
390
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 gfa 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 - 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
395 - Average degree
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
396 - 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
397 - Number of dead ends
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
398 - 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
399
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
400
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
401 .. class:: infomark
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
402
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
403 **Assembly manipulation**
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 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
406
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
407 ]]></help>
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
408 <expand macro="citations" />
5799092ffdff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
409 </tool>