Mercurial > repos > iuc > funannotate_sort

annotate funannotate_sort.xml @ 7:54961e026fe4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 90acc0e23230b2e29e1d38a90bca4009c84c7e67
author iuc
date Fri, 20 Oct 2023 10:09:10 +0000
parents 998b719a94cb
children 520e30695ec3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
1 <tool id="funannotate_sort" name="Sort assembly" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
2 <description></description>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
3 <macros>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
5 </macros>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
6 <requirements>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
7 <expand macro="requirements" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
8 </requirements>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
9 <version_command>funannotate check --show-versions</version_command>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
10 <command><![CDATA[
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
11 funannotate sort
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
12 --input '${input}'
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
13 --out '${output}'
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
14 --base '${base}'
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
15 --minlen ${minlen}
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
16 ]]></command>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
17 <inputs>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
18 <param argument="--input" type="data" format="fasta" label="Assembly to sort" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
19
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
20 <param argument="--base" type="text" value="scaffold" label="Base name to relabel contigs">
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
21 <validator type="regex" message="No special characters allowed">^(?:\w+)?$</validator>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
22 </param>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
23 <param argument="--minlen" type="integer" value="0" label="Shorter contigs are discarded" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
24 </inputs>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
25 <outputs>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
26 <data name='output' format='fasta' label="${tool.name} on ${on_string}: sorted assembly" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
27 </outputs>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
28 <tests>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
29 <test>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
30 <param name="input" value="genome.fa" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
31 <output name="output">
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
32 <assert_contents>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
33 <has_text text=">scaffold_1" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
34 <has_text text=">scaffold_4" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
35 </assert_contents>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
36 </output>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
37 </test>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
38 <test>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
39 <param name="input" value="genome.fa" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
40 <param name="base" value="something" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
41 <param name="minlen" value="2100" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
42 <output name="output">
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
43 <assert_contents>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
44 <has_text text=">something_1" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
45 <not_has_text text=">something_4" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
46 </assert_contents>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
47 </output>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
48 </test>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
49 </tests>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
50 <help><![CDATA[
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
51 Funannotate_ sort
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
52 -----------------
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
53
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
54 Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
55
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
56 This script sorts the input contigs by size (longest->shortest) and then relabels
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
57 the contigs with a simple name (e.g. scaffold_1). Augustus can have problems with
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
58 some complicated contig names.
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
59
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
60 .. _Funannotate: http://funannotate.readthedocs.io
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
61 ]]></help>
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
62 <expand macro="citations" />
998b719a94cb "planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
63 </tool>