Mercurial > repos > ufz > phabox_phavip

annotate phavip.xml @ 0:9fd3b56502eb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
author ufz
date Wed, 16 Apr 2025 09:42:31 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
1 <tool id="phabox_phavip" name="PhaBOX phavip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
2 <description>Protein annotation</description>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
3 <macros>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
4 <import>macros.xml</import>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
5 </macros>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
6 <xrefs>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
7 <xref type="bio.tools">phabox</xref>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
8 </xrefs>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
9 <requirements>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
10 <requirement type="package" version="@TOOL_VERSION@">phabox</requirement>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
11 </requirements>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
13 phabox2 --task phavip
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
14 @GENERAL@
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
15 ]]></command>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
16 <inputs>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
17 <expand macro="general"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
18 <param name="supp_outputs" type="select" optional="true" label="Supplementary outputs">
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
19 <option value="gene_annotation">Gene annotation</option>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
20 </param>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
21 </inputs>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
22 <outputs>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
23 <data name="out" format="tabular" from_work_dir="output/final_prediction/phavip_prediction.tsv"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
24 <data name="phavip_annotation" format="tabular" from_work_dir="output/final_prediction/phavip_supplementary/gene_annotation.tsv" label="${tool.name} on ${on_string}: Gene annotation">
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
25 <filter>supp_outputs and "gene_annotation" in supp_outputs</filter>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
26 </data>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
27 </outputs>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
28 <tests>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
29 <test expect_num_outputs="1">
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
30 <param name="dbdir" value="phaboxdb"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
31 <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
32 <output name="out">
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
33 <assert_contents>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
34 <has_line line="Accession&#9;Length&#9;Protein_num&#9;Annotated_num&#9;Annotation_rate"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
35 <has_n_lines n="391"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
36 <has_n_columns n="5"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
37 </assert_contents>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
38 </output>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
39 </test>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
40 <test expect_num_outputs="2">
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
41 <param name="dbdir" value="phaboxdb"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
42 <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
43 <param name="supp_outputs" value="gene_annotation"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
44 <output name="out">
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
45 <assert_contents>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
46 <has_line line="Accession&#9;Length&#9;Protein_num&#9;Annotated_num&#9;Annotation_rate"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
47 <has_n_lines n="391"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
48 <has_n_columns n="5"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
49 </assert_contents>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
50 </output>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
51 <output name="phavip_annotation">
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
52 <assert_contents>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
53 <has_line line="Genome&#9;ORF&#9;Start&#9;End&#9;Strand&#9;GC&#9;Annotation&#9;pident&#9;coverage"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
54 <has_n_lines n="8995"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
55 <has_n_columns n="9"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
56 </assert_contents>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
57 </output>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
58 </test>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
59 </tests>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
60 <help><![CDATA[
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
61
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
62 Please note that running task end_to_end, phamer, phagcn, phatyp, and cherry, will automatically run phavip.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
63 The output files are the same but the supplementary files will be dumped into the corresponding task.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
64
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
65
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
66 @COMMON_INPUT_DOC@
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
67
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
68 **Output**
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
69
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
70 @COMMON_OUTPUT_DOC@
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
71 - Protein_num: total number of predicted proteins.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
72 - Annotated_num: number of proteins that have significant alignments.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
73 - Annotation_rate: percentage of proteins that have annotations.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
74
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
75 In addition the gene annotation itself can be produced:
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
76
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
77 - Genome: the accession or the name of the input contigs.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
78 - ORF: the ID of the translated protein.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
79 - Start: start position on the genome.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
80 - End: end position on the genome.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
81 - Strand: forward (1) or backward(-1).
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
82 - GC: GC content.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
83 - Annotation: the annotation of the proteins.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
84
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
85 Please note that there are two kinds of hypothetical protein:
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
86
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
87 - hypothetical protein (no hit): a protein has no alignment results to the reference database.
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
88 - hypothetical protein (no hit): a protein has alignment results but the annotation is "hypothetical protein"
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
89
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
90
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
91 ]]></help>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
92 <expand macro="citations"/>
9fd3b56502eb planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
ufz
parents:
diff changeset
93 </tool>