Mercurial > repos > galaxyp > metagene_annotator

annotate metagene_annotator.xml @ 1:17c7ab82bfbc 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/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
author galaxyp
date Mon, 18 Mar 2024 12:34:58 +0000
parents b04960a7abf5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
1 <tool id="metagene_annotator" name="MetaGeneAnnotator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
2 <description>gene-finding program for prokaryote and phage (used by sixgill)</description>
1
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
3 <macros>
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
4 <token name="@TOOL_VERSION@">1.0</token>
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
5 <token name="@VERSION_SUFFIX@">1</token>
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
6 </macros>
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
7 <xrefs>
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
8 <xref type="bio.tools">metageneannotator</xref>
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
9 </xrefs>
0
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
10 <requirements>
1
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
11 <requirement type="package" version="@TOOL_VERSION@">metagene_annotator</requirement>
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
12 <requirement type="package" version="3.10">python</requirement>
0
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
13 </requirements>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
14 <command detect_errors="exit_code"><![CDATA[
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
15 #set $output_list = str($output_formats).split(',')
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
16 touch mga_output
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
17 #for $input in $inputs:
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
18 && mga ${input} $multiple_species >> mga_output
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
19 #end for
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
20 #if 'tsv' in $output_list or 'bed' in $output_list:
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
21 && python '$__tool_directory__/convert_mga.py' mga_output -v
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
22 #if 'tsv' in $output_list
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
23 --tsv '$mga_tsv'
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
24 #end if
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
25 #if 'bed' in $output_list
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
26 --bed '$mga_bed'
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
27 #end if
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
28 #end if
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
29 ]]></command>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
30 <inputs>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
31 <param name="inputs" type="data" format="fasta" multiple="true" label="prokaryote DNA sequences"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
32 <param name="multiple_species" type="boolean" truevalue="-m" falsevalue="-s" checked="true"
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
33 label="MetaGenomic - Sequences are from multiple organisms" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
34 <param name="output_formats" type="select" multiple="true" display="checkboxes" label="output formats">
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
35 <option value="txt" selected="true">MetaGeneAnnotator text report</option>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
36 <option value="tsv">MetaGeneAnnotator tabular report with sequence columns</option>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
37 <option value="bed">MetaGeneAnnotator in BED format</option>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
38 </param>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
39 </inputs>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
40 <outputs>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
41 <data name="mga_txt" format="txt" from_work_dir="mga_output" label="${tool.name} on ${on_string} metagenefile">
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
42 <filter>'txt' in output_formats</filter>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
43 </data>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
44 <data name="mga_tsv" format="tabular" label="${tool.name} on ${on_string} mga table">
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
45 <filter>'tsv' in output_formats</filter>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
46 <actions>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
47 <action name="column_names" type="metadata"
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
48 default="seq_ID,seq_model,seq_gc,seq_rbs,gene ID,start pos,end pos,strand,frame,complete/partial,gene score,used model,rbs start,rbs end,rbs score"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
49 </actions>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
50 </data>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
51 <data name="mga_bed" format="bed" label="${tool.name} on ${on_string} mga bed">
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
52 <filter>'bed' in output_formats</filter>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
53 <actions>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
54 <action name="column_names" type="metadata"
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
55 default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
56 </actions>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
57 </data>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
58 </outputs>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
59 <tests>
1
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
60 <test expect_num_outputs="1">
0
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
61 <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
62 <param name="multiple_species" value="True"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
63 <param name="output_formats" value="txt"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
64 <output name="mga_txt">
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
65 <assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
66 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = -1\s# self: -" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
67 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
68 </assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
69 </output>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
70 </test>
1
17c7ab82bfbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
galaxyp
parents: 0
diff changeset
71 <test expect_num_outputs="1">
0
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
72 <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
73 <param name="multiple_species" value="False"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
74 <param name="output_formats" value="txt"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
75 <output name="mga_txt">
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
76 <assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
77 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = 0.428571\s# self: b" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
78 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t12.48\d+\tb\t2002\t2007\t0.49\d+" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
79 </assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
80 </output>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
81 </test>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
82 <!-- Try these later
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
83 <test>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
84 <param name="inputs" value="metasequences1.fasta,metasequences2.fasta" ftype="fasta"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
85 <param name="multiple_species" value="True"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
86 <param name="output_formats" value="txt"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
87 <output name="mga_txt">
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
88 <assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
89 <has_text_matching expression="# 1/1.*# 10/1" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
90 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
91 </assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
92 </output>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
93 </test>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
94 <test>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
95 <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
96 <param name="multiple_species" value="True"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
97 <param name="output_formats" value="txt,tsv,bed"/>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
98 <output name="mga_txt">
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
99 <assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
100 <has_text_matching expression="# 1/1\s# gc = 0.275862, rbs = -1\s# self: -" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
101 <has_text_matching expression="gene_1\t1812\t1994\t-\t0\t11\t14.10\d+\tb\t2002\t2007\t2.11\d+" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
102 </assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
103 </output>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
104 <output name="mga_tsv">
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
105 <assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
106 <has_text_matching expression="#seq_id\tseq_model\tseq_gc\tseq_rbs" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
107 <has_text_matching expression="1/1\t-\t0.27\d+\t-1\tgene_1\t1812\t1994\t-\t0\t11\t14.1035\tb\t2002\t2007\t2.11\d+" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
108 </assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
109 </output>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
110 <output name="mga_bed">
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
111 <assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
112 <has_text_matching expression="1/1\t1811\t1994\t1/1:gene_1\t15\t-\t1811\t1994\t0\t1\t183\t0" />
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
113 </assert_contents>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
114 </output>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
115 </test>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
116 -->
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
117 </tests>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
118 <help><![CDATA[
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
119 **MetaGeneAnnotator (mga)**
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
120
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
121 A gene-finding program for prokaryote and phage.
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
122
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
123 The gene annotations can be used by sixgill_ when generating metapeptides from metagenomics shotgun sequencing.
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
124
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
125 .. image:: Sixgill_MetaGeneAnnotator_Workflow.png
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
126 :height: 213
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
127 :width: 625
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
128
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
129 usage:
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
130 mga [multi-fasta] <-m/-s>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
131
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
132 -m (multiple species sequences are individually treated)
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
133 -s (single species sequences are treated as a unit)
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
134
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
135 **Input:**
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
136 *A fasta file of metagenomic sequences*
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
137
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
138
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
139 **Outputs:**
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
140
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
141 *MetaGeneAnnotator text report*
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
142 Output from the MetaGeneAnnotator mga application::
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
143
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
144 # 1/1
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
145 # gc = 0.275862, rbs = -1
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
146 # self: -
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
147 gene_1 1812 1994 - 0 11 14.1035 b 2002 2007 2.11797
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
148 # 2/1
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
149 # gc = 0.338877, rbs = -1
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
150 # self: -
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
151 gene_1 1 414 + 0 01 25.748 b . . .
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
152 gene_2 614 790 + 0 11 0.774142 b . . .
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
153 gene_3 822 1079 + 0 11 20.6507 b . . .
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
154
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
155 output format description::
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
156
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
157 # [sequence name]
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
158 # gc = [gc%], rbs = [rbs%]
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
159 # self: [(b)acteria/(a)rchaea/(p)hage/unused(-)]
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
160 [gene ID] [start pos.] [end pos.] [strand] [frame] [complete/partial] [gene score] [used model] [rbs start] [rbs end] [rbs score]
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
161
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
162 explanations of output column:
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
163 *The value of [frame] (0/1/2) indicates the number of surplus (untranslated) nucleotides at the 5'-end of the predicted ORF.
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
164 *The value of [score] indicates the estimated score of predicted gene. All predicted genes are more than 0.
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
165 *The value of [complete/partial] indicates that the predicted gene structure is whether complete (contains both of start and stop codons[11]) or partial (lacks start[01] or stop[10] or both of them[00]).
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
166 *The value of [model] indicates a selected model ((s)elf/(b)acteria/(a)rchaea/(p)hage) for predicting the gene.
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
167
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
168
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
169 *MetaGeneAnnotator tabular report with sequence columns*
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
170 The mga output reformated as a tabular file::
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
171
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
172 #seq_id seq_model seq_gc seq_rbs gene ID start pos end pos strand frame complete/partial gene score used model rbs start rbs end rbs score
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
173 1/1 - 0.275862 -1 gene_1 1812 1994 - 0 11 14.1035 b 2002 2007 2.11797
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
174 2/1 - 0.338877 -1 gene_1 1 414 + 0 01 25.748 b . . .
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
175 2/1 - 0.338877 -1 gene_2 614 790 + 0 11 0.774142 b . . .
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
176 2/1 - 0.338877 -1 gene_3 822 1079 + 0 11 20.6507 b . . .
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
177
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
178
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
179 *MetaGeneAnnotator in BED format*
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
180 The mga output reformatted as a BED file which can be used to extract the DNA sequences for each gene from the fasta file::
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
181
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
182 1/1 1811 1994 1/1:gene_1 15 - 1811 1994 0 1 183 0
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
183 2/1 0 414 2/1:gene_1 26 + 0 414 0 1 414 0
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
184 2/1 613 790 2/1:gene_2 1 + 613 790 0 1 177 0
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
185 2/1 821 1079 2/1:gene_3 21 + 821 1079 0 1 258 0
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
186
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
187
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
188 .. _sixgill: https://github.com/dhmay/sixgill
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
189 ]]></help>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
190 <citations>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
191 <citation type="doi">10.1093/dnares/dsn027</citation>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
192 </citations>
b04960a7abf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c
galaxyp
parents:
diff changeset
193 </tool>