annotate biobox_add_taxid.xml @ 3:8d0b2def5e65 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 04a067550f7d61ca8ff489e3de64efd0da3abcf1
author iuc
date Sun, 08 Sep 2024 14:37:41 +0000
parents 450a61fc097f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
1 <tool id="biobox_add_taxid" name="Biobox add taxid" version="@SCRIPT_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
2 <description>Add taxid output from BAT or GTDB to biobox binning data</description>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
3 <macros>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
4 <import>macros.xml</import>
2
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
5 <token name="@SCRIPT_VERSION@">0.6</token>
0
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
6 </macros>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
7 <requirements>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
8 <requirement type="package" version="@SCRIPT_VERSION@">biobox_add_taxid</requirement>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
9 </requirements>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
10 <command detect_errors="exit_code">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
11 <![CDATA[
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
12
2
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
13 mkdir -p input taxonkit gtdb_to_taxdump &&
0
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
14
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
15 ln -s '${biobox_file}' '$biobox_file.element_identifier' &&
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
16
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
17 #for $i, $f in enumerate($tool_type.input):
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
18 ln -s '$f' 'input/${i}.tsv' &&
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
19 #end for
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
20
2
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
21 #if $tool_type.is_select == 'GTDB':
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
22 #for $i, $f in enumerate($gtdb_to_taxdump):
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
23 ln -s '$f' 'gtdb_to_taxdump/gtdb_to_taxdump_${i}.tsv' &&
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
24 #end for
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
25 #for $i, $f in enumerate($taxonkit):
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
26 ln -s '$f' 'taxonkit/taxonkit_${i}.tsv' &&
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
27 #end for
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
28 #end if
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
29
0
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
30 biobox_add_taxid.py
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
31 '$biobox_file.element_identifier'
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
32 '$tool_type.is_select'
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
33 'input'
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
34 #if $tool_type.is_select == 'GTDB':
2
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
35 -g 'gtdb_to_taxdump'
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
36 -t 'taxonkit'
0
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
37 -c $column
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
38 #end if
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
39 &&
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
40
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
41 #if $tool_type.is_select == 'GTDB':
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
42 cp *_add_taxid_GTDB* $output
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
43 #else:
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
44 cp *_add_taxid_BAT* $output
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
45 #end if
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
46
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
47 ]]>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
48 </command>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
49 <inputs>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
50 <param name="biobox_file" type="data" format="tabular" label="CAMI amber biobox file input" help="Input the CAMI amber biobox file here which are corespond with the biner and the BAT/GTDB output which did used the biner as input! "/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
51 <conditional name="tool_type">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
52 <param name="is_select" type="select" label="Select the tool which output should be used here" help="Select BAT when you use the bin2classifier file(s) or select GTDB when using the summary file(s)">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
53 <option value="BAT">BAT</option>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
54 <option value="GTDB">GTDB</option>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
55 </param>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
56 <when value="GTDB">
2
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
57 <param argument="--gtdb_to_taxdump" type="data" multiple="true" format="tabular" label="Input the output from gtdb_to_taxdump here" help="Use the output from gtdb_to_taxdump here since we need the mapped names from GTDB to NCBI to get the arcoding taxids from NCBI"/>
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
58 <param argument="--taxonkit" type="data" format="tabular" multiple="true" label="Input the output from Taxonkit here" help="Use the output from Taxonkit here since the need the mapped NCBI names to the arcording taxids"/>
0
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
59 <param argument="--column" type="data_column" data_ref="taxonkit" label="Input the colum with the NCBI names"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
60 <param name="input" type="data" multiple="true" format="tabular" label="Input the GTDB-Tk summary file(s) here"
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
61 help="Use the GTDB-Tk file(s) which are coresponding with the binning file!"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
62 </when>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
63 <when value="BAT">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
64 <param name="input" type="data" multiple="true" format="tabular" label="Input bin2classifier file(s) from BAT here"
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
65 help="Use the BAT file(s) which are coresponding with the binning file!"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
66 </when>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
67 </conditional>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
68 </inputs>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
69 <outputs>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
70 <data name="output" format="tabular" label="${tool.name}: BIOBOX ADD TAXID COLUMN"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
71 </outputs>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
72 <tests>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
73 <test expect_num_outputs="1">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
74 <param name="biobox_file" ftype="tabular" value="test_biobox_file.tsv"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
75 <conditional name="tool_type">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
76 <param name="is_select" value="BAT"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
77 <param name="input" ftype="tabular" value="test_bat_file.tsv"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
78 </conditional>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
79 <output name="output" file="test_biobox_file_add_taxid_bat.tsv"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
80 </test>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
81 <test expect_num_outputs="1">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
82 <param name="biobox_file" ftype="tabular" value="test_biobox_file.tsv"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
83 <conditional name="tool_type">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
84 <param name="is_select" value="GTDB"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
85 <param name="gtdb_to_taxdump" ftype="tabular" value="test_gtdb_to_taxdump_file.tsv"/>
2
450a61fc097f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
iuc
parents: 0
diff changeset
86 <param name="taxonkit" ftype="tabular" value="test_taxonkit_file_1.tsv,test_taxonkit_file_2.tsv"/>
0
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
87 <param name="column" value="1"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
88 <param name="input" ftype="tabular" value="test_gtdb_file.tsv"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
89 </conditional>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
90 <output name="output" file="test_biobox_file_add_taxid_gtdb.tsv"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
91 </test>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
92 </tests>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
93 <help>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
94 <![CDATA[
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
95
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
96 **USAGE OF THIS TOOL**
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
97
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
98 This tool was desgin for using the BAT/GTDB-Tk output to expand the CAMI amber biobox file with the taxid column to access taxa evaluation with amber!
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
99
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
100 **IMPORTAND NOTE WHEN USING GTDB OUTPUT**
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
101
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
102 Befor using GTDB-Tk output you have to use 2 other tools to map the GTDB names to the NCBI names and then map the NCBI names to there taxids.
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
103 To map the GTDB names to the NCBI names you extract the GTDB names from the summary file and with them you can now use the gtdb_to_taxdum tool!
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
104 After using the gtdb_to_taxdum tool you have the extract the NCBI names here and then use the tool Taxonkit[name2taxid] to finaly get the taxids.
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
105
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
106 **INPUTS**
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
107 - The CAMI amber biobox file
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
108 - BAT[bin2classifier] file(s) OR GTDB-Tk[Summary] file(s)
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
109 - The gtdb_to_taxdum output[WHEN USING GTDB-Tk]
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
110 - The Taxonkit[name2taxid] output[WHEN USING GTDB-Tk]
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
111
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
112 **OUTPUT**
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
113
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
114 A CAMI amber biobox file with a taxid colum
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
115 ]]>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
116 </help>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
117 <citations>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
118 <citation type="bibtex">@misc{BibEntry2024Aug,
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
119 title = {{biobox{$\_$}add{$\_$}taxid}},
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
120 author = {Santino Faack (SantaMcCloud)},
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
121 journal = {GitHub},
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
122 year = {2024},
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
123 month = aug,
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
124 note = {[Online; accessed 22. Aug. 2024]},
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
125 url = {https://github.com/SantaMcCloud/biobox_add_taxid/tree/release-0.3}
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
126 }</citation>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
127 </citations>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
iuc
parents:
diff changeset
128 </tool>