Mercurial > repos > iuc > biobox_add_taxid

comparison biobox_add_taxid.xml @ 2:450a61fc097f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 956c476d4eeed0334582438d715da88e170212c6
author iuc
date Sun, 08 Sep 2024 14:08:45 +0000
parents 1e10251b9615
children
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1:d368e312aebd 2:450a61fc097f
1 <tool id="biobox_add_taxid" name="Biobox add taxid" version="@SCRIPT_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="biobox_add_taxid" name="Biobox add taxid" version="@SCRIPT_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Add taxid output from BAT or GTDB to biobox binning data</description> 2 <description>Add taxid output from BAT or GTDB to biobox binning data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@SCRIPT_VERSION@">0.4</token> 5 <token name="@SCRIPT_VERSION@">0.6</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@SCRIPT_VERSION@">biobox_add_taxid</requirement> 8 <requirement type="package" version="@SCRIPT_VERSION@">biobox_add_taxid</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 12
13 mkdir -p input && 13 mkdir -p input taxonkit gtdb_to_taxdump &&
14 14
15 ln -s '${biobox_file}' '$biobox_file.element_identifier' && 15 ln -s '${biobox_file}' '$biobox_file.element_identifier' &&
16 16
17 #for $i, $f in enumerate($tool_type.input): 17 #for $i, $f in enumerate($tool_type.input):
18 ln -s '$f' 'input/${i}.tsv' && 18 ln -s '$f' 'input/${i}.tsv' &&
19 #end for 19 #end for
20 20
21 #if $tool_type.is_select == 'GTDB':
22 #for $i, $f in enumerate($gtdb_to_taxdump):
23 ln -s '$f' 'gtdb_to_taxdump/gtdb_to_taxdump_${i}.tsv' &&
24 #end for
25 #for $i, $f in enumerate($taxonkit):
26 ln -s '$f' 'taxonkit/taxonkit_${i}.tsv' &&
27 #end for
28 #end if
29
21 biobox_add_taxid.py 30 biobox_add_taxid.py
22 '$biobox_file.element_identifier' 31 '$biobox_file.element_identifier'
23 '$tool_type.is_select' 32 '$tool_type.is_select'
24 'input' 33 'input'
25 #if $tool_type.is_select == 'GTDB': 34 #if $tool_type.is_select == 'GTDB':
26 -g '$gtdb_to_taxdump' 35 -g 'gtdb_to_taxdump'
27 -t '$taxonkit' 36 -t 'taxonkit'
28 -c $column 37 -c $column
29 #end if 38 #end if
30 && 39 &&
31 40
32 #if $tool_type.is_select == 'GTDB': 41 #if $tool_type.is_select == 'GTDB':
43 <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)"> 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)">
44 <option value="BAT">BAT</option> 53 <option value="BAT">BAT</option>
45 <option value="GTDB">GTDB</option> 54 <option value="GTDB">GTDB</option>
46 </param> 55 </param>
47 <when value="GTDB"> 56 <when value="GTDB">
48 <param argument="--gtdb_to_taxdump" type="data" 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"/> 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"/>
49 <param argument="--taxonkit" type="data" format="tabular" 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"/> 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"/>
50 <param argument="--column" type="data_column" data_ref="taxonkit" label="Input the colum with the NCBI names"/> 59 <param argument="--column" type="data_column" data_ref="taxonkit" label="Input the colum with the NCBI names"/>
51 <param name="input" type="data" multiple="true" format="tabular" label="Input the GTDB-Tk summary file(s) here" 60 <param name="input" type="data" multiple="true" format="tabular" label="Input the GTDB-Tk summary file(s) here"
52 help="Use the GTDB-Tk file(s) which are coresponding with the binning file!"/> 61 help="Use the GTDB-Tk file(s) which are coresponding with the binning file!"/>
53 </when> 62 </when>
54 <when value="BAT"> 63 <when value="BAT">
72 <test expect_num_outputs="1"> 81 <test expect_num_outputs="1">
73 <param name="biobox_file" ftype="tabular" value="test_biobox_file.tsv"/> 82 <param name="biobox_file" ftype="tabular" value="test_biobox_file.tsv"/>
74 <conditional name="tool_type"> 83 <conditional name="tool_type">
75 <param name="is_select" value="GTDB"/> 84 <param name="is_select" value="GTDB"/>
76 <param name="gtdb_to_taxdump" ftype="tabular" value="test_gtdb_to_taxdump_file.tsv"/> 85 <param name="gtdb_to_taxdump" ftype="tabular" value="test_gtdb_to_taxdump_file.tsv"/>
77 <param name="taxonkit" ftype="tabular" value="test_taxonkit_file.tsv"/> 86 <param name="taxonkit" ftype="tabular" value="test_taxonkit_file_1.tsv,test_taxonkit_file_2.tsv"/>
78 <param name="column" value="1"/> 87 <param name="column" value="1"/>
79 <param name="input" ftype="tabular" value="test_gtdb_file.tsv"/> 88 <param name="input" ftype="tabular" value="test_gtdb_file.tsv"/>
80 </conditional> 89 </conditional>
81 <output name="output" file="test_biobox_file_add_taxid_gtdb.tsv"/> 90 <output name="output" file="test_biobox_file_add_taxid_gtdb.tsv"/>
82 </test> 91 </test>