annotate binning_refiner.xml @ 1:1c8d0916f97f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
author iuc
date Wed, 27 Apr 2022 18:46:46 +0000
parents f350d182f786
children 1b18b36bad5e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
1 <tool id="bin_refiner" name="Binning refiner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
2 <description>refines metagenome bins</description>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
3 <macros>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
5 </macros>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
8 #import re
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
9
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
10 ## Binning refiner prepends the -p param value
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
11 ## (which we set to be the string 'refined' in
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
12 ## the command line) to a hard-coded string (i.e.,
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
13 ## '_Binning_refiner_outputs') to set the base
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
14 ## output directory.
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
15
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
16 ## Binning_refiner requires 2 levels of directories
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
17 ## for the input bins.
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
18 mkdir -p input_bin_dir/bins &&
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
19 #for $f in $input_bins:
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
20 #set identifier = re.sub('[^\s\w\-]', '_', str($f.element_identifier))
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
21 #set file_name = $identifier + '.' + $f.ext
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
22 ## Binning_refiner doesn't handle gzipped files.
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
23 #if $f.ext.endswith(".gz")
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
24 gunzip -c '${f}' > 'input_bin_dir/bins/${file_name}' &&
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
25 #else:
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
26 ln -s '${f}' 'input_bin_dir/bins/${file_name}' &&
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
27 #end if
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
28 #end for
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
29
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
30 Binning_refiner
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
31 -i input_bin_dir
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
32 -p 'refined'
1
1c8d0916f97f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
iuc
parents: 0
diff changeset
33 -m $m
0
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
34 && mv 'refined_Binning_refiner_outputs/refined_contigs.txt' '$output_refined_contigs'
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
35 && mv 'refined_Binning_refiner_outputs/refined_sources_and_length.txt' '$output_sources_and_length'
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
36 ]]></command>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
37 <inputs>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
38 <param name="input_bins" format="fasta,fasta.gz" type="data" multiple="true" label="Binned fasta files"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
39 <param argument="-m" type="integer" value="512" label="Minimum size (Kbp) of refined bin" help="Bins smaller than this will be eliminated"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
40 </inputs>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
41 <outputs>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
42 <collection name="output_refined_bins" type="list" label="${tool.name} on ${on_string}: (refined bins)">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
43 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fasta" format="fasta" directory="refined_Binning_refiner_outputs/refined_refined_bins"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
44 </collection>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
45 <data name="output_refined_contigs" format="tabular" label="${tool.name} on ${on_string} (refined contigs)"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
46 <data name="output_sources_and_length" format="tabular" label="${tool.name} on ${on_string} (sources and length)"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
47 </outputs>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
48 <tests>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
49 <test expect_num_outputs="3">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
50 <param name="input_bins" value="MetaBAT_17.fa.gz,MetaBAT_18.fa.gz,MetaBAT_19.fa.gz,MetaBAT_20.fa.gz,MetaBAT_21.fa.gz,MetaBAT_22.fa.gz,MetaBAT_23.fa.gz,Concoct_1.fa.gz,Concoct_3.fa.gz,Concoct_8.fa.gz" ftype="fasta.gz"/>
1
1c8d0916f97f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
iuc
parents: 0
diff changeset
51 <param name="m" value="256"/>
1c8d0916f97f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
iuc
parents: 0
diff changeset
52 <output_collection name="output_refined_bins" type="list" count="8">
0
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
53 <element name="refined_1" ftype="fasta">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
54 <assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
55 <has_size value="1320640"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
56 <has_text text=">scaffold_2064"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
57 <has_n_lines n="21765"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
58 </assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
59 </element>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
60 <element name="refined_2" ftype="fasta">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
61 <assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
62 <has_size value="941488"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
63 <has_text text=">scaffold_1301"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
64 <has_n_lines n="15461"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
65 </assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
66 </element>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
67 <element name="refined_3" ftype="fasta">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
68 <assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
69 <has_size value="883642"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
70 <has_text text=">scaffold_262"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
71 <has_n_lines n="14495"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
72 </assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
73 </element>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
74 <element name="refined_4" ftype="fasta">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
75 <assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
76 <has_size value="758509"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
77 <has_text text=">scaffold_923"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
78 <has_n_lines n="12484"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
79 </assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
80 </element>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
81 <element name="refined_5" ftype="fasta">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
82 <assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
83 <has_size value="722197"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
84 <has_text text=">scaffold_232"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
85 <has_n_lines n="11849"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
86 </assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
87 </element>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
88 <element name="refined_6" ftype="fasta">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
89 <assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
90 <has_size value="637342"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
91 <has_text text=">scaffold_259"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
92 <has_n_lines n="10460"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
93 </assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
94 </element>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
95 <element name="refined_7" ftype="fasta">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
96 <assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
97 <has_size value="560996"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
98 <has_text text=">scaffold_1510"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
99 <has_n_lines n="9219"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
100 </assert_contents>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
101 </element>
1
1c8d0916f97f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
iuc
parents: 0
diff changeset
102 <element name="refined_8" ftype="fasta">
1c8d0916f97f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
iuc
parents: 0
diff changeset
103 <assert_contents>
1c8d0916f97f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
iuc
parents: 0
diff changeset
104 <has_size value="276224"/>
1c8d0916f97f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
iuc
parents: 0
diff changeset
105 <has_text text=">scaffold_955"/>
1c8d0916f97f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
iuc
parents: 0
diff changeset
106 <has_n_lines n="4554"/>
1c8d0916f97f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
iuc
parents: 0
diff changeset
107 </assert_contents>
1c8d0916f97f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 05bd671a4765eb97583bac21729b26bec808adcd"
iuc
parents: 0
diff changeset
108 </element>
0
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
109 </output_collection>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
110 <output name="output_refined_contigs" file="output_refined_contigs.tabular" ftype="tabular"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
111 <output name="output_sources_and_length" file="output_sources_and_length.tabular" ftype="tabular"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
112 </test>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
113 </tests>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
114 <help><![CDATA[
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
115 **What it does**
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
116
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
117 Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
118 especially with respect to contamination levels.
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
119
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
120 The tool accepts one or more fasta datasets (i.e., bins) that were produced by metagenome binning tools
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
121 (CONCOCT MaxBin2, MetaBAT2 and others).
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
122
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
123 All refined bins larger than the specified "Minimum size (Kbp) of refined bin" will be output as a dataset
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
124 collection of fasta files. Additional outputs include a tabular dataset containing the id of the contigs
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
125 in each refined bin (refined contigs) and another tabular dataset containing the size of each refined bin
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
126 and the origin of its contigs (sources and length).
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
127
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
128 **More information**
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
129
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
130 https://github.com/songweizhi/Binning_refiner
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
131
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
132 ]]></help>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
133 <expand macro="citations"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
parents:
diff changeset
134 </tool>