annotate Fasta_to_Contig2Bin.xml @ 2:c9b07cfc911c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit adf83f3747e7c2a7f5b305671718fc6789ea804e
author iuc
date Mon, 26 Dec 2022 17:47:54 +0000
parents 5033d753964b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
1 <tool id="Fasta_to_Contig2Bin" name="Converts genome bins in fasta format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
2 <description>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
3 to scaffolds-to-bin table
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
4 </description>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
5 <macros>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
6 <import>macros.xml</import>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
7 </macros>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
8 <expand macro="biotools"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
9 <expand macro="requirements"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
10 <expand macro="version"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
12 #import re
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
13 mkdir "inputs" &&
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
14 #for $i in $inputs
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
15 #set file_name = $i.file_name
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
16 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
17 ln -s '$file_name' 'inputs/${identifier}.fasta' &&
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
18 #end for
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
19 Fasta_to_Contig2Bin.sh
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
20 --extension fasta
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
21 --input_folder 'inputs'
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
22 > '$contigs2bin'
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
23 ]]></command>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
24 <inputs>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
25 <param name="inputs" type="data_collection" collection_type="list" format="fasta" label="Bin sequences"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
26 </inputs>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
27 <outputs>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
28 <data name="contigs2bin" format="tabular"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
29 </outputs>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
30 <tests>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
31 <test expect_num_outputs="1">
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
32 <param name="inputs">
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
33 <collection type="list">
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
34 <element name="001" value="maxbin2.001.fasta" ftype="fasta"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
35 <element name="002" value="maxbin2.002.fasta" ftype="fasta"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
36 </collection>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
37 </param>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
38 <output name="contigs2bin" ftype="tabular">
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
39 <assert_contents>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
40 <has_text text="contig-201_2"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
41 <has_text text="001"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
42 <has_text text="contig-201_798"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
43 <has_text text="002"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
44 </assert_contents>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
45 </output>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
46 </test>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
47 </tests>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
48 <help><![CDATA[
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
49 @HELP_HEADER@
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
50 ]]></help>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
51 <expand macro="citations"/>
5033d753964b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
iuc
parents:
diff changeset
52 </tool>