Mercurial > repos > iuc > fasta_to_contig2bin
comparison Fasta_to_Contig2Bin.xml @ 0:5033d753964b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
| author | iuc |
|---|---|
| date | Mon, 27 Jun 2022 12:41:53 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:5033d753964b |
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| 1 <tool id="Fasta_to_Contig2Bin" name="Converts genome bins in fasta format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| 2 <description> | |
| 3 to scaffolds-to-bin table | |
| 4 </description> | |
| 5 <macros> | |
| 6 <import>macros.xml</import> | |
| 7 </macros> | |
| 8 <expand macro="biotools"/> | |
| 9 <expand macro="requirements"/> | |
| 10 <expand macro="version"/> | |
| 11 <command detect_errors="exit_code"><![CDATA[ | |
| 12 #import re | |
| 13 mkdir "inputs" && | |
| 14 #for $i in $inputs | |
| 15 #set file_name = $i.file_name | |
| 16 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) | |
| 17 ln -s '$file_name' 'inputs/${identifier}.fasta' && | |
| 18 #end for | |
| 19 Fasta_to_Contig2Bin.sh | |
| 20 --extension fasta | |
| 21 --input_folder 'inputs' | |
| 22 > '$contigs2bin' | |
| 23 ]]></command> | |
| 24 <inputs> | |
| 25 <param name="inputs" type="data_collection" collection_type="list" format="fasta" label="Bin sequences"/> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data name="contigs2bin" format="tabular"/> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test expect_num_outputs="1"> | |
| 32 <param name="inputs"> | |
| 33 <collection type="list"> | |
| 34 <element name="001" value="maxbin2.001.fasta" ftype="fasta"/> | |
| 35 <element name="002" value="maxbin2.002.fasta" ftype="fasta"/> | |
| 36 </collection> | |
| 37 </param> | |
| 38 <output name="contigs2bin" ftype="tabular"> | |
| 39 <assert_contents> | |
| 40 <has_text text="contig-201_2"/> | |
| 41 <has_text text="001"/> | |
| 42 <has_text text="contig-201_798"/> | |
| 43 <has_text text="002"/> | |
| 44 </assert_contents> | |
| 45 </output> | |
| 46 </test> | |
| 47 </tests> | |
| 48 <help><![CDATA[ | |
| 49 @HELP_HEADER@ | |
| 50 ]]></help> | |
| 51 <expand macro="citations"/> | |
| 52 </tool> |