Mercurial > repos > iuc > fasta_to_contig2bin

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit adf83f3747e7c2a7f5b305671718fc6789ea804e
author iuc
date Mon, 26 Dec 2022 17:47:35 +0000
parents de45fc119798
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de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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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@">
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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2 <description>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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3 to scaffolds-to-bin table
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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4 </description>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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5 <macros>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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6 <import>macros.xml</import>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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7 </macros>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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8 <expand macro="biotools"/>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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9 <expand macro="requirements"/>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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10 <expand macro="version"/>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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11 <command detect_errors="exit_code"><![CDATA[
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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12 #import re
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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13 mkdir "inputs" &&
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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14 #for $i in $inputs
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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15 #set file_name = $i.file_name
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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16 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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17 ln -s '$file_name' 'inputs/${identifier}.fasta' &&
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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18 #end for
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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19 Fasta_to_Contig2Bin.sh
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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20 --extension fasta
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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21 --input_folder 'inputs'
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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22 > '$contigs2bin'
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23 ]]></command>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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24 <inputs>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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25 <param name="inputs" type="data_collection" collection_type="list" format="fasta" label="Bin sequences"/>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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26 </inputs>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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27 <outputs>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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28 <data name="contigs2bin" format="tabular"/>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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29 </outputs>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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30 <tests>
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31 <test expect_num_outputs="1">
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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32 <param name="inputs">
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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33 <collection type="list">
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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34 <element name="001" value="maxbin2.001.fasta" ftype="fasta"/>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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35 <element name="002" value="maxbin2.002.fasta" ftype="fasta"/>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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36 </collection>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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37 </param>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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38 <output name="contigs2bin" ftype="tabular">
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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39 <assert_contents>
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40 <has_text text="contig-201_2"/>
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41 <has_text text="001"/>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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42 <has_text text="contig-201_798"/>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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43 <has_text text="002"/>
de45fc119798 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
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44 </assert_contents>
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45 </output>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 @HELP_HEADER@
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50 ]]></help>
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51 <expand macro="citations"/>
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52 </tool>