Mercurial > repos > iuc > concoct_extract_fasta_bins

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 86e1afebec29c10ef1e31196b23c24fde2d086da
author iuc
date Sun, 12 Nov 2023 14:31:16 +0000
parents bcd8d64f82b7
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1 <tool id="concoct_extract_fasta_bins" name="CONCOCT: Extract a fasta file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>for each cluster</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## CONCOCT doesn't handle gzipped files.
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10 #if $fasta_file.ext.endswith(".gz")
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11 gunzip -c '$fasta_file' > 'contigs.fa' &&
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12 #else:
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13 ln -s '$fasta_file' 'contigs.fa' &&
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14 #end if
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15
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16 mkdir outdir &&
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17 extract_fasta_bins.py
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18 'contigs.fa'
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19 '$cluster_file'
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20 --output_path 'outdir'
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21 ]]></command>
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22 <inputs>
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23 <param name="fasta_file" type="data" format="fasta,fasta.gz" label="Original contig file"/>
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24 <param name="cluster_file" type="data" format="csv" label="CONCOCT clusters"/>
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25 </inputs>
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26 <outputs>
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27 <collection name="bins" type="list" label="${tool.name} on ${on_string} : Bins">
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28 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="outdir"/>
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29 </collection>
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30 </outputs>
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31 <tests>
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32 <test expect_num_outputs="1">
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33 <param name="fasta_file" value="composition.fa.gz" ftype="fasta.gz"/>
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34 <param name="cluster_file" value="clusters.csv" ftype="csv"/>
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35 <output_collection name="bins" type="list" count="54">
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36 <element name="0" ftype="fasta">
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37 <assert_contents>
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38 <has_size value="1194"/>
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39 <has_text text="contig-223000058 1140 nucleotides"/>
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40 <has_n_lines n="20"/>
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41 </assert_contents>
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42 </element>
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43 <element name="52" ftype="fasta">
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44 <assert_contents>
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45 <has_size value="5356"/>
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46 <has_text text="contig-161000004 1031 nucleotides"/>
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47 <has_n_lines n="90"/>
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48 </assert_contents>
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49 </element>
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50 </output_collection>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54 **What it does**
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55
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56 Performs metagenomic binning of fasta contigs by extracting a fasta file for each cluster defined in a CONCOCT clustering file.
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57
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58 The tool accepts two inputs; the fasta contigs file and the CONCOCT clustering file that was produced using the same fasta contigs input. A collection of fasta files is produced.
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59
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60 @HELP_OVERVIEW@
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61 ]]></help>
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62 <expand macro="citations"/>
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63 </tool>