Mercurial > repos > iuc > concoct_extract_fasta_bins

annotate extract_fasta_bins.xml @ 0:1bc8fd1b3ed0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
author iuc
date Fri, 18 Feb 2022 14:17:48 +0000
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1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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1 <tool id="concoct_extract_fasta_bins" name="Extract a fasta file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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2 <description>for each cluster in a CONCOCT clustering file</description>
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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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="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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8 mkdir outdir &&
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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9 python '$__tool_directory__/extract_fasta_bins.py'
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10 #if $input_fasta.is_of_type('fasta.gz'):
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11 --gzipped
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12 #end if
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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13 --input_fasta '$input_fasta'
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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14 --input_cluster '$input_cluster'
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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15 --output_path 'outdir'
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16 ]]></command>
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17 <inputs>
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18 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="Fasta file"/>
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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19 <param argument="--input_cluster" type="data" format="tabular" label="CONCOCT clustering file"/>
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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20 </inputs>
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21 <outputs>
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22 <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)">
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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23 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="outdir"/>
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24 </collection>
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25 </outputs>
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26 <tests>
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27 <test expect_num_outputs="1">
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28 <param name="input_fasta" value="input1.fa.gz" ftype="fasta.gz"/>
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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29 <param name="input_cluster" value="inputcluster1.tabular" ftype="tabular"/>
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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30 <output_collection name="bins" type="list" count="2">
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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31 <element name="77" ftype="fasta">
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32 <assert_contents>
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33 <has_size value="2194"/>
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34 <has_text text="NODE_1_length_2054_cov_17.474684"/>
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35 <has_n_lines n="37"/>
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36 </assert_contents>
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37 </element>
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38 <element name="93" ftype="fasta">
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39 <assert_contents>
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40 <has_size value="16531"/>
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41 <has_text text="NODE_2_length_16156_cov_8.219856"/>
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42 <has_n_lines n="272"/>
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43 </assert_contents>
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44 </element>
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45 </output_collection>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 **What it does**
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50
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51 Performs metagenomic binning of fasta contigs by extracting a fasta file for each cluster defined in a
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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52 CONCOCT clustering file.
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53
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54 The tool accepts two inputs; the fasta contigs file and the CONCOCT clustering file that was produced using
1bc8fd1b3ed0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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55 the same fasta contigs input. A collection of fasta files is produced.
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56 ]]></help>
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57 <expand macro="citations"/>
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58 </tool>