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annotate concoct.xml @ 6:16672a3c9b65 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 6bcf71ac8fae2a84117069dc00b3c4cac6d20fa5
author iuc
date Sat, 26 Aug 2023 02:42:23 +0000
parents 28e8d2bd6aba
children eae7ee167917
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1 <tool id="concoct" name="CONCOCT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>for metagenome binning</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="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 ## CONCOCT doesn't handle gzipped files.
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9 #if $composition_file.ext.endswith(".gz")
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10 gunzip -c '$composition_file' > 'composition_file.fa' &&
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11 #else:
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12 ln -s '$composition_file' 'composition_file.fa' &&
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13 #end if
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15 mkdir outdir &&
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16 concoct
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17 --coverage_file '$coverage_file'
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18 --composition_file 'composition_file.fa'
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19 --clusters $advanced.clusters
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20 --kmer_length $advanced.kmer_length
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21 --threads \${GALAXY_SLOTS:-4}
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22 --length_threshold $advanced.length_threshold
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23 --read_length $advanced.read_length
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24 --total_percentage_pca $advanced.total_percentage_pca
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25 --basename 'outdir/'
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26 --seed $advanced.seed
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27 --iterations $advanced.iterations
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28 $advanced.no_cov_normalization
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29 $output.no_total_coverage
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30 --no_original_data
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31 $output.converge_out
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32 ]]></command>
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33 <inputs>
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34 <param argument="--coverage_file" type="data" format="tabular" label="Coverage file" help="Table where each row correspond to a contig, and each column correspond to a sample. The values are the average coverage for this contig in that sample"/>
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35 <param argument="--composition_file" type="data" format="fasta,fasta.gz" label="Composition file with sequences" help="It is named the composition file since it is used to calculate the kmer composition (the genomic signature) of each contig."/>
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36 <section name="advanced" title="Advanced options">
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37 <param argument="--clusters" type="integer" min="0" value="400" label="Maximum number of clusters for the Variational Gaussian Mixture Model (VGMM) algorithm"/>
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38 <param argument="--kmer_length" type="integer" min="0" value="4" label="Kmer length"/>
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39 <param argument="--length_threshold" type="integer" min="0" value="1000" label="Sequence length threshold" help="Contigs shorter than this value will not be included"/>
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40 <param argument="--read_length" type="integer" min="0" value="100" label="Read length for coverage"/>
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41 <param argument="--total_percentage_pca" type="integer" min="0" value="90" label="Percentage of variance explained by the principal components for the combined data"/>
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42 <param argument="--seed" type="integer" min="0" value="1" label="Seed for clustering" help="Zero value will use random seed"/>
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43 <param argument="--iterations" type="integer" min="0" value="500" label="Maximum number of iterations for the Variational Bayes Gaussian Mixture Models (VBGMM)"/>
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44 <param argument="--no_cov_normalization" type="boolean" truevalue="--no_cov_normalization" falsevalue="" checked="false" label="Skip normalization and only do log transorm of the coverage?" help="By default, the coverage is normalized for samples, then normalized for contigs and finally log transformed. By setting this flag you skip the normalization and only do log transorm of the coverage."/>
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45 </section>
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46 <section name="output" title="Output">
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47 <param argument="--no_total_coverage" type="boolean" truevalue="--no_total_coverage" falsevalue="" checked="false" label="Eliminate the total coverage column from the coverage data matrix?" help="By default, total coverage is included, independently of coverage normalization but previous to log transformation. Use this tag to escape this behaviour."/>
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48 <param argument="--converge_out" type="boolean" truevalue="--converge_out" falsevalue="" checked="false" label="Write convergence information to files?"/>
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49 <param name="log" type="boolean" checked="false" label="Output process log file?"/>
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50 </section>
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51 </inputs>
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52 <outputs>
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53 <data name="output_clustering" format="csv" from_work_dir="outdir/clustering_gt*" label="${tool.name} on ${on_string}: Clusters"/>
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54 <data name="process_log" format="txt" from_work_dir="outdir/log.txt" label="${tool.name} on ${on_string}: Log">
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55 <filter>output['log']</filter>
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56 </data>
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57 <data name="output_pca_components" format="csv" from_work_dir="outdir/PCA_components_data_gt*" label="${tool.name} on ${on_string}: PCA components"/>
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58 <data name="output_pca_transformed" format="csv" from_work_dir="outdir/PCA_transformed_data_gt*" label="${tool.name} on ${on_string}: PCA transformed clusters"/>
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59 </outputs>
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60 <tests>
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61 <test expect_num_outputs="4">
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62 <param name="coverage_file" value="coverage" ftype="tabular"/>
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63 <param name="composition_file" value="composition.fa" ftype="fasta"/>
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64 <section name="advanced">
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65 <param name="clusters" value="400"/>
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66 <param name="kmer_length" value="4"/>
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67 <param name="length_threshold" value="1000"/>
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68 <param name="read_length" value="100"/>
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69 <param name="total_percentage_pca" value="100"/>
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70 <param name="seed" value="1"/>
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71 <param name="iterations" value="500"/>
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72 <param name="no_cov_normalization" value=""/>
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73 </section>
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74 <section name="output">
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75 <param name="no_total_coverage" value=""/>
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76 <param name="converge_out" value=""/>
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77 <param name="log" value="true"/>
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78 </section>
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79 <output name="process_log" ftype="txt" compare="contains">
0
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
parents:
diff changeset
80 <assert_contents>
4
28e8d2bd6aba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit e59b5a00326e0a3bba00c1232a35cbf40a77a7be
iuc
parents: 3
diff changeset
81 <has_size value="786" delta="4"/>
3
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
82 <has_text text="CONCOCT Finished"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
83 </assert_contents>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
84 </output>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
85 <output name="output_pca_components" ftype="csv">
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
86 <assert_contents>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
87 <has_size value="362924" delta="10"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
88 <has_text text="-5.90697200e-02"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
89 </assert_contents>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
90 </output>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
91 <output name="output_pca_transformed" ftype="csv">
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
92 <assert_contents>
6
16672a3c9b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 6bcf71ac8fae2a84117069dc00b3c4cac6d20fa5
iuc
parents: 4
diff changeset
93 <has_size value="834200" delta="50"/>
3
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
94 <has_text text="contig-21000001"/>
0
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
parents:
diff changeset
95 </assert_contents>
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
parents:
diff changeset
96 </output>
3
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
97 <output name="output_clustering" ftype="csv">
0
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
parents:
diff changeset
98 <assert_contents>
3
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
99 <has_size value="6923" delta="10"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
100 <has_text text="contig-21000001,"/>
0
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
parents:
diff changeset
101 </assert_contents>
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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102 </output>
3
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
103 </test>
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iuc
parents: 2
diff changeset
104 <test expect_num_outputs="3">
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
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diff changeset
105 <param name="coverage_file" value="coverage" ftype="tabular"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
106 <param name="composition_file" value="composition.fa.gz" ftype="fasta.gz"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
107 <section name="advanced">
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
108 <param name="clusters" value="400"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
109 <param name="kmer_length" value="4"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
110 <param name="length_threshold" value="1000"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
111 <param name="read_length" value="100"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
112 <param name="total_percentage_pca" value="100"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
113 <param name="seed" value="1"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
114 <param name="iterations" value="500"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
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115 <param name="no_cov_normalization" value=""/>
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116 </section>
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117 <section name="output">
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iuc
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diff changeset
118 <param name="no_total_coverage" value=""/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
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119 <param name="converge_out" value=""/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
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120 <param name="log" value="false"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
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121 </section>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
122 <output name="output_pca_components" ftype="csv">
0
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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123 <assert_contents>
3
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
124 <has_size value="362924" delta="10"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
125 <has_text text="-5.90697200e-02"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
126 </assert_contents>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
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127 </output>
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iuc
parents: 2
diff changeset
128 <output name="output_pca_transformed" ftype="csv">
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
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129 <assert_contents>
6
16672a3c9b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 6bcf71ac8fae2a84117069dc00b3c4cac6d20fa5
iuc
parents: 4
diff changeset
130 <has_size value="834200" delta="50"/>
3
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
131 <has_text text="contig-21000001"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
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132 </assert_contents>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
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133 </output>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
134 <output name="output_clustering" ftype="csv">
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
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135 <assert_contents>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
136 <has_size value="6923" delta="10"/>
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents: 2
diff changeset
137 <has_text text="contig-21000001,"/>
0
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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138 </assert_contents>
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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139 </output>
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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140 </test>
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141 </tests>
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iuc
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142 <help><![CDATA[
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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143 **What it does**
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144
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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145 CONCOCT (Clustering cONtigs with COverage and ComposiTion) performs unsupervised binning of metagenomic contigs by
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
iuc
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146 using nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately
3
3842ef1b2f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
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147 (up to species level) bin metagenomic contigs.
0
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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148
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149 The tool accepts 2 inputs; a tabular file where each row corresponds to a contig and each column corresponds to a
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150 sample (the values are the average coverage for this contig in that sample) and a file containing sequences in
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diff changeset
151 fasta format.
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152
1
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parents: 0
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153 Three outputs are produced; clustering of the > 1000 kmer count, the PCA transformed matrix and the PCA components.
0
06c0eb033025 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 49b42f61ff37c3c33dd15c195e5705e1db066c37"
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154
1
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parents: 0
diff changeset
155 @HELP_OVERVIEW@
0
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diff changeset
156 ]]></help>
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diff changeset
157 <expand macro="citations"/>
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158 </tool>