Mercurial > repos > iuc > concoct
comparison concoct.xml @ 6:337ba922753a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 6bcf71ac8fae2a84117069dc00b3c4cac6d20fa5
| author | iuc |
|---|---|
| date | Sat, 26 Aug 2023 02:41:24 +0000 |
| parents | d9600883e676 |
| children |
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| 5:1686800f8452 | 6:337ba922753a |
|---|---|
| 36 <section name="advanced" title="Advanced options"> | 36 <section name="advanced" title="Advanced options"> |
| 37 <param argument="--clusters" type="integer" min="0" value="400" label="Maximum number of clusters for the Variational Gaussian Mixture Model (VGMM) algorithm"/> | 37 <param argument="--clusters" type="integer" min="0" value="400" label="Maximum number of clusters for the Variational Gaussian Mixture Model (VGMM) algorithm"/> |
| 38 <param argument="--kmer_length" type="integer" min="0" value="4" label="Kmer length"/> | 38 <param argument="--kmer_length" type="integer" min="0" value="4" label="Kmer length"/> |
| 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"/> | 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"/> |
| 40 <param argument="--read_length" type="integer" min="0" value="100" label="Read length for coverage"/> | 40 <param argument="--read_length" type="integer" min="0" value="100" label="Read length for coverage"/> |
| 41 <param argument="--total_percentage_pca" type="integer" min="0" value="100" label="Percentage of variance explained by the principal components for the combined data"/> | 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"/> |
| 42 <param argument="--seed" type="integer" min="0" value="1" label="Seed for clustering" help="Zero value will use random seed"/> | 42 <param argument="--seed" type="integer" min="0" value="1" label="Seed for clustering" help="Zero value will use random seed"/> |
| 43 <param argument="--iterations" type="integer" min="0" value="500" label="Maximum number of iterations for the Variational Bayes Gaussian Mixture Models (VBGMM)"/> | 43 <param argument="--iterations" type="integer" min="0" value="500" label="Maximum number of iterations for the Variational Bayes Gaussian Mixture Models (VBGMM)"/> |
| 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."/> | 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."/> |
| 45 </section> | 45 </section> |
| 46 <section name="output" title="Output"> | 46 <section name="output" title="Output"> |
| 88 <has_text text="-5.90697200e-02"/> | 88 <has_text text="-5.90697200e-02"/> |
| 89 </assert_contents> | 89 </assert_contents> |
| 90 </output> | 90 </output> |
| 91 <output name="output_pca_transformed" ftype="csv"> | 91 <output name="output_pca_transformed" ftype="csv"> |
| 92 <assert_contents> | 92 <assert_contents> |
| 93 <has_size value="834200" delta="10"/> | 93 <has_size value="834200" delta="50"/> |
| 94 <has_text text="contig-21000001"/> | 94 <has_text text="contig-21000001"/> |
| 95 </assert_contents> | 95 </assert_contents> |
| 96 </output> | 96 </output> |
| 97 <output name="output_clustering" ftype="csv"> | 97 <output name="output_clustering" ftype="csv"> |
| 98 <assert_contents> | 98 <assert_contents> |
| 125 <has_text text="-5.90697200e-02"/> | 125 <has_text text="-5.90697200e-02"/> |
| 126 </assert_contents> | 126 </assert_contents> |
| 127 </output> | 127 </output> |
| 128 <output name="output_pca_transformed" ftype="csv"> | 128 <output name="output_pca_transformed" ftype="csv"> |
| 129 <assert_contents> | 129 <assert_contents> |
| 130 <has_size value="834200" delta="10"/> | 130 <has_size value="834200" delta="50"/> |
| 131 <has_text text="contig-21000001"/> | 131 <has_text text="contig-21000001"/> |
| 132 </assert_contents> | 132 </assert_contents> |
| 133 </output> | 133 </output> |
| 134 <output name="output_clustering" ftype="csv"> | 134 <output name="output_clustering" ftype="csv"> |
| 135 <assert_contents> | 135 <assert_contents> |