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comparison 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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equal deleted inserted replaced
5:147577841bb8 6:16672a3c9b65
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>