Mercurial > repos > iuc > cnvkit_call

comparison call.xml @ 3:b7b790a1cae0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5
author iuc
date Fri, 13 Dec 2024 23:54:51 +0000
parents 46f2af94b1bf
children e570209e97bf
comparison
equal deleted inserted replaced
2:46f2af94b1bf 3:b7b790a1cae0
96 <data name="out_sample_Bintest" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" /> 96 <data name="out_sample_Bintest" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
97 </outputs> 97 </outputs>
98 <tests> 98 <tests>
99 <test expect_num_outputs="1"> 99 <test expect_num_outputs="1">
100 <param name="input_sample_file" ftype="tabular" value="tumor.cns" /> 100 <param name="input_sample_file" ftype="tabular" value="tumor.cns" />
101 <param name="zygosity_freq" value="0.25" /> 101 <section name="additional_SNP_allelic_process">
102 <param name="min_variant_depth" value="40" /> 102 <param name="zygosity_freq" value="0.25" />
103 <param name="purity" value="1" /> 103 <param name="min_variant_depth" value="40" />
104 </section>
105 <section name="advanced_settings">
106 <param name="purity" value="1" />
107 </section>
104 <output name="out_sample_Bintest"> 108 <output name="out_sample_Bintest">
105 <assert_contents><has_text_matching expression="chrM"/></assert_contents> 109 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
106 </output> 110 </output>
107 </test> 111 </test>
108 <test expect_num_outputs="1"> 112 <test expect_num_outputs="1">
109 <conditional name="Sample_sex"> 113 <section name="advanced_settings">
110 <param name="sex" value="yes" /> 114 <conditional name="Sample_sex">
111 </conditional> 115 <param name="sex" value="yes" />
116 </conditional>
117 <param name="purity" value="1" />
118 </section>
112 <param name="input_sample_file" ftype="tabular" value="tumor.cns" /> 119 <param name="input_sample_file" ftype="tabular" value="tumor.cns" />
113 <param name="min_variant_depth" value="40" /> 120 <section name="additional_SNP_allelic_process">
114 <param name="purity" value="1" /> 121 <param name="min_variant_depth" value="40" />
122 </section>
115 <output name="out_sample_Bintest"> 123 <output name="out_sample_Bintest">
116 <assert_contents><has_text_matching expression="chrM"/></assert_contents> 124 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
117 </output> 125 </output>
118 </test> 126 </test>
119 </tests> 127 </tests>