Mercurial > repos > iuc > cnvkit_reference

comparison reference.xml @ 4:b45fa373a972 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 23:57:41 +0000
parents 0c3db8ec44b0
children 403825b9349a
comparison
equal deleted inserted replaced
3:c6102e8e3deb 4:b45fa373a972
96 <outputs> 96 <outputs>
97 <data name="out_referene_tas" format="tabular" label="${tool.name} on ${on_string}: TAS-on-target coverage" from_work_dir="ref-tas.cnn" /> 97 <data name="out_referene_tas" format="tabular" label="${tool.name} on ${on_string}: TAS-on-target coverage" from_work_dir="ref-tas.cnn" />
98 </outputs> 98 </outputs>
99 <tests> 99 <tests>
100 <test expect_num_outputs="1"> 100 <test expect_num_outputs="1">
101 <conditional name="reference_source"> 101 <conditional name="CNV_reference">
102 <param name="ref_selector" value="history"/> 102 <param name="CNV_reference_availabel" value="yes" />
103 <param name="fasta" ftype="fasta" value="genome.fasta" /> 103 <section name="advanced_settings">
104 </conditional> 104 <conditional name="reference_source">
105 <param name="CNV_reference_availabel" value="yes" /> 105 <param name="ref_selector" value="history"/>
106 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" /> 106 <param name="fasta" ftype="fasta" value="genome.fasta" />
107 <param name="no_gc" value="1" /> 107 </conditional>
108 </section>
109 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
110 <section name="disable_some_of_the_bias_corrections">
111 <param name="no_gc" value="1" />
112 </section>
113 </conditional>
108 <output name="out_referene_tas" file="ref-tas.cnn" /> 114 <output name="out_referene_tas" file="ref-tas.cnn" />
109 </test> 115 </test>
110 <test expect_num_outputs="1"> 116 <test expect_num_outputs="1">
111 <conditional name="reference_source"> 117 <conditional name="CNV_reference">
112 <param name="ref_selector" value="cached"/> 118 <param name="CNV_reference_availabel" value="yes" />
113 <param name="fasta" value="test_buildid"/> 119 <section name="advanced_settings">
114 </conditional> 120 <conditional name="reference_source">
115 <param name="CNV_reference_availabel" value="yes" /> 121 <param name="ref_selector" value="cached"/>
116 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" /> 122 <param name="fasta" value="test_buildid"/>
117 <param name="no_gc" value="1" /> 123 </conditional>
124 </section>
125 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
126 <section name="disable_some_of_the_bias_corrections">
127 <param name="no_gc" value="1" />
128 </section>
129 </conditional>
118 <output name="out_referene_tas" file="ref-tas.cnn" /> 130 <output name="out_referene_tas" file="ref-tas.cnn" />
119 </test> 131 </test>
120 <test expect_num_outputs="1"> 132 <test expect_num_outputs="1">
121 <conditional name="reference_source"> 133 <conditional name="CNV_reference">
122 <param name="ref_selector" value="cached"/> 134 <param name="CNV_reference_availabel" value="yes" />
123 <param name="fasta" value="test_buildid"/> 135 <section name="advanced_settings">
124 </conditional> 136 <conditional name="reference_source">
125 <param name="CNV_reference_availabel" value="yes" /> 137 <param name="ref_selector" value="cached"/>
126 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" /> 138 <param name="fasta" value="test_buildid"/>
127 <param name="no_gc" value="1" /> 139 </conditional>
140 </section>
141 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" />
142 <section name="disable_some_of_the_bias_corrections">
143 <param name="no_gc" value="1" />
144 </section>
145 </conditional>
128 <output name="out_referene_tas"> 146 <output name="out_referene_tas">
129 <assert_contents><has_text text="chromosome"/></assert_contents> 147 <assert_contents><has_text text="chromosome"/></assert_contents>
130 </output> 148 </output>
131 </test> 149 </test>
132 <test expect_num_outputs="1"> 150 <test expect_num_outputs="1">
133 <conditional name="reference_source"> 151 <conditional name="CNV_reference">
134 <param name="ref_selector" value="cached"/> 152 <param name="CNV_reference_availabel" value="no" />
135 <param name="fasta" value="test_buildid"/> 153 <section name="advanced_settings">
136 </conditional> 154 <conditional name="reference_source">
137 <param name="CNV_reference_availabel" value="no" /> 155 <param name="ref_selector" value="cached"/>
138 <param name="targets" ftype="bed" value="capture.target.bed" /> 156 <param name="fasta" value="test_buildid"/>
139 <param name="no_gc" value="1" /> 157 </conditional>
158 </section>
159 <param name="targets" ftype="bed" value="capture.target.bed" />
160 <section name="disable_some_of_the_bias_corrections">
161 <param name="no_gc" value="1" />
162 </section>
163 </conditional>
140 <output name="out_referene_tas"> 164 <output name="out_referene_tas">
141 <assert_contents><has_text text="chromosome"/></assert_contents> 165 <assert_contents><has_text text="chromosome"/></assert_contents>
142 </output> 166 </output>
143 </test> 167 </test>
144 <test expect_num_outputs="1"> 168 <test expect_num_outputs="1">
145 <conditional name="reference_source"> 169 <conditional name="CNV_reference">
146 <param name="ref_selector" value="cached"/> 170 <param name="CNV_reference_availabel" value="no" />
147 <param name="fasta" value="test_buildid"/> 171 <section name="advanced_settings">
148 </conditional> 172 <conditional name="reference_source">
149 <conditional name="Sample_sex"> 173 <param name="ref_selector" value="cached"/>
150 <param name="sex" value="no" /> 174 <param name="fasta" value="test_buildid"/>
151 </conditional> 175 </conditional>
152 <param name="CNV_reference_availabel" value="no" /> 176 <conditional name="Sample_sex">
153 <param name="targets" ftype="bed" value="capture.target.bed" /> 177 <param name="sex" value="no" />
154 <param name="no_gc" value="1" /> 178 </conditional>
179 </section>
180 <param name="targets" ftype="bed" value="capture.target.bed" />
181 <section name="disable_some_of_the_bias_corrections">
182 <param name="no_gc" value="1" />
183 </section>
184 </conditional>
155 <output name="out_referene_tas"> 185 <output name="out_referene_tas">
156 <assert_contents><has_text text="chromosome"/></assert_contents> 186 <assert_contents><has_text text="chromosome"/></assert_contents>
157 </output> 187 </output>
158 </test> 188 </test>
159 </tests> 189 </tests>