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comparison music_compare.xml @ 1:4447ed460308 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
author bgruening
date Mon, 02 May 2022 09:58:49 +0000
parents 10bf0f89035f
children
comparison
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0:10bf0f89035f 1:4447ed460308
29 </repeat> 29 </repeat>
30 </macro> 30 </macro>
31 </macros> 31 </macros>
32 <expand macro="requirements" /> 32 <expand macro="requirements" />
33 <command detect_errors="exit_code" ><![CDATA[ 33 <command detect_errors="exit_code" ><![CDATA[
34 cat '$conf' >> /dev/stderr &&
34 mkdir report_data && 35 mkdir report_data &&
35 Rscript --vanilla '$__tool_directory__/scripts/compare.R' '$conf' 36 Rscript --vanilla '$__tool_directory__/scripts/compare.R' '$conf'
36 ]]></command> 37 ]]></command>
37 <configfiles> 38 <configfiles>
38 <configfile name="conf" > 39 <configfile name="conf" >
75 ) 76 )
76 #end if 77 #end if
77 #end for 78 #end for
78 ) 79 )
79 80
80 heat_grouped_p = as.logical('$heat_grouped_p')
81 out_filt = list(cells = null_str_vec('$filter.out_list_cells'), 81 out_filt = list(cells = null_str_vec('$filter.out_list_cells'),
82 facts = null_str_vec('$filter.out_list_facts')) 82 facts = null_str_vec('$filter.out_list_facts'))
83
83 est_method = null_str_vec('$est_method') 84 est_method = null_str_vec('$est_method')
85 dendro_setting = null_str_vec('$dendro_setting')
84 86
85 out_heatmulti_pdf = '$out_heatmulti_pdf' 87 out_heatmulti_pdf = '$out_heatmulti_pdf'
86 out_heatsumm_pdf = '$out_heatsumm_pdf' 88 out_heatsumm_pdf = '$out_heatsumm_pdf'
87 </configfile> 89 </configfile>
88 </configfiles> 90 </configfiles>
130 </repeat> 132 </repeat>
131 <param name="est_method" type="select" label="Method to use" help="One to compare across all" > 133 <param name="est_method" type="select" label="Method to use" help="One to compare across all" >
132 <option value="MuSiC" selected="true" >MuSiC</option> 134 <option value="MuSiC" selected="true" >MuSiC</option>
133 <option value="NNLS" selected="true" >NNLS</option> 135 <option value="NNLS" selected="true" >NNLS</option>
134 </param> 136 </param>
135 <param name="heat_grouped_p" type="boolean" label="Individual heatmaps grouped by scRNA dataset?" checked="true" /> 137 <param name="dendro_setting" type="select" label="Cluster heatmaps?"
138 help="Samples, Cells and Datasets can all be clustered by similarity.">
139 <option value="None" selected="true" >No, preserve order of Rows and Columns</option>
140 <option value="Both">Cluster both Rows and Columns</option>
141 <option value="Cols">Cluster only Columns</option>
142 <option value="Rows">Cluster only Rows</option>
143 </param>
136 <section name="filter" title="Filter Summary Plots" > 144 <section name="filter" title="Filter Summary Plots" >
137 <param name="out_list_cells" type="text" label="Show only these cell types (blank for all)" 145 <param name="out_list_cells" type="text" label="Show only these cell types (blank for all)"
138 help="Comma-delimited list. Cell types given in the above scRNA datasets are still used for deconvolution (bulk reads are still assigned to discrete cell types), but we merely select the ones we want to show." /> 146 help="Comma-delimited list. Cell types given in the above scRNA datasets are still used for deconvolution (bulk reads are still assigned to discrete cell types), but we merely select the ones we want to show." />
139 <param name="out_list_facts" type="text" label="Show only these factors (blank for all)" 147 <param name="out_list_facts" type="text" label="Show only these factors (blank for all)"
140 help="Comma-delimited list. Factors must exist in those inferred from the above bulk datasets." /> 148 help="Comma-delimited list. Factors must exist in those inferred from the above bulk datasets." />
153 <tests> 161 <tests>
154 <test expect_num_outputs="4" > 162 <test expect_num_outputs="4" >
155 <!-- NNLS Test with severe output filtering --> 163 <!-- NNLS Test with severe output filtering -->
156 <expand macro="test_input" /> 164 <expand macro="test_input" />
157 <param name="est_method" value="NNLS" /> 165 <param name="est_method" value="NNLS" />
158 <param name="heat_grouped_p" value="true" />
159 <section name="filter" > 166 <section name="filter" >
160 <param name="out_list_cells" value="PT,Podo,Fib,Endo" /> 167 <param name="out_list_cells" value="PT,Podo,Fib,Endo" />
161 <param name="out_list_facts" value="APOL1,Pheno1" /> 168 <param name="out_list_facts" value="APOL1,Pheno1" />
162 </section> 169 </section>
163 <output name="out_heatsumm_pdf" value="out_filt1.pdf" compare="sim_size" /> 170 <output name="out_heatsumm_pdf" value="out_filt1.pdf" compare="sim_size" />
164 </test> 171 </test>
165 <test expect_num_outputs="4" > 172 <test expect_num_outputs="4" >
166 <!-- NNLS Test with only factor filtering --> 173 <!-- NNLS Test with only factor filtering -->
167 <expand macro="test_input" /> 174 <expand macro="test_input" />
168 <param name="est_method" value="NNLS" /> 175 <param name="est_method" value="NNLS" />
169 <param name="heat_grouped_p" value="true" />
170 <section name="filter" > 176 <section name="filter" >
171 <param name="out_list_facts" value="APOL1,Pheno1" /> 177 <param name="out_list_facts" value="APOL1,Pheno1" />
172 </section> 178 </section>
173 <output name="out_heatmulti_pdf" value="out_heat2.pdf" compare="sim_size" /> 179 <output name="out_heatmulti_pdf" value="out_heat2.pdf" compare="sim_size" />
174 </test> 180 </test>
175 <test expect_num_outputs="4" > 181 <test expect_num_outputs="4" >
182 <!-- NNLS Test with factor filtering and dendrograms -->
183 <expand macro="test_input" />
184 <param name="est_method" value="NNLS" />
185 <param name="dendro_setting" value="Both" />
186 <section name="filter" >
187 <param name="out_list_facts" value="APOL1,Pheno1" />
188 </section>
189 <output name="out_heatmulti_pdf" value="out_heat2.pdf" compare="sim_size" />
190 </test>
191 <test expect_num_outputs="4" >
176 <!-- MuSiC Test with no filtering --> 192 <!-- MuSiC Test with no filtering -->
177 <expand macro="test_input" /> 193 <expand macro="test_input" />
178 <param name="est_method" value="MuSiC" /> 194 <param name="est_method" value="MuSiC" />
179 <param name="heat_grouped_p" value="true" />
180 <output_collection name="dtables" count="3"> 195 <output_collection name="dtables" count="3">
181 <element name="Data Table" ftype="tabular" > 196 <element name="Data Table" ftype="tabular" >
182 <assert_contents> 197 <assert_contents>
183 <has_text_matching expression="B\:\:APOL1\.G1NF42\s+PT\s+B\s+APOL1\s+0.56\d+\s+19035\d+" /> 198 <has_text_matching expression="B\:\:APOL1\.G1NF42\s+PT\s+B\s+APOL1\s+0.56\d+\s+19035\d+" />
184 </assert_contents> 199 </assert_contents>