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comparison dropletutils.xml @ 5:d5e4b59d5331 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7"
author iuc
date Wed, 29 Jan 2020 20:07:15 +0000
parents a75b34ff05f0
children a79cf05ca77d
comparison
equal deleted inserted replaced
4:a75b34ff05f0 5:d5e4b59d5331
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="dropletutils" name="DropletUtils" version="@PACKAGE_VERSION@+@GALAXY_VERSION@" > 2 <tool id="dropletutils" name="DropletUtils" version="@PACKAGE_VERSION@+@GALAXY_VERSION@" >
3 <description>Utilities for handling droplet-based single-cell RNA-seq data</description> 3 <description>Utilities for handling droplet-based single-cell RNA-seq data</description>
4 <macros> 4 <macros>
5 <token name="@PACKAGE_VERSION@" >1.2.1</token> 5 <token name="@PACKAGE_VERSION@" >1.2.1</token>
6 <token name="@GALAXY_VERSION@" >5</token> 6 <token name="@GALAXY_VERSION@" >galaxy6</token>
7 <token name="@TXIN@">tenx.input</token> 7 <token name="@TXIN@">tenx.input</token>
8 <token name="@TXOUT@">tenx.output</token> 8 <token name="@TXOUT@">tenx.output</token>
9 <xml name="test_dirin" > 9 <xml name="test_dirin" >
10 <conditional name="tenx_format"> 10 <conditional name="tenx_format">
11 <param name="use" value="directory" /> 11 <param name="use" value="directory" />
78 #end if 78 #end if
79 79
80 out.type='$operation.outformat' 80 out.type='$operation.outformat'
81 #if str($operation.outformat) == 'directory': 81 #if str($operation.outformat) == 'directory':
82 files\$out='@TXOUT@' 82 files\$out='@TXOUT@'
83 #else if str($operation.outformat) == 'h5ad': 83 #else if str($operation.outformat) == 'h5':
84 files\$out='$fileout_h5ad' 84 files\$out='$fileout_h5'
85 #else if str($operation.outformat) == 'tsv': 85 #else if str($operation.outformat) == 'tsv':
86 files\$out='$fileout_tsv' 86 files\$out='$fileout_tsv'
87 #end if 87 #end if
88 88
89 #else if str($operation.use) == 'barcode_rank': 89 #else if str($operation.use) == 'barcode_rank':
97 </configfiles> 97 </configfiles>
98 <inputs> 98 <inputs>
99 <conditional name="tenx_format"> 99 <conditional name="tenx_format">
100 <param name="use" type="select" label="Format for the input matrix"> 100 <param name="use" type="select" label="Format for the input matrix">
101 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option> 101 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option>
102 <option value="h5ad" selected="true" >AnnData/H5</option> 102 <option value="h5" selected="true" >H5</option>
103 <option value="tsv">Tabular</option> 103 <option value="tsv">Tabular</option>
104 </param> 104 </param>
105 <when value="directory"> 105 <when value="directory">
106 <param name="input" type="data" format="mtx,txt" label="Count Data"/> 106 <param name="input" type="data" format="mtx,txt" label="Count Data"/>
107 <param name="input_genes" type="data" format="tabular,tsv,txt" label="Genes List"/> 107 <param name="input_genes" type="data" format="tabular,tsv,txt" label="Genes List"/>
108 <param name="input_barcodes" type="data" format="tabular,tsv,txt" label="Barcodes List"/> 108 <param name="input_barcodes" type="data" format="tabular,tsv,txt" label="Barcodes List"/>
109 </when> 109 </when>
110 <when value="h5ad"> 110 <when value="h5">
111 <param name="input" type="data" format="h5ad" label="Count Data"/> 111 <param name="input" type="data" format="h5" label="Count Data"/>
112 </when> 112 </when>
113 <when value="tsv"> 113 <when value="tsv">
114 <param name="input" type="data" format="tabular,tsv" label="Count Data" help="The first column must contain gene names, and the first row must contain barcode identifiers." /> 114 <param name="input" type="data" format="tabular,tsv" label="Count Data" help="The first column must contain gene names, and the first row must contain barcode identifiers." />
115 </when> 115 </when>
116 </conditional> 116 </conditional>
135 <param name="fdr_thresh" type="float" min="0" max="1" value="0.01" label="FDR Threshold" help="False Discovery Rate threshold at which droplets with significant deviations from the ambient profile are detected at this threshold. If set to 0, the threshold is ignored." /> 135 <param name="fdr_thresh" type="float" min="0" max="1" value="0.01" label="FDR Threshold" help="False Discovery Rate threshold at which droplets with significant deviations from the ambient profile are detected at this threshold. If set to 0, the threshold is ignored." />
136 </when> 136 </when>
137 </conditional> 137 </conditional>
138 <param name="outformat" type="select" label="Format for output matrices"> 138 <param name="outformat" type="select" label="Format for output matrices">
139 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option> 139 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option>
140 <option value="h5ad" selected="true" >AnnData/H5</option> 140 <option value="h5" selected="true" >H5</option>
141 <option value="tsv">Tabular</option> 141 <option value="tsv">Tabular</option>
142 </param> 142 </param>
143 </when> 143 </when>
144 <when value="barcode_rank"> 144 <when value="barcode_rank">
145 <param name="lower" type="integer" min="1" value="100" label="Lower Bound" help="Lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets."/> 145 <param name="lower" type="integer" min="1" value="100" label="Lower Bound" help="Lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets."/>
149 </inputs> 149 </inputs>
150 <outputs> 150 <outputs>
151 <data name="fileout_tsv" format="tsv" label="${tool.name} Count Matrix on ${on_string}"> 151 <data name="fileout_tsv" format="tsv" label="${tool.name} Count Matrix on ${on_string}">
152 <filter>operation['use']=='filter' and operation['outformat'] == 'tsv' </filter> 152 <filter>operation['use']=='filter' and operation['outformat'] == 'tsv' </filter>
153 </data> 153 </data>
154 <data name="fileout_h5ad" format="h5ad" label="${tool.name} AnnData on ${on_string}"> 154 <data name="fileout_h5" format="h5" label="${tool.name} H5 Matrix on ${on_string}">
155 <filter>operation['use']=='filter' and operation['outformat'] == 'h5ad'</filter> 155 <filter>operation['use']=='filter' and operation['outformat'] == 'h5'</filter>
156 </data> 156 </data>
157 <data name="barcodes_out" format="tsv" from_work_dir="@TXOUT@/barcodes.tsv" label="${tool.name} 10X Barcodes on ${on_string}" > 157 <data name="barcodes_out" format="tsv" from_work_dir="@TXOUT@/barcodes.tsv" label="${tool.name} 10X Barcodes on ${on_string}" >
158 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter> 158 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter>
159 </data> 159 </data>
160 <data name="genes_out" format="tsv" from_work_dir="@TXOUT@/genes.tsv" label="${tool.name} 10X Genes on ${on_string}" > 160 <data name="genes_out" format="tsv" from_work_dir="@TXOUT@/genes.tsv" label="${tool.name} 10X Genes on ${on_string}" >
175 <!-- ::: Default Drops --> 175 <!-- ::: Default Drops -->
176 <test expect_num_outputs="1"> 176 <test expect_num_outputs="1">
177 <expand macro="test_dirin" /> 177 <expand macro="test_dirin" />
178 <conditional name="operation"> 178 <conditional name="operation">
179 <param name="use" value="filter" /> 179 <param name="use" value="filter" />
180 <param name="outformat" value="h5ad" /><!-- H5AD --> 180 <param name="outformat" value="h5" /><!-- H5 -->
181 </conditional> 181 </conditional>
182 <output name="fileout_h5ad" value="defs_defaultdrops.h5ad" compare="sim_size" delta="10" /> 182 <output name="fileout_h5" value="defs_defaultdrops.h5" compare="sim_size" delta="10" />
183 </test> 183 </test>
184 <test expect_num_outputs="1"> 184 <test expect_num_outputs="1">
185 <expand macro="test_dirin" /> 185 <expand macro="test_dirin" />
186 <conditional name="operation"> 186 <conditional name="operation">
187 <param name="use" value="filter" /> 187 <param name="use" value="filter" />
208 <!-- ::: Empty Drops --> 208 <!-- ::: Empty Drops -->
209 <test expect_num_outputs="3"> 209 <test expect_num_outputs="3">
210 <expand macro="test_dirin" /> 210 <expand macro="test_dirin" />
211 <conditional name="operation"> 211 <conditional name="operation">
212 <param name="use" value="filter" /> 212 <param name="use" value="filter" />
213 <param name="outformat" value="h5ad" /> 213 <param name="outformat" value="h5" />
214 <conditional name="method"> 214 <conditional name="method">
215 <param name="use" value="emptydrops" /> 215 <param name="use" value="emptydrops" />
216 <param name="lower" value="150" /> 216 <param name="lower" value="150" />
217 <param name="fdr_thresh" value="0.02" /> 217 <param name="fdr_thresh" value="0.02" />
218 </conditional> 218 </conditional>
219 </conditional> 219 </conditional>
220 <output name="fileout_h5ad" value="defs_emptydrops_150_0002.h5ad" compare="sim_size" delta="10" /> 220 <output name="fileout_h5" value="defs_emptydrops_150_0002.h5" compare="sim_size" delta="10" />
221 <output name="table" > 221 <output name="table" >
222 <assert_contents> 222 <assert_contents>
223 <has_n_columns n="9" /> 223 <has_n_columns n="9" />
224 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> 224 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
225 <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" /> 225 <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
227 </assert_contents> 227 </assert_contents>
228 </output> 228 </output>
229 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" /> 229 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" />
230 </test> 230 </test>
231 <!-- Other format input tests --> 231 <!-- Other format input tests -->
232 <!-- ::: Empty Drops, same as above but input is h5ad --> 232 <!-- ::: Empty Drops, same as above but input is h5 -->
233 <test expect_num_outputs="3"> 233 <test expect_num_outputs="3">
234 <conditional name="tenx_format" > 234 <conditional name="tenx_format" >
235 <param name="use" value="h5ad" /> 235 <param name="use" value="h5" />
236 <param name="input" value="in_matrix.h5ad" /> 236 <param name="input" value="in_matrix.h5" />
237 </conditional> 237 </conditional>
238 <conditional name="operation"> 238 <conditional name="operation">
239 <param name="use" value="filter" /> 239 <param name="use" value="filter" />
240 <param name="outformat" value="h5ad" /> 240 <param name="outformat" value="h5" />
241 <conditional name="method"> 241 <conditional name="method">
242 <param name="use" value="emptydrops" /> 242 <param name="use" value="emptydrops" />
243 <param name="lower" value="150" /> 243 <param name="lower" value="150" />
244 <param name="fdr_thresh" value="0.02" /> 244 <param name="fdr_thresh" value="0.02" />
245 </conditional> 245 </conditional>
246 </conditional> 246 </conditional>
247 <output name="fileout_h5ad" value="defs_emptydrops_150_0002a.h5ad" compare="sim_size" delta="400" /> 247 <output name="fileout_h5" value="defs_emptydrops_150_0002a.h5" compare="sim_size" delta="400" />
248 <output name="table" > 248 <output name="table" >
249 <assert_contents> 249 <assert_contents>
250 <has_n_columns n="9" /> 250 <has_n_columns n="9" />
251 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> 251 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
252 <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" /> 252 <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />