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comparison dropletutils.xml @ 2:58105e5efa8d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
author iuc
date Fri, 06 Sep 2019 10:55:49 -0400
parents 94ee8160ace3
children 2bbf0052aaa9
comparison
equal deleted inserted replaced
1:94ee8160ace3 2:58105e5efa8d
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@" >2</token> 6 <token name="@GALAXY_VERSION@" >3</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" />
123 <param name="use" type="select" label="Method" help="The DefaultDrops method calls cells according to the number of UMIs associated with each barcode as implemented by CellRanger. The EmptyDrops method identifies empty droplets using a smart ambient background model." > 123 <param name="use" type="select" label="Method" help="The DefaultDrops method calls cells according to the number of UMIs associated with each barcode as implemented by CellRanger. The EmptyDrops method identifies empty droplets using a smart ambient background model." >
124 <option value="defaultdrops" selected="true">DefaultDrops</option> 124 <option value="defaultdrops" selected="true">DefaultDrops</option>
125 <option value="emptydrops">EmptyDrops</option> 125 <option value="emptydrops">EmptyDrops</option>
126 </param> 126 </param>
127 <when value="defaultdrops"> 127 <when value="defaultdrops">
128 <param name="expected" type="integer" min="10" value="3000" label="Expected Number of Cells" help="The expected number of cells in the sample." /> 128 <param name="expected" type="integer" min="1" value="3000" label="Expected Number of Cells" help="The expected number of cells in the sample." />
129 <param name="upperquant" type="float" min="0.1" max="1.0" value="0.99" label="Upper Quantile" help="The quantile of the top expected barcodes to consider." /> 129 <param name="upperquant" type="float" min="0" max="1.0" value="0.99" label="Upper Quantile" help="The quantile of the top expected barcodes to consider." />
130 <param name="lowerprop" type="float" min="0.1" max="1.0" value="0.1" label="Lower Proportion" help="The fraction of molecules of the upper quantile that must be exceeded for a cell barcode to be detected." /> 130 <param name="lowerprop" type="float" min="0" max="1.0" value="0.1" label="Lower Proportion" help="The fraction of molecules of the upper quantile that must be exceeded for a cell barcode to be detected." />
131 </when> 131 </when>
132 <when value="emptydrops"> 132 <when value="emptydrops">
133 <param name="lower" type="integer" min="10" value="100" label="Lower-bound Threshold" help="The lower-bound threshold of the total UMI count at which barcodes beneath this are assumed to be empty droplets." /> 133 <param name="lower" type="integer" min="1" value="100" label="Lower-bound Threshold" help="The lower-bound threshold of the total UMI count at which barcodes beneath this are assumed to be empty droplets." />
134 <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." /> 134 <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 </when> 135 </when>
136 </conditional> 136 </conditional>
137 <param name="outformat" type="select" label="Format for output matrices"> 137 <param name="outformat" type="select" label="Format for output matrices">
138 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option> 138 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option>
139 <option value="h5ad" selected="true" >AnnData/H5</option> 139 <option value="h5ad" selected="true" >AnnData/H5</option>
140 <option value="tsv">Tabular</option> 140 <option value="tsv">Tabular</option>
141 </param> 141 </param>
142 </when> 142 </when>
143 <when value="barcode_rank"> 143 <when value="barcode_rank">
144 <param name="lower" type="integer" min="10" 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."/> 144 <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 </when> 145 </when>
146 </conditional> 146 </conditional>
147 <param name="seed" type="integer" value="100" label="Random Seed" /> 147 <param name="seed" type="integer" value="100" label="Random Seed" />
148 </inputs> 148 </inputs>
149 <outputs> 149 <outputs>
219 <output name="fileout_h5ad" value="defs_emptydrops_150_0002.h5ad" compare="sim_size" delta="10" /> 219 <output name="fileout_h5ad" value="defs_emptydrops_150_0002.h5ad" compare="sim_size" delta="10" />
220 <output name="table" > 220 <output name="table" >
221 <assert_contents> 221 <assert_contents>
222 <has_n_columns n="9" /> 222 <has_n_columns n="9" />
223 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> 223 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
224 <has_line_matching expression="^1\sGGAAGAAGAA\s0\sNA\sNA\sNA\sNA\sNA\sNA" /> 224 <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
225 <has_line_matching expression="^11100\sGCTGAAGCAA\s71\sNA\sNA\sNA\sNA\sNA\sNA" /> 225 <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166.644236503983\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
226 </assert_contents> 226 </assert_contents>
227 </output> 227 </output>
228 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="100" /> 228 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="100" />
229 </test> 229 </test>
230 <!-- Other format input tests --> 230 <!-- Other format input tests -->
246 <output name="fileout_h5ad" value="defs_emptydrops_150_0002a.h5ad" compare="sim_size" delta="200" /> 246 <output name="fileout_h5ad" value="defs_emptydrops_150_0002a.h5ad" compare="sim_size" delta="200" />
247 <output name="table" > 247 <output name="table" >
248 <assert_contents> 248 <assert_contents>
249 <has_n_columns n="9" /> 249 <has_n_columns n="9" />
250 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> 250 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
251 <has_line_matching expression="^1\sGGAAGAAGAA\s20\sNA\sNA\sNA\sNA\sNA\sNA" /> 251 <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
252 <has_line_matching expression="^11100\sGCTGAAGCAA\s203\s-222.833111872316\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" /> 252 <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196.181449214729\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
253 </assert_contents> 253 </assert_contents>
254 </output> 254 </output>
255 <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="100" /> 255 <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="100" />
256 </test> 256 </test>
257 <!-- Output a directory --> 257 <!-- Output a directory -->