Mercurial > repos > iuc > dropletutils
comparison dropletutils.xml @ 2:a8aa294401be draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"
author | iuc |
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date | Fri, 06 Sep 2019 10:56:16 -0400 |
parents | cfe1e6c28d95 |
children | f0de368eabca |
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1:cfe1e6c28d95 | 2:a8aa294401be |
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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 --> |