Mercurial > repos > iuc > dropletutils
diff dropletutils.xml @ 6:8855361fcfc5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"
| author | iuc |
|---|---|
| date | Thu, 10 Dec 2020 13:50:06 +0000 |
| parents | cdf4443d5625 |
| children | 2c1200fba922 |
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--- a/dropletutils.xml Wed Jan 29 15:07:38 2020 -0500 +++ b/dropletutils.xml Thu Dec 10 13:50:06 2020 +0000 @@ -1,9 +1,22 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="dropletutils" name="DropletUtils" version="@PACKAGE_VERSION@+@GALAXY_VERSION@" > +<tool id="dropletutils" name="DropletUtils" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > <description>Utilities for handling droplet-based single-cell RNA-seq data</description> + <xrefs> + <xref type="bio.tools">dropletutils</xref> + </xrefs> + <edam_topics> + <edam_topic>topic_0203</edam_topic> + <edam_topic>topic_3168</edam_topic> + <edam_topic>topic_3170</edam_topic> + <edam_topic>topic_3308</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_1812</edam_operation> + <edam_operation>operation_3200</edam_operation> + </edam_operations> <macros> - <token name="@PACKAGE_VERSION@" >1.2.1</token> - <token name="@GALAXY_VERSION@" >galaxy6</token> + <token name="@TOOL_VERSION@">1.10.0</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@TXIN@">tenx.input</token> <token name="@TXOUT@">tenx.output</token> <xml name="test_dirin" > @@ -16,9 +29,10 @@ </xml> </macros> <requirements> - <requirement type="package" version="@PACKAGE_VERSION@">bioconductor-dropletutils</requirement> - <requirement type="package" version="1.2_17" >r-matrix</requirement> - <requirement type="package" version="1.10.1" >bioconductor-scater</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-dropletutils</requirement> + <requirement type="package" version="1.18.0" >bioconductor-scater</requirement> + <requirement type="package" version="4.0">r-base</requirement> + <requirement type="package" version="1.2_18">r-matrix</requirement> <requirement type="package" version="1">fonts-conda-ecosystem</requirement> </requirements> <version_command><![CDATA[ @@ -45,14 +59,14 @@ <configfiles> <configfile name="droplet_conf" > ## defaults -empty.fdr_threshold = 0.01 -eparams=formals(emptyDrops) -dparams=formals(defaultDrops) -bparams=formals(barcodeRanks) +empty_fdr_threshold = 0.01 +eparams = formals(emptyDrops) +dparams = formals(defaultDrops) +bparams = formals(barcodeRanks) ## File params -in.type='$tenx_format.use' -out.type=NULL +intype='$tenx_format.use' +outtype=NULL files=list() files\$table='$table' @@ -74,10 +88,10 @@ #else if str($operation.method.use) == 'emptydrops': do.method="emptyDrops" eparams\$lower=as.integer('$operation.method.lower') -empty.fdr_threshold=as.numeric('$operation.method.fdr_thresh') +empty_fdr_threshold=as.numeric('$operation.method.fdr_thresh') #end if -out.type='$operation.outformat' +outtype='$operation.outformat' #if str($operation.outformat) == 'directory': files\$out='@TXOUT@' #else if str($operation.outformat) == 'h5': @@ -172,8 +186,8 @@ </outputs> <tests> <!-- Directory input tests --> - <!-- ::: Default Drops --> <test expect_num_outputs="1"> + <!-- ::: Default Drops --> <expand macro="test_dirin" /> <conditional name="operation"> <param name="use" value="filter" /> @@ -196,17 +210,17 @@ </assert_contents> </output> </test> - <!-- :: Barcode Ranks --> <test expect_num_outputs="1"> + <!-- :: Barcode Ranks --> <expand macro="test_dirin" /> <conditional name="operation"> <param name="use" value="barcode_rank" /> <param name="lower" value="120" /> </conditional> - <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="400"/> + <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="600"/> </test> - <!-- ::: Empty Drops --> <test expect_num_outputs="3"> + <!-- ::: Empty Drops --> <expand macro="test_dirin" /> <conditional name="operation"> <param name="use" value="filter" /> @@ -221,16 +235,16 @@ <output name="table" > <assert_contents> <has_n_columns n="9" /> - <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> - <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" /> - <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166.644236503983\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" /> + <has_line_matching expression="^\sbar_names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis_cell\sis_cellandlimited" /> + <has_line_matching expression="^994\sGGCATTACAA\s338\s-246\.(.*TRUE){3}$" /> + <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166\.(.*TRUE){3}$" /> </assert_contents> </output> <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" /> </test> <!-- Other format input tests --> - <!-- ::: Empty Drops, same as above but input is h5 --> <test expect_num_outputs="3"> + <!-- ::: Empty Drops, same as above but input is h5 --> <conditional name="tenx_format" > <param name="use" value="h5" /> <param name="input" value="in_matrix.h5" /> @@ -248,9 +262,9 @@ <output name="table" > <assert_contents> <has_n_columns n="9" /> - <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" /> - <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" /> - <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196.181449214729\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" /> + <has_line_matching expression="^\sbar_names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis_cell\sis_cellandlimited" /> + <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198\.(.*TRUE){3}$" /> + <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196\.(.*TRUE){3}$" /> </assert_contents> </output> <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="400" />