Mercurial > repos > iuc > baredsc_combine_2d
diff baredsc_combine_2d.xml @ 0:ac9434b9fc27 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
| author | iuc |
|---|---|
| date | Mon, 02 Oct 2023 13:23:59 +0000 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/baredsc_combine_2d.xml Mon Oct 02 13:23:59 2023 +0000 @@ -0,0 +1,140 @@ +<tool id="baredsc_combine_2d" name="Combine multiple 2D Models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> + <description>from baredSC</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_topics"/> + <edam_operations> + <edam_operation>operation_2495</edam_operation> + <edam_operation>operation_3463</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">baredsc</xref> + </xrefs> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ## Create symlinks + #for $i, $output in enumerate($MCMC.outputs): + ln -s '$output' '${i}.npz' && + #end for + + combineMultipleModels_2d + ## Required inputs: + @REQUIRED_INPUTS_2D@ + + ## Filter cells + @FILTER_CELLS@ + + @COMBINE_OUTPUTS@ + ## MCMC + @MCMC_2D@ + ## Plots + @PLOTS@ + @PRETTYBINS_SPLITY_COLORSCALE_2D@ + ## Advanced + @ADVANCED_COMMON_X@ + @ADVANCED_COMMON_COMPLEMENT_2D@ + ## Outputs + --figure baredSC.$plots.image_file_format && + mkdir output && + @ORDER_OUTPUTS_2D@ + ]]></command> + <inputs> + <expand macro="macro_input_counts"/> + <expand macro="macro_two_genes"/> + <expand macro="macro_filter_cells"/> + <section name="MCMC" title="MCMC parameters"> + <expand macro="combine_outputs" d="2" /> + <expand macro="macro_MCMC_params_common_axis" axis="x" /> + <expand macro="macro_MCMC_params_common_axis" axis="y" /> + <expand macro="macro_scale_seed"/> + </section> + <section name="plots" title="Customize plots"> + <expand macro="macro_plots"/> + <expand macro="macro_prettybins_axis" axis="x"/> + <expand macro="macro_prettybins_axis" axis="y"/> + <expand macro="macro_colorscale"/> + <expand macro="macro_splity"/> + </section> + <section name="advanced" title="Advanced parameters" expanded="false"> + <expand macro="macro_advanced_common_axis" axis="x" default_osamppdf="4"/> + <expand macro="macro_advanced_common_axis" axis="y" default_osamppdf="4"/> + <expand macro="macro_advanced_evidence"/> + <expand macro="macro_scaleprior"/> + </section> + </inputs> + <outputs> + <data format="tabular" name="pdf2d" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: mean PDF in matrix format" from_work_dir="output/baredSC_pdf2d.txt"/> + <data format="tabular" name="pdf2d_flat" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: PDF with error bar, one bin per line" from_work_dir="output/baredSC_pdf2d_flat.txt"> + <actions> + <action name="column_names" type="metadata" default="x,y,low,mean,high,median" /> + </actions> + </data> + <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: plot" from_work_dir="baredSC"> + <change_format> + <when input="plots.image_file_format" value="png" format="png" /> + <when input="plots.image_file_format" value="svg" format="svg" /> + <when input="plots.image_file_format" value="pdf" format="pdf" /> + </change_format> + </data> + <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: plots and txt"> + <discover_datasets pattern="baredSC_(?P<identifier_0>\S+)\.(?P<ext>.*)"/> + </collection> + </outputs> + <tests> + <!-- First test --> + <test> + <conditional name="input_counts"> + <param name="filetype" value="tabular"/> + <param name="input" value="nih3t3_generated_2d_2.txt"/> + </conditional> + <param name="geneXColName" value="0.5_0_0_0.5_x"/> + <param name="geneYColName" value="0.5_0_0_0.5_y"/> + <section name="MCMC"> + <param name="outputs" value="2d_small_1gauss.npz,2d_small_2gauss.npz"/> + <param name="nx" value="10"/> + <param name="ny" value="12"/> + </section> + <section name="plots"> + <param name="prettyBinsx" value="20"/> + <param name="prettyBinsy" value="20"/> + </section> + <output name="pdf2d" ftype="tabular"> + <assert_contents> + <has_n_lines n="21"/> + </assert_contents> + </output> + <output name="pdf2d_flat" ftype="tabular"> + <assert_contents> + <has_text_matching expression="x\s+y\s+low\s+mean\s+high\s+median"/> + <has_n_lines n="401"/> + </assert_contents> + </output> + <output name="plot" ftype="png"> + <assert_contents> + <has_size value="37414" delta="3000"/> + </assert_contents> + </output> + <output_collection name="other_outputs" count="3" type="list"> + <element name="corr" ftype="txt"> + <assert_contents> + <has_n_lines n="2"/> + <has_line_matching expression="mean\tmedian\tlow\thigh"/> + <has_text_matching expression="0\.9[0-9]+\s+0\.9[0-9]+\s+0\.8[0-9]+\s+0\.9[0-9]+"/> + </assert_contents> + </element> + <element name="individuals" ftype="png"> + <assert_contents> + <has_size value="56721" delta="5000"/> + </assert_contents> + </element> + <element name="median" ftype="png"> + <assert_contents> + <has_size value="37412" delta="4000"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <expand macro="helpcitations"/> +</tool> \ No newline at end of file