Mercurial > repos > iuc > baredsc_2d
diff baredsc_2d.xml @ 0:aa379e925d98 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 13:23:27 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/baredsc_2d.xml Mon Oct 02 13:23:27 2023 +0000 @@ -0,0 +1,343 @@ +<tool id="baredsc_2d" name="baredSC 2d" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> + <description>Compute distribution for a pair of genes</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[ + baredSC_2d + ## Required inputs: + @REQUIRED_INPUTS_2D@ + + ## Filter cells + @FILTER_CELLS@ + ## MCMC + @MCMC_2D@ + @BAREDSC_COMMON@ + ## Plots + @PLOTS@ + @PRETTYBINS_SPLITY_COLORSCALE_2D@ + ## Advanced + @ADVANCED_COMMON_X@ + @ADVANCED_COMMON_COMPLEMENT_2D@ + @ADVANCED_BAREDSC_COMMON@ + ## Outputs + --output output + --figure baredSC.$plots.image_file_format + --logevidence logevidence.txt && + mkdir QC && + mv baredSC_convergence.* QC && + mv baredSC_p.$plots.image_file_format QC && + mv baredSC_corner.* QC && + mkdir output && + mv baredSC_neff.txt 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="macro_MCMC_params_common_axis" axis="x" /> + <expand macro="macro_MCMC_params_common_axis" axis="y" /> + <expand macro="macro_scale_seed"/> + <expand macro="macro_MCMC_common_baredSC"/> + </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_advanced_common_baredSC"/> + <expand macro="macro_scaleprior"/> + </section> + </inputs> + <outputs> + <data format="npz" name="output" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: Numpy archive" from_work_dir="output.npz"/> + <data format="txt" name="neff" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: Neff" from_work_dir="output/baredSC_neff.txt"/> + <collection type="list" name="qc_plots" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: QC plots"> + <discover_datasets pattern="baredSC_(?P<identifier_0>\S+)\.(?P<ext>.*)" directory="QC"/> + </collection> + <data format="tabular" name="pdf2d" label="${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 ${geneYColName}: plots and txt"> + <discover_datasets pattern="baredSC_(?P<identifier_0>\S+)\.(?P<ext>.*)"/> + </collection> + <data format="txt" name="logevidence" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: Log evidence" from_work_dir="logevidence.txt"/> + </outputs> + <tests> + <!-- First test I decreased the number of samples and bins to make it quicker--> + <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="nnorm" value="2"/> + <param name="nx" value="10"/> + <param name="ny" value="12"/> + <conditional name="automaticRestart"> + <param name="set_minNeff" value="no"/> + </conditional> + <param name="nsampMCMC" value="20000"/> + </section> + <section name="plots"> + <param name="prettyBinsx" value="50"/> + <param name="prettyBinsy" value="50"/> + </section> + <output name="output"> + <assert_contents> + <has_size value="524174" delta="50000"/> + </assert_contents> + </output> + <output name="neff"> + <assert_contents> + <has_text_matching expression="^1[0-2][0-9]\."/> + </assert_contents> + </output> + <output_collection name="qc_plots" count="3" type="list"> + <element name="convergence" ftype="png"> + <assert_contents> + <has_size value="35116" delta="3000"/> + </assert_contents> + </element> + <element name="p" ftype="png"> + <assert_contents> + <has_size value="279538" delta="20000"/> + </assert_contents> + </element> + <element name="corner" ftype="png"> + <assert_contents> + <has_size value="1450978" delta="100000"/> + </assert_contents> + </element> + </output_collection> + <output name="pdf2d" ftype="tabular"> + <assert_contents> + <has_n_lines n="51"/> + <has_line_matching expression="xy\t0\.025\t0\.07500000000000001\t0\.125\t0\.17500000000000002\t0\.225\t0\.275\t0\.32500000000000007\t0\.375\t0\.42500000000000004\t0\.475\t0\.525\t0\.5750000000000001\t0\.625\t0\.675\t0\.7250000000000001\t0\.775\t0\.8250000000000001\t0\.875\t0\.925\t0\.9750000000000001\t1\.025\t1\.0750000000000002\t1\.125\t1\.1750000000000003\t1\.225\t1\.275\t1\.3250000000000002\t1\.375\t1\.4250000000000003\t1\.475\t1\.525\t1\.5750000000000002\t1\.625\t1\.6750000000000003\t1\.725\t1\.775\t1\.8250000000000002\t1\.875\t1\.9250000000000003\t1\.975\t2\.0250000000000004\t2\.075\t2\.125\t2\.175\t2\.225\t2\.2750000000000004\t2\.325\t2\.375\t2\.4250000000000003\t2\.475"/> + <has_text_matching expression="2\.5[0-9]+e-02\s+3\.[0-9]+e-02\s+[56]\.[0-9]+e-02"/> + </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="2501"/> + <has_line_matching expression="0\.025\s+0\.025[0-9]+\s+0\.002[0-9]+\s+0\.03[0-9]+\s+0\.0[67][0-9]+\s+0\.0[12][0-9]+"/> + </assert_contents> + </output> + <output name="plot" ftype="png"> + <assert_contents> + <has_size value="40843" delta="4000"/> + </assert_contents> + </output> + <output_collection name="other_outputs" count="4" type="list"> + <element name="p" ftype="txt"> + <assert_contents> + <has_line_matching expression="name\s+low\s+median\s+high"/> + <has_line_matching expression="xy_mux[01]\s+0\.3[0-9]+\s+0\.3[0-9]+\s+0\.3[0-9]+"/> + <has_text_matching expression="xy_mux[01]\s+0\.9[0-9]+\s+1\.0[0-9]+\s+1\.0[0-9]+" /> + <has_n_lines n="12"/> + </assert_contents> + </element> + <element name="corr" ftype="txt"> + <assert_contents> + <has_n_lines n="2"/> + <has_line_matching expression="mean\tmedian\tlow\thigh\tpval\terror"/> + <has_text_matching expression="0\.9[0-9]+\s+0\.9[0-9]+\s+0\.8[0-9]+\s+0\.9[0-9]+\s+0\.00[7-9][0-9]+\s+0\.00[7-9][0-9]+\s+"/> + </assert_contents> + </element> + <element name="individuals" ftype="png"> + <assert_contents> + <has_size value="56538" delta="5000"/> + </assert_contents> + </element> + <element name="median" ftype="png"> + <assert_contents> + <has_size value="40829" delta="4000"/> + </assert_contents> + </element> + </output_collection> + <output name="logevidence"> + <assert_contents> + <has_text_matching expression="^-81[0-9][0-9]\."/> + </assert_contents> + </output> + </test> + <!-- Second test pdf filtering cells title log scale--> + <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"/> + <conditional name="filter"> + <param name="nb" value="1"/> + <param name="metadata1ColName" value="0_0.5_0.5_0_group"/> + <param name="metadata1Values" value="1.0"/> + </conditional> + <section name="MCMC"> + <param name="xmin" value="-12"/> + <param name="xmax" value="-7"/> + <param name="nx" value="25"/> + <param name="ymin" value="-12"/> + <param name="ymax" value="-7"/> + <param name="ny" value="25"/> + <param name="nnorm" value="2"/> + <param name="nsampMCMC" value="10000"/> + <conditional name="automaticRestart"> + <param name="set_minNeff" value="yes"/> + <param name="minNeff" value="200"/> + </conditional> + <conditional name="scale"> + <param name="type" value="log"/> + </conditional> + </section> + <section name="plots"> + <param name="title" value="TEST2"/> + <param name="image_file_format" value="pdf"/> + <param name="splity" value="-10.5 -9.5"/> + </section> + <output name="output"> + <assert_contents> + <has_size value="2690419" delta="200000"/> + </assert_contents> + </output> + <output name="neff"> + <assert_contents> + <has_text_matching expression="^(10|9)[0-9][0-9]\."/> + </assert_contents> + </output> + <output_collection name="qc_plots" count="3" type="list"> + <element name="convergence" ftype="pdf"> + <assert_contents> + <has_size value="28184" delta="2000"/> + </assert_contents> + </element> + <element name="p" ftype="pdf"> + <assert_contents> + <has_size value="800065" delta="80000"/> + </assert_contents> + </element> + <element name="corner" ftype="pdf"> + <assert_contents> + <has_size value="1431497" delta="200000"/> + </assert_contents> + </element> + </output_collection> + <output name="pdf2d" ftype="tabular"> + <assert_contents> + <has_n_lines n="26"/> + <has_line_matching expression="xy\s+-11\.9\s+-11\.7\s+-11\.5\s+-11\.3\s+-11\.1\s+-10\.9\s+-10\.7\s+-10\.5\s+-10\.3\s+-10\.1\s+-9\.9\s+-9\.7\s+-9\.5\s+-9\.3\s+-9\.1\s+-8\.9\s+-8\.7\s+-8\.5\s+-8\.3\s+-8\.1\s+-7\.9\s+-7\.699999999999999\s+-7\.5\s+-7\.299999999999999\s+-7\.1"/> + <has_text_matching expression="-1\.19[0-9]+e\+01\s+"/> + </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="626"/> + </assert_contents> + </output> + <output name="plot" ftype="pdf"> + <assert_contents> + <has_size value="15541" delta="1000"/> + </assert_contents> + </output> + <output_collection name="other_outputs" count="10" type="list"> + <element name="p" ftype="txt"> + <assert_contents> + <has_line_matching expression="name\s+low\s+median\s+high"/> + <has_line_matching expression="xy_mux[01]\s+-8\.6[0-9]+\s+-8\.6[0-9]+\s+-8\.5[0-9]+"/> + <has_text_matching expression="xy_mux[01]\s+-10\.2[0-9]+\s+-10\.1[0-9]+\s+-10\.0[0-9]+" /> + <has_n_lines n="12"/> + </assert_contents> + </element> + <element name="corr" ftype="txt"> + <assert_contents> + <has_n_lines n="2"/> + <has_line_matching expression="mean\tmedian\tlow\thigh\tpval\terror"/> + <has_text_matching expression="0\.9[0-9]+\s+0\.9[0-9]+\s+0\.8[0-9]+\s+0\.9[0-9]+\s+0\.00[10|9][0-9]+\s+0\.00[10|9][0-9]+\s+"/> + </assert_contents> + </element> + <element name="individuals" ftype="pdf"> + <assert_contents> + <has_size value="38594" delta="3000"/> + </assert_contents> + </element> + <element name="median" ftype="pdf"> + <assert_contents> + <has_size value="15482" delta="1000"/> + </assert_contents> + </element> + <element name="split-10.5" ftype="pdf"> + <assert_contents> + <has_size value="11801" delta="1000"/> + </assert_contents> + </element> + <element name="split-10.5_renorm" ftype="pdf"> + <assert_contents> + <has_size value="13138" delta="1000"/> + </assert_contents> + </element> + <element name="split-10.5_pdf"> + <assert_contents> + <has_text_matching expression="x\s+low1\s+mean1\s+high1\s+low2\s+mean2\s+high2"/> + <has_n_lines n="26"/> + <has_text_matching expression="-1\.19[0-9]+e\+01"/> + </assert_contents> + </element> + <element name="split-9.5" ftype="pdf"> + <assert_contents> + <has_size value="11919" delta="1000"/> + </assert_contents> + </element> + <element name="split-9.5_renorm" ftype="pdf"> + <assert_contents> + <has_size value="13145" delta="1000"/> + </assert_contents> + </element> + <element name="split-9.5_pdf"> + <assert_contents> + <has_text_matching expression="x\s+low1\s+mean1\s+high1\s+low2\s+mean2\s+high2"/> + <has_n_lines n="26"/> + <has_text_matching expression="-1\.19[0-9]+e\+01\s+"/> + </assert_contents> + </element> + </output_collection> + <output name="logevidence"> + <assert_contents> + <has_text_matching expression="^-40[0-9][0-9]\."/> + </assert_contents> + </output> + </test> + </tests> + <expand macro="helpcitations"/> +</tool> \ No newline at end of file