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Changeset 0:02b1fe7aed76 (2023-10-02)

Next changeset 1:4fff5a293013 (2023-10-16)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32

diff -r 000000000000 -r 02b1fe7aed76 baredsc_1d.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/baredsc_1d.xml Mon Oct 02 13:24:52 2023 +0000

[

b'@@ -0,0 +1,303 @@\n+<tool id="baredsc_1d" name="baredSC 1d" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">\n+ <description>Compute distribution for a single gene</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edam_topics"/>\n+ <edam_operations>\n+ <edam_operation>operation_2495</edam_operation>\n+ </edam_operations>\n+ <xrefs>\n+ <xref type="bio.tools">baredsc</xref>\n+ </xrefs>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ baredSC_1d\n+ ## Required inputs:\n+ @REQUIRED_INPUTS_1D@\n+\n+ ## Filter cells\n+ @FILTER_CELLS@\n+ ## MCMC\n+ @MCMC_1D@\n+ @BAREDSC_COMMON@\n+ ## Plots\n+ @PLOTS@\n+ @PRETTYBINS_1D@\n+ ## Advanced\n+ @ADVANCED_COMMON_X@\n+ @ADVANCED_BAREDSC_COMMON@\n+ ## Outputs\n+ --output output\n+ --figure baredSC.$plots.image_file_format\n+ --logevidence logevidence.txt &&\n+ mkdir QC output &&\n+ mv baredSC_convergence.* QC &&\n+ mv baredSC_p.$plots.image_file_format QC &&\n+ mv baredSC_corner.* QC &&\n+ mv baredSC_neff.txt output &&\n+ @ORDER_OUTPUTS_1D@\n+ ]]></command>\n+ <inputs>\n+ <expand macro="macro_input_counts"/>\n+ <expand macro="macro_single_gene"/>\n+ <expand macro="macro_filter_cells"/>\n+ <section name="MCMC" title="MCMC parameters">\n+ <expand macro="macro_MCMC_params_common_axis" axis="x" />\n+ <expand macro="macro_scale_seed"/>\n+ <expand macro="macro_MCMC_common_baredSC"/>\n+ </section>\n+ <section name="plots" title="Customize plots">\n+ <expand macro="macro_plots"/>\n+ <expand macro="macro_prettybins_1d"/>\n+ </section>\n+ <section name="advanced" title="Advanced parameters" expanded="false">\n+ <expand macro="macro_advanced_common_axis" axis="x"/>\n+ <expand macro="macro_advanced_evidence"/>\n+ <expand macro="macro_advanced_common_baredSC"/>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data format="npz" name="output" label="${tool.name} on $getVar(\'input_counts.input\', \'input_counts.inputAnnData\') for ${geneColName}: Numpy archive" from_work_dir="output.npz"/>\n+ <data format="txt" name="neff" label="${tool.name} on $getVar(\'input_counts.input\', \'input_counts.inputAnnData\') for ${geneColName}: Neff" from_work_dir="output/baredSC_neff.txt"/>\n+ <collection type="list" name="qc_plots" label="${tool.name} on $getVar(\'input_counts.input\', \'input_counts.inputAnnData\') for ${geneColName}: QC plots">\n+ <discover_datasets pattern="baredSC_(?P<identifier_0>\\S+)\\.(?P<ext>.*)" directory="QC"/>\n+ </collection>\n+ <data format="tabular" name="pdf" label="${tool.name} on $getVar(\'input_counts.input\', \'input_counts.inputAnnData\') for ${geneColName}: PDF with error bar" from_work_dir="output/baredSC_pdf.txt">\n+ <actions>\n+ <action name="column_names" type="metadata" default="x,low,mean,high,median" />\n+ </actions>\n+ </data>\n+ <data format="png" name="plot" label="${tool.name} on $getVar(\'input_counts.input\', \'input_counts.inputAnnData\') for ${geneColName}: plot" from_work_dir="baredSC">\n+ <change_format>\n+ <when input="plots.image_file_format" value="png" format="png" />\n+ <when input="plots.image_file_format" value="svg" format="svg" />\n+ <when input="plots.image_file_format" value="pdf" format="pdf" />\n+ </change_format>\n+ </data>\n+ <collection type="list" name="other_outputs" label="${tool.name} on $getVar(\'input_counts.input\', \'input_counts.inputAnnData\') for ${geneColName}: plots and txt">\n+ <discover_datasets pattern="baredSC_(?P<identifier_0>\\S+)\\.(?P<ext>.*)"/>\n+ </collection>\n+ <data format="txt" name="logevidence" label="${tool.name} on $getVar(\'input'..b'ntents>\n+ </output>\n+ <output name="neff">\n+ <assert_contents>\n+ <has_text_matching expression="^317[56]\\."/>\n+ </assert_contents>\n+ </output>\n+ <output_collection name="qc_plots" count="3" type="list">\n+ <element name="convergence" ftype="pdf">\n+ <assert_contents>\n+ <has_size value="25976" delta="2000"/>\n+ </assert_contents>\n+ </element>\n+ <element name="p" ftype="pdf">\n+ <assert_contents>\n+ <has_size value="479327" delta="20000"/>\n+ </assert_contents>\n+ </element>\n+ <element name="corner" ftype="pdf">\n+ <assert_contents>\n+ <has_size value="223275" delta="20000"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ \n+ <output name="pdf" ftype="tabular">\n+ <assert_contents>\n+ <has_text_matching expression="x\\s+low\\s+mean\\s+high\\s+median"/>\n+ <has_n_lines n="201"/>\n+ <has_line_matching expression="-8\\.5\\s+0\\.4[0-9]+\\s+0\\.5[0-9]+\\s+0\\.6[0-9]+\\s+0\\.5[0-9]+"/>\n+ </assert_contents>\n+ </output>\n+ <output name="plot" ftype="pdf">\n+ <assert_contents>\n+ <has_size value="111517" delta="10000"/>\n+ </assert_contents>\n+ </output>\n+ <output_collection name="other_outputs" count="7" type="list">\n+ <element name="individuals" ftype="pdf">\n+ <assert_contents>\n+ <has_size value="95638" delta="10000"/>\n+ </assert_contents>\n+ </element>\n+ <element name="p" ftype="txt">\n+ <assert_contents>\n+ <has_line_matching expression="name\\s+low\\s+median\\s+high"/>\n+ <has_line_matching expression="mu[01]\\s+-8\\.8[0-9]+\\s+-8\\.7[0-9]+\\s+-8\\.6[0-9]+"/>\n+ <has_text_matching expression="scale[01]\\s+0\\.1[0-9]+\\s+0\\.2[0-9]+\\s+0\\.2[0-9]+" />\n+ <has_n_lines n="6"/>\n+ </assert_contents>\n+ </element>\n+ <element name="with_posterior" ftype="pdf">\n+ <assert_contents>\n+ <has_size value="112356" delta="10000"/>\n+ </assert_contents>\n+ </element>\n+ <element name="posterior_per_cell" ftype="txt">\n+ <assert_contents>\n+ <has_n_lines n="1164"/>\n+ <has_line_matching expression="mu\\s+sd"/>\n+ </assert_contents>\n+ </element>\n+ <element name="posterior_andco" ftype="pdf">\n+ <assert_contents>\n+ <has_size value="66922" delta="6000"/>\n+ </assert_contents>\n+ </element>\n+ <element name="posterior_individuals" ftype="pdf">\n+ <assert_contents>\n+ <has_size value="77887" delta="7000"/>\n+ </assert_contents>\n+ </element>\n+ <element name="means" ftype="txt">\n+ <assert_contents>\n+ <has_n_lines n="100000"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output name="logevidence">\n+ <assert_contents>\n+ <has_text_matching expression="^-20[78][0-9]\\."/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <expand macro="helpcitations"/>\n+</tool>\n'

diff -r 000000000000 -r 02b1fe7aed76 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Oct 02 13:24:52 2023 +0000

[

b'@@ -0,0 +1,313 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">1.1.1</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">baredsc</requirement>\n+ <requirement type="package" version="1.12">gzip</requirement>\n+ </requirements>\n+ <version_command><![CDATA[baredSC_1d --version]]></version_command>\n+ </xml>\n+ <xml name="helpcitations">\n+ <help><![CDATA[\n+\n+ .. class:: infomark\n+ \n+ **BARED (Bayesian Approach to Retreive Expression Distribution of) Single Cell**\n+ \n+ baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. It uses the raw counts and the total number of UMI for each cell. The PDF is approximated by a number of 1d or 2d gaussians provided by the user. The likelihood is estimated using the asumption that the raw counts follow a Poisson distribution of parameter equal to the proportion of mRNA for the gene in the cell multiplied by the total number of UMI identified in this cell.\n+ \n+ To get a description of outputs, please read the `Documentation <https://baredsc.readthedocs.io/en/latest/index.html>`_\n+\n+ This is a description of the figure with the results. \n+\n+ - When the 1d version is used, it displays the mean PDF in solid red line, the median in black dashed lines (/!\\backslash the integral of the median is not equal to 1) with the confidence interval of 1 sigma (68%), 2 sigma (95%) and 3 sigma (99.7%) as well as in green, the kernel density estimate of the input values, the detected expression (``log(1 + targetSum * raw / total UMI)``).\n+\n+ - When the 2d version is used, it displays the PDF as a heatmap as well as a projection on the x and y axis. On the projection, the confidence interval 68% is indicated as a shaded area as well as the mean with a solid red line and the median with a dashed black line. On the top right corner, the correlation is indicated with the confidence interval 68% as well as a confidence interval on the one-sided p-value (the probability that the correlation is the opposite sign of the mean, one sigma confidence interval).\n+\n+ Usually you should run baredSC_1d or baredSC_2d with 1 to 4 gaussians. Then you combine the different models with combineMultipleModels_1d or combineMultipleModels_2d.\n+ \n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1186/s12859-021-04507-8</citation>\n+ </citations>\n+ </xml>\n+ <xml name="edam_topics">\n+ <edam_topics>\n+ <edam_topic>topic_3170</edam_topic>\n+ <edam_topic>topic_4028</edam_topic>\n+ <edam_topic>topic_2269</edam_topic>\n+ </edam_topics>\n+ </xml>\n+ <xml name="macro_input_counts">\n+ <conditional name="input_counts">\n+ <param name="filetype" type="select" label="Input type">\n+ <option value="tabular">Tabular</option>\n+ <option value="anndata">Anndata (for example from Scanpy)</option>\n+ </param>\n+ <when value="tabular">\n+ <param argument="--input" type="data" format="tabular" label="Input table (with header)" help="Expected format is one line per cell, columns with raw counts and one column \'nCount_RNA\' with the total number of UMI per cell (optionally other meta data to filter)" />\n+ </when>\n+ <when value="anndata">\n+ <param argument="--inputAnnData" type="data" format="anndata" label="AnnData containing raw counts" />\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="macro_single_gene">\n+ <param argument="--geneColName" type="text" value="" label="Name of the column with gene counts."/>\n+'..b'tadata1ColName\'\n+ --metadata1Values \'$filter.metadata1Values\'\n+ --metadata2ColName \'$filter.metadata2ColName\'\n+ --metadata2Values \'$filter.metadata2Values\'\n+ --metadata3ColName \'$filter.metadata3ColName\'\n+ --metadata3Values \'$filter.metadata3Values\'\n+ #end if \n+ ]]></token>\n+ <token name="@MCMC_1D@" ><![CDATA[\n+ --xmin $MCMC.xmin\n+ --xmax $MCMC.xmax\n+ --xscale \'$MCMC.scale.type\'\n+ #if str( $MCMC.scale.type ) == "Seurat":\n+ --targetSum $MCMC.scale.targetSum\n+ #end if\n+ --nx $MCMC.nx\n+ --minScale $MCMC.minScalex\n+ --seed $MCMC.seed\n+ ]]></token>\n+ <token name="@MCMC_2D@" ><![CDATA[\n+ --xmin $MCMC.xmin\n+ --xmax $MCMC.xmax\n+ --nx $MCMC.nx\n+ --minScalex $MCMC.minScalex\n+ --ymin $MCMC.ymin\n+ --ymax $MCMC.ymax\n+ --ny $MCMC.ny\n+ --minScaley $MCMC.minScaley\n+ --scale \'$MCMC.scale.type\'\n+ #if str( $MCMC.scale.type ) == "Seurat":\n+ --targetSum $MCMC.scale.targetSum\n+ #end if\n+ --seed $MCMC.seed\n+ ]]></token>\n+ <token name="@BAREDSC_COMMON@" ><![CDATA[\n+ --nnorm $MCMC.nnorm\n+ --nsampMCMC $MCMC.nsampMCMC\n+ #if str( $MCMC.automaticRestart.set_minNeff ) == "yes":\n+ --minNeff $MCMC.automaticRestart.minNeff\n+ #end if\n+ ]]></token>\n+ <token name="@PLOTS@" ><![CDATA[\n+ #if str( $plots.title ) != \'\':\n+ --title \'$plots.title\'\n+ #end if\n+ #if $plots.removeFirstSamples != -1:\n+ --removeFirstSamples $plots.removeFirstSamples\n+ #end if\n+ --nsampInPlot $plots.nsampInPlot\n+ ]]></token>\n+ <token name="@PRETTYBINS_1D@" ><![CDATA[\n+ #if $plots.prettyBins != -1:\n+ --prettyBins $plots.prettyBins\n+ #end if \n+ ]]></token>\n+ <token name="@PRETTYBINS_SPLITY_COLORSCALE_2D@" ><![CDATA[\n+ #if $plots.prettyBinsx != -1:\n+ --prettyBinsx $plots.prettyBinsx\n+ #end if\n+ #if $plots.prettyBinsy != -1:\n+ --prettyBinsy $plots.prettyBinsy\n+ #end if\n+ ## splity is space separated floats\n+ #if str($plots.splity) != \'\':\n+ --splity $plots.splity\n+ #end if\n+ #if str($plots.log1pColorScale) != \'\':\n+ \'$plots.log1pColorScale\'\n+ #end if\n+ ]]></token>\n+ <token name="@ADVANCED_COMMON_X@" ><![CDATA[\n+ --osampx $advanced.osampx\n+ --osampxpdf $advanced.osampxpdf\n+ --coviscale $advanced.coviscale\n+ --nis $advanced.nis\n+ ]]></token>\n+ <token name="@ADVANCED_COMMON_COMPLEMENT_2D@" ><![CDATA[\n+ --osampy $advanced.osampy\n+ --osampypdf $advanced.osampypdf\n+ --scalePrior $advanced.scalePrior\n+ ]]></token>\n+ <token name="@ADVANCED_BAREDSC_COMMON@" ><![CDATA[\n+ #if str( $advanced.burn.custom ) == "yes":\n+ #if str( $advanced.burn.nsampBurnMCMC ) != "-1":\n+ --nsampBurnMCMC $advanced.burn.nsampBurnMCMC\n+ #end if\n+ --T0BurnMCMC $advanced.burn.T0BurnMCMC\n+ #end if\n+ ]]></token>\n+ <token name="@COMBINE_OUTPUTS@"><![CDATA[\n+ --outputs\n+ #for $i, $output in enumerate($MCMC.outputs):\n+ $i\n+ #end for\n+ ]]></token>\n+ <token name="@ORDER_OUTPUTS_1D@"><![CDATA[\n+ mv baredSC_pdf.txt output &&\n+ mv baredSC.$plots.image_file_format baredSC &&\n+ gunzip baredSC_means.txt.gz\n+ ]]></token>\n+ <token name="@ORDER_OUTPUTS_2D@"><![CDATA[\n+ mv baredSC_pdf2d.txt output &&\n+ mv baredSC_pdf2d_flat.txt output &&\n+ mv baredSC.$plots.image_file_format baredSC\n+ #if str($plots.splity) != \'\':\n+ #for $value in str($plots.splity).split(\' \'):\n+ && mv baredSC_split\'$value\'.txt baredSC_split\'$value\'_pdf.txt\n+ #end for\n+ #end if\n+ ]]></token>\n+</macros>\n\\ No newline at end of file\n'

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diff -r 000000000000 -r 02b1fe7aed76 test-data/2d_small_2gauss_corr.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2d_small_2gauss_corr.txt Mon Oct 02 13:24:52 2023 +0000

@@ -0,0 +1,2 @@
+mean median low high pval error
+0.902971588834658 0.9030205591240211 0.8808479278110088 0.9249439927709214 0.007859609399117668 0.007859609399117668

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diff -r 000000000000 -r 02b1fe7aed76 test-data/2d_small_2gauss_neff.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2d_small_2gauss_neff.txt Mon Oct 02 13:24:52 2023 +0000

@@ -0,0 +1,1 @@
+127.23278590819812

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diff -r 000000000000 -r 02b1fe7aed76 test-data/2d_small_2gauss_p.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2d_small_2gauss_p.txt Mon Oct 02 13:24:52 2023 +0000

@@ -0,0 +1,12 @@
+name low median high
+xy_mux0 0.3421735749355604 0.36400142067277885 0.38414407467979367
+xy_muy0 0.3602753667616778 0.3797834812619477 0.3997083085113705
+xy_scalex0 0.128373484740148 0.13754306887169315 0.154475100117708
+xy_scaley0 0.11267797849970684 0.13404387324572375 0.1636497454683696
+xy_corr0 -0.056936609709389754 0.20134274953150133 0.4823245136404016
+xy_amp1 0.4683630960583824 0.4935067017747425 0.5184297378623833
+xy_mux1 0.9950898144773097 1.0128387895441175 1.0323483080264237
+xy_muy1 0.9882799141570242 1.0073935336038764 1.0262810747590292
+xy_scalex1 0.12680233831791496 0.1317913482460104 0.1439711554909536
+xy_scaley1 0.10695025120288884 0.11525119819932761 0.13138587521715606
+xy_corr1 0.27825576244514594 0.5311286235242539 0.7541979912185461

diff -r 000000000000 -r 02b1fe7aed76 test-data/2d_small_2gauss_pdf2d.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2d_small_2gauss_pdf2d.txt Mon Oct 02 13:24:52 2023 +0000

b'@@ -0,0 +1,51 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diff -r 000000000000 -r 02b1fe7aed76 test-data/2d_small_2gauss_pdf2d_flat.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2d_small_2gauss_pdf2d_flat.txt Mon Oct 02 13:24:52 2023 +0000

b'@@ -0,0 +1,2501 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diff -r 000000000000 -r 02b1fe7aed76 test-data/2d_test2_split-10.5.txt
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diff -r 000000000000 -r 02b1fe7aed76 test-data/2d_test2_split-9.5_renorm.pdf

Binary file test-data/2d_test2_split-9.5_renorm.pdf has changed

diff -r 000000000000 -r 02b1fe7aed76 test-data/generate_small_inputs_for_combine.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/generate_small_inputs_for_combine.sh Mon Oct 02 13:24:52 2023 +0000

@@ -0,0 +1,6 @@
+for nnorm in 1 2; do
+ baredSC_1d --input test-data/nih3t3_generated_2d_2.txt --geneColName 0.5_0_0_0.5_x --nnorm ${nnorm} --output test-data/small_${nnorm}gauss --figure test-data/small_${nnorm}gauss.png --nx 10 --prettyBins 100 --nsampMCMC 20000 --force
+done
+for nnorm in 1 2; do
+ baredSC_2d --input test-data/nih3t3_generated_2d_2.txt --geneXColName '0.5_0_0_0.5_x' --geneYColName '0.5_0_0_0.5_y' --nnorm ${nnorm} --output test-data/2d_small_${nnorm}gauss --figure test-data/2d_small_${nnorm}gauss.png --nx 10 --ny 12 --prettyBinsx 50 --prettyBinsy 50 --nsampMCMC 20000 --force
+done

diff -r 000000000000 -r 02b1fe7aed76 test-data/nih3t3_generated_2d_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nih3t3_generated_2d_2.txt Mon Oct 02 13:24:52 2023 +0000

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diff -r 000000000000 -r 02b1fe7aed76 test-data/small_2gauss_neff.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_2gauss_neff.txt Mon Oct 02 13:24:52 2023 +0000

@@ -0,0 +1,1 @@
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diff -r 000000000000 -r 02b1fe7aed76 test-data/small_2gauss_p.png

Binary file test-data/small_2gauss_p.png has changed

diff -r 000000000000 -r 02b1fe7aed76 test-data/small_2gauss_p.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_2gauss_p.txt Mon Oct 02 13:24:52 2023 +0000

@@ -0,0 +1,6 @@
+name low median high
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+scale0 0.15226068811267196 0.24583330904194123 0.37859276190581687
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diff -r 000000000000 -r 02b1fe7aed76 test-data/small_2gauss_pdf.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_2gauss_pdf.txt Mon Oct 02 13:24:52 2023 +0000

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diff -r 000000000000 -r 02b1fe7aed76 test-data/small_2gauss_posterior_andco.png

Binary file test-data/small_2gauss_posterior_andco.png has changed

diff -r 000000000000 -r 02b1fe7aed76 test-data/small_2gauss_posterior_individuals.png

Binary file test-data/small_2gauss_posterior_individuals.png has changed

diff -r 000000000000 -r 02b1fe7aed76 test-data/small_2gauss_posterior_per_cell.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_2gauss_posterior_per_cell.txt Mon Oct 02 13:24:52 2023 +0000

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