Mercurial > repos > iuc > baredsc_1d
diff baredsc_1d.xml @ 0:02b1fe7aed76 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
| author | iuc |
|---|---|
| date | Mon, 02 Oct 2023 13:24:52 +0000 |
| parents | |
| children | 4fff5a293013 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/baredsc_1d.xml Mon Oct 02 13:24:52 2023 +0000 @@ -0,0 +1,303 @@ +<tool id="baredsc_1d" name="baredSC 1d" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> + <description>Compute distribution for a single gene</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_topics"/> + <edam_operations> + <edam_operation>operation_2495</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">baredsc</xref> + </xrefs> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + baredSC_1d + ## Required inputs: + @REQUIRED_INPUTS_1D@ + + ## Filter cells + @FILTER_CELLS@ + ## MCMC + @MCMC_1D@ + @BAREDSC_COMMON@ + ## Plots + @PLOTS@ + @PRETTYBINS_1D@ + ## Advanced + @ADVANCED_COMMON_X@ + @ADVANCED_BAREDSC_COMMON@ + ## Outputs + --output output + --figure baredSC.$plots.image_file_format + --logevidence logevidence.txt && + mkdir QC output && + mv baredSC_convergence.* QC && + mv baredSC_p.$plots.image_file_format QC && + mv baredSC_corner.* QC && + mv baredSC_neff.txt output && + @ORDER_OUTPUTS_1D@ + ]]></command> + <inputs> + <expand macro="macro_input_counts"/> + <expand macro="macro_single_gene"/> + <expand macro="macro_filter_cells"/> + <section name="MCMC" title="MCMC parameters"> + <expand macro="macro_MCMC_params_common_axis" axis="x" /> + <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_1d"/> + </section> + <section name="advanced" title="Advanced parameters" expanded="false"> + <expand macro="macro_advanced_common_axis" axis="x"/> + <expand macro="macro_advanced_evidence"/> + <expand macro="macro_advanced_common_baredSC"/> + </section> + </inputs> + <outputs> + <data format="npz" name="output" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Numpy archive" from_work_dir="output.npz"/> + <data format="txt" name="neff" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Neff" from_work_dir="output/baredSC_neff.txt"/> + <collection type="list" name="qc_plots" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: QC plots"> + <discover_datasets pattern="baredSC_(?P<identifier_0>\S+)\.(?P<ext>.*)" directory="QC"/> + </collection> + <data format="tabular" name="pdf" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: PDF with error bar" from_work_dir="output/baredSC_pdf.txt"> + <actions> + <action name="column_names" type="metadata" default="x,low,mean,high,median" /> + </actions> + </data> + <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: plot" from_work_dir="baredSC"> + <change_format> + <when input="plots.image_file_format" value="png" format="png" /> + <when input="plots.image_file_format" value="svg" format="svg" /> + <when input="plots.image_file_format" value="pdf" format="pdf" /> + </change_format> + </data> + <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: plots and txt"> + <discover_datasets pattern="baredSC_(?P<identifier_0>\S+)\.(?P<ext>.*)"/> + </collection> + <data format="txt" name="logevidence" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Log evidence" from_work_dir="logevidence.txt"/> + </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="geneColName" value="0.5_0_0_0.5_x"/> + <section name="MCMC"> + <param name="nnorm" value="1"/> + </section> + <section name="plots"> + <param name="title" value="first gene 1 gauss"/> + </section> + <output name="output"> + <assert_contents> + <has_size value="1257974" delta="100000"/> + </assert_contents> + </output> + <output name="neff"> + <assert_contents> + <has_text_matching expression="^80[0-9][0-9]\."/> + </assert_contents> + </output> + <output_collection name="qc_plots" count="3" type="list"> + <element name="convergence" ftype="png"> + <assert_contents> + <has_size value="23021" delta="2000"/> + </assert_contents> + </element> + <element name="p" ftype="png"> + <assert_contents> + <has_size value="45302" delta="4000"/> + </assert_contents> + </element> + <element name="corner" ftype="png"> + <assert_contents> + <has_size value="66254" delta="6000"/> + </assert_contents> + </element> + </output_collection> + <!--In the next output pdf means probability density function--> + <output name="pdf" ftype="tabular"> + <assert_contents> + <has_text_matching expression="x\s+low\s+mean\s+high\s+median"/> + <has_n_lines n="101"/> + <has_line_matching expression="0\.0125\s+0\.2[0-9]+\s+0\.2[0-9]+\s+0\.2[0-9]+\s+0\.2[0-9]+"/> + </assert_contents> + </output> + <output name="plot" ftype="png"> + <assert_contents> + <has_size value="239991" delta="20000"/> + </assert_contents> + </output> + <output_collection name="other_outputs" count="7" type="list"> + <element name="individuals" ftype="png"> + <assert_contents> + <has_size value="54420" delta="5000"/> + </assert_contents> + </element> + <element name="p" ftype="txt"> + <assert_contents> + <has_line_matching expression="name\s+low\s+median\s+high"/> + <has_line_matching expression="mu0\s+0\.6[0-9]+\s+0\.6[0-9]+\s+0\.6[0-9]+"/> + <has_text_matching expression="scale0\s+0\.3[0-9]+\s+0\.3[0-9]+\s+0\.3[0-9]+" /> + <has_n_lines n="3"/> + </assert_contents> + </element> + <element name="with_posterior" ftype="png"> + <assert_contents> + <has_size value="243443" delta="20000"/> + </assert_contents> + </element> + <element name="posterior_per_cell" ftype="txt"> + <assert_contents> + <has_n_lines n="2362"/> + <has_line_matching expression="mu\s+sd"/> + </assert_contents> + </element> + <element name="posterior_andco" ftype="png"> + <assert_contents> + <has_size value="194143" delta="10000"/> + </assert_contents> + </element> + <element name="posterior_individuals" ftype="png"> + <assert_contents> + <has_size value="135293" delta="10000"/> + </assert_contents> + </element> + <element name="means" ftype="txt"> + <assert_contents> + <has_n_lines n="75001"/> + </assert_contents> + </element> + </output_collection> + <output name="logevidence"> + <assert_contents> + <has_text_matching expression="^-42[0-9][0-9]\."/> + </assert_contents> + </output> + </test> + <!-- Second test pdf filtering cells pretty log scale--> + <test> + <conditional name="input_counts"> + <param name="filetype" value="tabular"/> + <param name="input" value="nih3t3_generated_2d_2.txt"/> + </conditional> + <param name="geneColName" value="0.5_0_0_0.5_x"/> + <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="-15"/> + <param name="xmax" value="-7"/> + <param name="nx" value="25"/> + <param name="nnorm" value="2"/> + <param name="nsampMCMC" value="20000"/> + <conditional name="automaticRestart"> + <param name="set_minNeff" value="yes"/> + <param name="minNeff" value="400"/> + </conditional> + <conditional name="scale"> + <param name="type" value="log"/> + </conditional> + </section> + <section name="plots"> + <param name="image_file_format" value="pdf"/> + <param name="prettyBins" value="200"/> + </section> + <output name="output"> + <assert_contents> + <has_size value="3198024" delta="300000"/> + </assert_contents> + </output> + <output name="neff"> + <assert_contents> + <has_text_matching expression="^317[56]\."/> + </assert_contents> + </output> + <output_collection name="qc_plots" count="3" type="list"> + <element name="convergence" ftype="pdf"> + <assert_contents> + <has_size value="25976" delta="2000"/> + </assert_contents> + </element> + <element name="p" ftype="pdf"> + <assert_contents> + <has_size value="479327" delta="20000"/> + </assert_contents> + </element> + <element name="corner" ftype="pdf"> + <assert_contents> + <has_size value="223275" delta="20000"/> + </assert_contents> + </element> + </output_collection> + <!--In the next output pdf means probability density function--> + <output name="pdf" ftype="tabular"> + <assert_contents> + <has_text_matching expression="x\s+low\s+mean\s+high\s+median"/> + <has_n_lines n="201"/> + <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]+"/> + </assert_contents> + </output> + <output name="plot" ftype="pdf"> + <assert_contents> + <has_size value="111517" delta="10000"/> + </assert_contents> + </output> + <output_collection name="other_outputs" count="7" type="list"> + <element name="individuals" ftype="pdf"> + <assert_contents> + <has_size value="95638" delta="10000"/> + </assert_contents> + </element> + <element name="p" ftype="txt"> + <assert_contents> + <has_line_matching expression="name\s+low\s+median\s+high"/> + <has_line_matching expression="mu[01]\s+-8\.8[0-9]+\s+-8\.7[0-9]+\s+-8\.6[0-9]+"/> + <has_text_matching expression="scale[01]\s+0\.1[0-9]+\s+0\.2[0-9]+\s+0\.2[0-9]+" /> + <has_n_lines n="6"/> + </assert_contents> + </element> + <element name="with_posterior" ftype="pdf"> + <assert_contents> + <has_size value="112356" delta="10000"/> + </assert_contents> + </element> + <element name="posterior_per_cell" ftype="txt"> + <assert_contents> + <has_n_lines n="1164"/> + <has_line_matching expression="mu\s+sd"/> + </assert_contents> + </element> + <element name="posterior_andco" ftype="pdf"> + <assert_contents> + <has_size value="66922" delta="6000"/> + </assert_contents> + </element> + <element name="posterior_individuals" ftype="pdf"> + <assert_contents> + <has_size value="77887" delta="7000"/> + </assert_contents> + </element> + <element name="means" ftype="txt"> + <assert_contents> + <has_n_lines n="100000"/> + </assert_contents> + </element> + </output_collection> + <output name="logevidence"> + <assert_contents> + <has_text_matching expression="^-20[78][0-9]\."/> + </assert_contents> + </output> + </test> + </tests> + <expand macro="helpcitations"/> +</tool>