--- /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 ${geneColName}: QC plots">
+            <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)" directory="QC"/>
+        </collection>
+        <data format="tabular" name="pdf" label="${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 ${geneColName}: plots and txt">
+            <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)"/>
+        </collection>
+        <data format="txt" name="logevidence" label="${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>