diff baredsc_combine_1d.xml @ 0:c32347702e12 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
author iuc
date Mon, 02 Oct 2023 13:24:26 +0000
parents
children 050cf43887d3
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/baredsc_combine_1d.xml	Mon Oct 02 13:24:26 2023 +0000
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+<tool id="baredsc_combine_1d" name="Combine multiple 1D 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_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
+
+    ## Run
+    combineMultipleModels_1d
+    ## Required inputs:
+    @REQUIRED_INPUTS_1D@
+
+    ## Filter cells
+    @FILTER_CELLS@
+
+    @COMBINE_OUTPUTS@
+    ## MCMC
+    @MCMC_1D@
+    ## Plots
+    @PLOTS@
+    @PRETTYBINS_1D@
+    ## Advanced
+    @ADVANCED_COMMON_X@
+    ## Outputs
+    --figure baredSC.$plots.image_file_format &&
+    mkdir output &&
+    @ORDER_OUTPUTS_1D@
+    ]]></command>
+    <inputs>
+        <expand macro="macro_input_counts"/>
+        <expand macro="macro_single_gene"/>
+        <expand macro="macro_filter_cells"/>
+        <section name="MCMC" title="MCMC parameters">
+            <expand macro="combine_outputs" d="1" />
+            <expand macro="macro_MCMC_params_common_axis" axis="x" />
+            <expand macro="macro_scale_seed"/>
+        </section>
+        <section name="plots" title="Customize plots">
+            <expand macro="macro_plots"/>
+            <expand macro="macro_prettybins_1d"/>
+        </section>
+        <section name="advanced" title="Advanced parameters" expanded="false">
+            <expand macro="macro_advanced_common_axis" axis="x"/>
+            <expand macro="macro_advanced_evidence"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="pdf" label="${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>
+    </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="outputs" value="small_1gauss.npz,small_2gauss.npz"/>
+                <param name="nx" value="10"/>
+            </section>
+            <section name="plots">
+                <param name="title" value="first gene combine 1 and 2 gauss"/>
+                <param name="prettyBins" value="100"/>
+            </section>
+            <!--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\.12[0-9]+\s+0\.37[0-9]+\s+0\.64[0-9]+\s+0\.33[0-9]+"/>
+                </assert_contents>
+            </output>
+            <output name="plot" ftype="png">
+                <assert_contents>
+                    <has_size value="244510" delta="20000"/>
+                </assert_contents>
+            </output>
+            <output_collection name="other_outputs" count="6" type="list">
+                <element name="individuals" ftype="png">
+                    <assert_contents>
+                        <has_size value="120034" delta="10000"/>
+                    </assert_contents>
+                </element>
+                <element name="with_posterior" ftype="png">
+                    <assert_contents>
+                        <has_size value="253397" 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="213773" delta="10000"/>
+                    </assert_contents>
+                </element>
+                <element name="posterior_individuals" ftype="png">
+                    <assert_contents>
+                        <has_size value="108794" delta="10000"/>
+                    </assert_contents>
+                </element>
+                <element name="means" ftype="txt">
+                    <assert_contents>
+                        <has_n_lines n="15001"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <assert_stdout>
+                <has_text text="You have 2361 cells."/>
+                <has_text text="Using 12 samples from output 0."/>
+                <has_text text="Using 1 samples from output 0."/>
+            </assert_stdout>
+        </test>
+    </tests>
+    <expand macro="helpcitations"/>
+</tool>
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