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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
author iuc
date Mon, 02 Oct 2023 13:22:34 +0000
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1 <tool id="baredsc_combine_1d" name="Combine multiple 1D Models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description>from baredSC</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_topics"/>
7 <edam_operations>
8 <edam_operation>operation_2495</edam_operation>
9 </edam_operations>
10 <xrefs>
11 <xref type="bio.tools">baredsc</xref>
12 </xrefs>
13 <expand macro="requirements"/>
14 <command detect_errors="exit_code"><![CDATA[
15 ## Create symlinks
16 #for $i, $output in enumerate($MCMC.outputs):
17 ln -s '$output' '${i}.npz' &&
18 #end for
19
20 ## Run
21 combineMultipleModels_1d
22 ## Required inputs:
23 @REQUIRED_INPUTS_1D@
24
25 ## Filter cells
26 @FILTER_CELLS@
27
28 @COMBINE_OUTPUTS@
29 ## MCMC
30 @MCMC_1D@
31 ## Plots
32 @PLOTS@
33 @PRETTYBINS_1D@
34 ## Advanced
35 @ADVANCED_COMMON_X@
36 ## Outputs
37 --figure baredSC.$plots.image_file_format &&
38 mkdir output &&
39 @ORDER_OUTPUTS_1D@
40 ]]></command>
41 <inputs>
42 <expand macro="macro_input_counts"/>
43 <expand macro="macro_single_gene"/>
44 <expand macro="macro_filter_cells"/>
45 <section name="MCMC" title="MCMC parameters">
46 <expand macro="combine_outputs" d="1" />
47 <expand macro="macro_MCMC_params_common_axis" axis="x" />
48 <expand macro="macro_scale_seed"/>
49 </section>
50 <section name="plots" title="Customize plots">
51 <expand macro="macro_plots"/>
52 <expand macro="macro_prettybins_1d"/>
53 </section>
54 <section name="advanced" title="Advanced parameters" expanded="false">
55 <expand macro="macro_advanced_common_axis" axis="x"/>
56 <expand macro="macro_advanced_evidence"/>
57 </section>
58 </inputs>
59 <outputs>
60 <data format="tabular" name="pdf" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: PDF with error bar" from_work_dir="output/baredSC_pdf.txt">
61 <actions>
62 <action name="column_names" type="metadata" default="x,low,mean,high,median" />
63 </actions>
64 </data>
65 <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: plot" from_work_dir="baredSC">
66 <change_format>
67 <when input="plots.image_file_format" value="png" format="png" />
68 <when input="plots.image_file_format" value="svg" format="svg" />
69 <when input="plots.image_file_format" value="pdf" format="pdf" />
70 </change_format>
71 </data>
72 <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: plots and txt">
73 <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)"/>
74 </collection>
75 </outputs>
76 <tests>
77 <!-- First test -->
78 <test>
79 <conditional name="input_counts">
80 <param name="filetype" value="tabular"/>
81 <param name="input" value="nih3t3_generated_2d_2.txt"/>
82 </conditional>
83 <param name="geneColName" value="0.5_0_0_0.5_x"/>
84 <section name="MCMC">
85 <param name="outputs" value="small_1gauss.npz,small_2gauss.npz"/>
86 <param name="nx" value="10"/>
87 </section>
88 <section name="plots">
89 <param name="title" value="first gene combine 1 and 2 gauss"/>
90 <param name="prettyBins" value="100"/>
91 </section>
92 <!--In the next output pdf means probability density function-->
93 <output name="pdf" ftype="tabular">
94 <assert_contents>
95 <has_text_matching expression="x\s+low\s+mean\s+high\s+median"/>
96 <has_n_lines n="101"/>
97 <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]+"/>
98 </assert_contents>
99 </output>
100 <output name="plot" ftype="png">
101 <assert_contents>
102 <has_size value="244510" delta="20000"/>
103 </assert_contents>
104 </output>
105 <output_collection name="other_outputs" count="6" type="list">
106 <element name="individuals" ftype="png">
107 <assert_contents>
108 <has_size value="120034" delta="10000"/>
109 </assert_contents>
110 </element>
111 <element name="with_posterior" ftype="png">
112 <assert_contents>
113 <has_size value="253397" delta="20000"/>
114 </assert_contents>
115 </element>
116 <element name="posterior_per_cell" ftype="txt">
117 <assert_contents>
118 <has_n_lines n="2362"/>
119 <has_line_matching expression="mu\s+sd"/>
120 </assert_contents>
121 </element>
122 <element name="posterior_andco" ftype="png">
123 <assert_contents>
124 <has_size value="213773" delta="10000"/>
125 </assert_contents>
126 </element>
127 <element name="posterior_individuals" ftype="png">
128 <assert_contents>
129 <has_size value="108794" delta="10000"/>
130 </assert_contents>
131 </element>
132 <element name="means" ftype="txt">
133 <assert_contents>
134 <has_n_lines n="15001"/>
135 </assert_contents>
136 </element>
137 </output_collection>
138 <assert_stdout>
139 <has_text text="You have 2361 cells."/>
140 <has_text text="Using 12 samples from output 0."/>
141 <has_text text="Using 1 samples from output 0."/>
142 </assert_stdout>
143 </test>
144 </tests>
145 <expand macro="helpcitations"/>
146 </tool>