Mercurial > repos > iuc > baredsc_combine_2d

comparison baredsc_combine_2d.xml @ 0:ac9434b9fc27 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
author iuc
date Mon, 02 Oct 2023 13:23:59 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:ac9434b9fc27
1 <tool id="baredsc_combine_2d" name="Combine multiple 2D 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_operation>operation_3463</edam_operation>
10 </edam_operations>
11 <xrefs>
12 <xref type="bio.tools">baredsc</xref>
13 </xrefs>
14 <expand macro="requirements"/>
15 <command detect_errors="exit_code"><![CDATA[
16 ## Create symlinks
17 #for $i, $output in enumerate($MCMC.outputs):
18 ln -s '$output' '${i}.npz' &&
19 #end for
20
21 combineMultipleModels_2d
22 ## Required inputs:
23 @REQUIRED_INPUTS_2D@
24
25 ## Filter cells
26 @FILTER_CELLS@
27
28 @COMBINE_OUTPUTS@
29 ## MCMC
30 @MCMC_2D@
31 ## Plots
32 @PLOTS@
33 @PRETTYBINS_SPLITY_COLORSCALE_2D@
34 ## Advanced
35 @ADVANCED_COMMON_X@
36 @ADVANCED_COMMON_COMPLEMENT_2D@
37 ## Outputs
38 --figure baredSC.$plots.image_file_format &&
39 mkdir output &&
40 @ORDER_OUTPUTS_2D@
41 ]]></command>
42 <inputs>
43 <expand macro="macro_input_counts"/>
44 <expand macro="macro_two_genes"/>
45 <expand macro="macro_filter_cells"/>
46 <section name="MCMC" title="MCMC parameters">
47 <expand macro="combine_outputs" d="2" />
48 <expand macro="macro_MCMC_params_common_axis" axis="x" />
49 <expand macro="macro_MCMC_params_common_axis" axis="y" />
50 <expand macro="macro_scale_seed"/>
51 </section>
52 <section name="plots" title="Customize plots">
53 <expand macro="macro_plots"/>
54 <expand macro="macro_prettybins_axis" axis="x"/>
55 <expand macro="macro_prettybins_axis" axis="y"/>
56 <expand macro="macro_colorscale"/>
57 <expand macro="macro_splity"/>
58 </section>
59 <section name="advanced" title="Advanced parameters" expanded="false">
60 <expand macro="macro_advanced_common_axis" axis="x" default_osamppdf="4"/>
61 <expand macro="macro_advanced_common_axis" axis="y" default_osamppdf="4"/>
62 <expand macro="macro_advanced_evidence"/>
63 <expand macro="macro_scaleprior"/>
64 </section>
65 </inputs>
66 <outputs>
67 <data format="tabular" name="pdf2d" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: mean PDF in matrix format" from_work_dir="output/baredSC_pdf2d.txt"/>
68 <data format="tabular" name="pdf2d_flat" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: PDF with error bar, one bin per line" from_work_dir="output/baredSC_pdf2d_flat.txt">
69 <actions>
70 <action name="column_names" type="metadata" default="x,y,low,mean,high,median" />
71 </actions>
72 </data>
73 <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: plot" from_work_dir="baredSC">
74 <change_format>
75 <when input="plots.image_file_format" value="png" format="png" />
76 <when input="plots.image_file_format" value="svg" format="svg" />
77 <when input="plots.image_file_format" value="pdf" format="pdf" />
78 </change_format>
79 </data>
80 <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: plots and txt">
81 <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)"/>
82 </collection>
83 </outputs>
84 <tests>
85 <!-- First test -->
86 <test>
87 <conditional name="input_counts">
88 <param name="filetype" value="tabular"/>
89 <param name="input" value="nih3t3_generated_2d_2.txt"/>
90 </conditional>
91 <param name="geneXColName" value="0.5_0_0_0.5_x"/>
92 <param name="geneYColName" value="0.5_0_0_0.5_y"/>
93 <section name="MCMC">
94 <param name="outputs" value="2d_small_1gauss.npz,2d_small_2gauss.npz"/>
95 <param name="nx" value="10"/>
96 <param name="ny" value="12"/>
97 </section>
98 <section name="plots">
99 <param name="prettyBinsx" value="20"/>
100 <param name="prettyBinsy" value="20"/>
101 </section>
102 <output name="pdf2d" ftype="tabular">
103 <assert_contents>
104 <has_n_lines n="21"/>
105 </assert_contents>
106 </output>
107 <output name="pdf2d_flat" ftype="tabular">
108 <assert_contents>
109 <has_text_matching expression="x\s+y\s+low\s+mean\s+high\s+median"/>
110 <has_n_lines n="401"/>
111 </assert_contents>
112 </output>
113 <output name="plot" ftype="png">
114 <assert_contents>
115 <has_size value="37414" delta="3000"/>
116 </assert_contents>
117 </output>
118 <output_collection name="other_outputs" count="3" type="list">
119 <element name="corr" ftype="txt">
120 <assert_contents>
121 <has_n_lines n="2"/>
122 <has_line_matching expression="mean\tmedian\tlow\thigh"/>
123 <has_text_matching expression="0\.9[0-9]+\s+0\.9[0-9]+\s+0\.8[0-9]+\s+0\.9[0-9]+"/>
124 </assert_contents>
125 </element>
126 <element name="individuals" ftype="png">
127 <assert_contents>
128 <has_size value="56721" delta="5000"/>
129 </assert_contents>
130 </element>
131 <element name="median" ftype="png">
132 <assert_contents>
133 <has_size value="37412" delta="4000"/>
134 </assert_contents>
135 </element>
136 </output_collection>
137 </test>
138 </tests>
139 <expand macro="helpcitations"/>
140 </tool>