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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:07:24 -0400
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-1:000000000000 0:1a30a61effea
1 <tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy1">
2 <description>produce an iteration over a defined parameter</description>
3 <macros>
4 <import>scanpy_macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 mkdir outputs;
11 #if str( $input_type.parameter_values ) == "list_comma_separated_values":
12 for param in \$(echo '$input_type.input_values' | sed 's/,/ /g'); do
13 echo \$param > outputs/'$parameter_name'_\$param\.txt;
14 done
15 #else if str( $input_type.parameter_values ) == "step_increase_values":
16 for param in \$(seq '$input_type.start_value' '$input_type.step' '$input_type.end_value'); do
17 echo \$param > outputs/'$parameter_name'_\$param\.txt;
18 done
19 #end if
20 ]]></command>
21
22 <inputs>
23 <param type="select" name="parameter_name" label="Choose the format of the expression data" help="Use compressed txt, Scanpy or Seurat objects">
24 <option value="perplexity" selected="True">Perplexity</option>
25 <option value="resolution">Resolution</option>
26 </param>
27 <conditional name="input_type">
28 <param type="select" name="parameter_values" label="Choose the format of the input values" help="step increase values or list of all the parameter values">
29 <option value="list_comma_separated_values" selected="True">List of all parameter values to be iterated</option>
30 <option value="step_increase_values">Step increase values to be iterated</option>
31 </param>
32 <when value="list_comma_separated_values">
33 <param type="text" value="0.1, 0.3, 0.5, 0.7, 1.0, 2.0, 3.0, 4.0, 5.0" name="input_values" label="User input values" help="List of all comma separated values for the parameter"/>
34 </when>
35 <when value="step_increase_values">
36 <param type="float" value="1" name="start_value" label="Starting value" help="Initial value for the parameter"/>
37 <param type="float" value="2" name="step" label="Step" help="Increment to use from first to last value"/>
38 <param type="float" value="10" name="end_value" label="Ending value" help="Final value for the parameter. The final value is not included if increments of step don't match the last value."/>
39 </when>
40 </conditional>
41 </inputs>
42
43 <outputs>
44 <collection name="parameter_iteration" type="list" label="Parameter iterated">
45 <discover_datasets pattern="__name_and_ext__" directory="outputs"/>
46 </collection>
47 </outputs>
48
49 <tests>
50 <test>
51 <param name="parameter_name" value="perplexity"/>
52 <conditional name="input_type">
53 <param name="parameter_values" value="list_comma_separated_values"/>
54 <param name="input_values" value="1, 5, 10"/>
55 </conditional>
56 <output_collection name="parameter_iteration" count="3">
57 <element name="perplexity_1" file="perplexity_1.txt" ftype="txt" compare="sim_size"/>
58 <element name="perplexity_5" file="perplexity_5.txt" ftype="txt" compare="sim_size"/>
59 <element name="perplexity_10" file="perplexity_10.txt" ftype="txt" compare="sim_size"/>
60 </output_collection>
61 </test>
62 </tests>
63
64 <help><![CDATA[
65 .. class:: infomark
66
67 **What it does**
68
69 Given start, step and end, it will iterate parameters for either perplexity or
70 resolution.
71
72 **Inputs**
73
74 * Parameter name: either Resolution or Perplexity.
75 * Starting value: float for Resolution, integer for Perplexity.
76 * Step: float for Resolution, integer for Perplexity.
77 * End value: float for Resolution, integer for Perplexity.
78
79 **Outputs**
80
81 * Collection of parameters to be passed to either Scanpy run tSNE (perplexity) or Scanpy find clusters (resolution).
82
83 @VERSION_HISTORY@
84 ]]></help>
85 <expand macro="citations"/>
86 </tool>