Mercurial > repos > ebi-gxa > scanpy_parameter_iterator
comparison scanpy-parameter-iterator.xml @ 12:7c4d44c14ceb draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit dcb8b19d34c3e2bf822996ca2e80de111c30b27e"
author | ebi-gxa |
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date | Mon, 08 Jun 2020 04:43:24 -0400 |
parents | 1a30a61effea |
children | ae4debc68f4a |
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11:645f12f44a6d | 12:7c4d44c14ceb |
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1 <tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy1"> | 1 <tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy2"> |
2 <description>produce an iteration over a defined parameter</description> | 2 <description>produce an iteration over a defined parameter</description> |
3 <macros> | 3 <macros> |
4 <import>scanpy_macros.xml</import> | 4 <import>scanpy_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <requirements> | 6 <requirements> |
18 done | 18 done |
19 #end if | 19 #end if |
20 ]]></command> | 20 ]]></command> |
21 | 21 |
22 <inputs> | 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"> | 23 <param type="select" name="parameter_name" label="Parameter name" help="Select a type of parameter"> |
24 <option value="perplexity" selected="True">Perplexity</option> | 24 <option value="perplexity" selected="True">Perplexity</option> |
25 <option value="resolution">Resolution</option> | 25 <option value="resolution">Resolution</option> |
26 <option value="n_neighbors">Number of neighbors</option> | |
26 </param> | 27 </param> |
27 <conditional name="input_type"> | 28 <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 <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="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 <option value="step_increase_values">Step increase values to be iterated</option> |
64 <help><![CDATA[ | 65 <help><![CDATA[ |
65 .. class:: infomark | 66 .. class:: infomark |
66 | 67 |
67 **What it does** | 68 **What it does** |
68 | 69 |
69 Given start, step and end, it will iterate parameters for either perplexity or | 70 Given start, step and end, it will iterate parameters for either perplexity (for t-SNE), resolution (clustering) |
70 resolution. | 71 or number of neighbours (neighbour graph construction). |
71 | 72 |
72 **Inputs** | 73 **Inputs** |
73 | 74 |
74 * Parameter name: either Resolution or Perplexity. | 75 * Parameter name: either Resolution or Perplexity. |
75 * Starting value: float for Resolution, integer for Perplexity. | 76 * Starting value: float for Resolution, integer for Perplexity. |