Mercurial > repos > bgruening > hicexplorer_chicqualitycontrol

comparison chicQualityControl.xml @ 8:b892fa1fcaec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:54:38 +0000
parents db4a82804126
children a63e9713c39d
comparison
equal deleted inserted replaced
7:fadd03fbc4f5 8:b892fa1fcaec
26 && mv histogram.$image_file_format histogram 26 && mv histogram.$image_file_format histogram
27 && mv sparsity.$image_file_format sparsity 27 && mv sparsity.$image_file_format sparsity
28 ]]> </command> 28 ]]> </command>
29 <inputs> 29 <inputs>
30 <expand macro="matrix_h5_cooler_multiple_macro" /> 30 <expand macro="matrix_h5_cooler_multiple_macro" />
31 <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to build the background model." /> 31 <param argument="--referencePoints" type="data" format="interval" label="Reference points" help="Bed file contains all reference points which should be used to build the background model." />
32 <param argument="--sparsity" type="float" value="0.05" label="Sparsity threshold" help='Viewpoints with a sparsity less than given are considered of bad quality. If multiple matrices are given, the viewpoint is removed as soon as it is of bad quality in at least one matrix.' /> 32 <param argument="--sparsity" type="float" value="0.05" label="Sparsity threshold" help="Viewpoints with a sparsity less than given are considered of bad quality. If multiple matrices are given, the viewpoint is removed as soon as it is of bad quality in at least one matrix." />
33 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' /> 33 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help="Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin." />
34 34
35 <param name='dpi' type='integer' value='300' min="100" max="2000" optional='true' label='DPI for image' help='Change the default resolution of the plot.' /> 35 <param name="dpi" type="integer" value="300" min="100" max="2000" optional="true" label="DPI for image" help="Change the default resolution of the plot." />
36 <param name="image_file_format" type="select" label="Image output format"> 36 <param name="image_file_format" type="select" label="Image output format">
37 <option value="png" selected="True">png</option> 37 <option value="png" selected="True">png</option>
38 <option value="svg">svg</option> 38 <option value="svg">svg</option>
39 <option value="pdf">pdf</option> 39 <option value="pdf">pdf</option>
40 </param> 40 </param>
41 </inputs>
41 42
42 </inputs>
43 <outputs> 43 <outputs>
44 <data name="raw_reference_points" from_work_dir="reference_points_raw_filter" format="interval" label="${tool.name} on [${on_string}]: Reference points raw" /> 44 <data name="raw_reference_points" from_work_dir="reference_points_raw_filter" format="interval" label="${tool.name} on [${on_string}]: Reference points raw" />
45 <data name="rejected_reference_points" from_work_dir="reference_points_rejected_filter" format="interval" label="${tool.name} on [${on_string}]: Reference points rejected" /> 45 <data name="rejected_reference_points" from_work_dir="reference_points_rejected_filter" format="interval" label="${tool.name} on [${on_string}]: Reference points rejected" />
46 <data name="accepted_reference_points" from_work_dir="reference_points" format="interval" label="${tool.name} on [${on_string}]: Reference points accepted" /> 46 <data name="accepted_reference_points" from_work_dir="reference_points" format="interval" label="${tool.name} on [${on_string}]: Reference points accepted" />
47 <data name="failed_reference_points" from_work_dir="reference_points_failed_reference_points" format="interval" label="${tool.name} on [${on_string}]: Reference points failed" /> 47 <data name="failed_reference_points" from_work_dir="reference_points_failed_reference_points" format="interval" label="${tool.name} on [${on_string}]: Reference points failed" />
48
49 <data name="report" from_work_dir="reference_points_report" format="txt" label="${tool.name} on [${on_string}]: Report" /> 48 <data name="report" from_work_dir="reference_points_report" format="txt" label="${tool.name} on [${on_string}]: Report" />
50
51 <data name="plot_histrogram" from_work_dir="histogram" format="png" label="${tool.name} on [${on_string}]: Histrogram plot"> 49 <data name="plot_histrogram" from_work_dir="histogram" format="png" label="${tool.name} on [${on_string}]: Histrogram plot">
52 <change_format> 50 <change_format>
53 <when input="image_file_format" value="svg" format="svg" /> 51 <when input="image_file_format" value="svg" format="svg" />
54 <when input="image_file_format" value="pdf" format="pdf" /> 52 <when input="image_file_format" value="pdf" format="pdf" />
55 </change_format> 53 </change_format>
59 <when input="image_file_format" value="svg" format="svg" /> 57 <when input="image_file_format" value="svg" format="svg" />
60 <when input="image_file_format" value="pdf" format="pdf" /> 58 <when input="image_file_format" value="pdf" format="pdf" />
61 </change_format> 59 </change_format>
62 </data> 60 </data>
63 </outputs> 61 </outputs>
62
64 <tests> 63 <tests>
65 <test> 64 <test>
66 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" /> 65 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
67 <param name="referencePoints" value="cHi-C/referencePoints.bed" /> 66 <param name="referencePoints" value="cHi-C/referencePoints.bed" />
68 <param name='sparsity' value='0.05' /> 67 <param name="sparsity" value="0.05" />
69
70 <output name="accepted_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed" ftype="interval" /> 68 <output name="accepted_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed" ftype="interval" />
71 <output name="raw_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter" ftype="interval" /> 69 <output name="raw_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter" ftype="interval" />
72 <output name="rejected_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter" ftype="interval" /> 70 <output name="rejected_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter" ftype="interval" />
73 <output name="failed_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_failed_reference_points" ftype="interval" /> 71 <output name="failed_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_failed_reference_points" ftype="interval" />
74 <output name="report" file="cHi-C/chicQualityControl/new_referencepoints.bed_report" ftype="txt" /> 72 <output name="report" file="cHi-C/chicQualityControl/new_referencepoints.bed_report" ftype="txt" />
75 73 <output name="plot_histrogram" file="cHi-C/chicQualityControl/histogram.png" ftype="png" compare="sim_size" />
76 <output name="plot_histrogram" file="cHi-C/chicQualityControl/histogram.png" ftype="png" compare='sim_size' />
77 <output name="plot_sparsity" file="cHi-C/chicQualityControl/sparsity.png" ftype="png" compare="sim_size" /> 74 <output name="plot_sparsity" file="cHi-C/chicQualityControl/sparsity.png" ftype="png" compare="sim_size" />
78
79 </test> 75 </test>
80 </tests> 76 </tests>
81 <help><![CDATA[ 77 <help><![CDATA[
82 78
83 Compute the quality of viewpoints 79 Compute the quality of viewpoints