Mercurial > repos > bgruening > hicexplorer_chicqualitycontrol

comparison chicQualityControl.xml @ 6:db4a82804126 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:23:20 +0000
parents 0e149d0c112c
children b892fa1fcaec
comparison
equal deleted inserted replaced
5:44d6bef89faa 6:db4a82804126
1 <tool id="hicexplorer_chicqualitycontrol" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_chicqualitycontrol" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>generates an estimate of the quality of each viewpoint</description> 2 <description>generates an estimate of the quality of each viewpoint</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">chicQualityControl</token> 4 <token name="@BINARY@">chicQualityControl</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
11 ln -s '$m' ${counter}_matrix.$m.ext && 11 ln -s '$m' ${counter}_matrix.$m.ext &&
12 #end for 12 #end for
13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) 13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
14 14
15 @BINARY@ 15 @BINARY@
16
17 --matrices $m 16 --matrices $m
18 --referencePoints '$referencePoints' 17 --referencePoints '$referencePoints'
19 --sparsity $sparsity 18 --sparsity $sparsity
20 --fixateRange $fixateRange 19 --fixateRange $fixateRange
21 --dpi $dpi 20 --dpi $dpi
24 --outFileNameHistogram histogram.$image_file_format 23 --outFileNameHistogram histogram.$image_file_format
25 --outFileNameSparsity sparsity.$image_file_format 24 --outFileNameSparsity sparsity.$image_file_format
26 25
27 && mv histogram.$image_file_format histogram 26 && mv histogram.$image_file_format histogram
28 && mv sparsity.$image_file_format sparsity 27 && mv sparsity.$image_file_format sparsity
29 ]]></command> 28 ]]> </command>
30 <inputs> 29 <inputs>
31 <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." />
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.' />
32 34
33 <param argument="--referencePoints" type="data" format='interval' 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.' />
34 label="Reference points"
35 help="Bed file contains all reference points which should be used to build the background model." />
36 <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.'/>
37
38 <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.'/>
39
40 <param name='dpi' type='integer' value='300' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
41 <param name="image_file_format" type="select" label="Image output format"> 36 <param name="image_file_format" type="select" label="Image output format">
42 <option value="png" selected="True">png</option> 37 <option value="png" selected="True">png</option>
43 <option value="svg">svg</option> 38 <option value="svg">svg</option>
44 <option value="pdf">pdf</option> 39 <option value="pdf">pdf</option>
45 </param> 40 </param>
46 41
47 </inputs> 42 </inputs>
48 <outputs> 43 <outputs>
49 <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 [${on_string}]: Reference points raw" />
50 <data name="rejected_reference_points" from_work_dir="reference_points_rejected_filter" format="interval" label="${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 [${on_string}]: Reference points rejected" />
51 <data name="accepted_reference_points" from_work_dir="reference_points" format="interval" label="${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 [${on_string}]: Reference points accepted" />
52 <data name="failed_reference_points" from_work_dir="reference_points_failed_reference_points" format="interval" label="${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 [${on_string}]: Reference points failed" />
53 48
54 <data name="report" from_work_dir="reference_points_report" format="txt" label="${tool.name} on [${on_string}]: Report"/> 49 <data name="report" from_work_dir="reference_points_report" format="txt" label="${tool.name} on [${on_string}]: Report" />
55 50
56 <data name="plot_histrogram" from_work_dir="histogram" format="png" label="${tool.name} on [${on_string}]: Histrogram plot"> 51 <data name="plot_histrogram" from_work_dir="histogram" format="png" label="${tool.name} on [${on_string}]: Histrogram plot">
57 <change_format> 52 <change_format>
58 <when input="image_file_format" value="svg" format="svg" /> 53 <when input="image_file_format" value="svg" format="svg" />
59 <when input="image_file_format" value="pdf" format="pdf" /> 54 <when input="image_file_format" value="pdf" format="pdf" />
60 </change_format> 55 </change_format>
66 </change_format> 61 </change_format>
67 </data> 62 </data>
68 </outputs> 63 </outputs>
69 <tests> 64 <tests>
70 <test> 65 <test>
71 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 66 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
72 <param name="referencePoints" value="cHi-C/referencePoints.bed"/> 67 <param name="referencePoints" value="cHi-C/referencePoints.bed" />
73 <param name='sparsity' value='0.05'/> 68 <param name='sparsity' value='0.05' />
74 69
75 <output name="accepted_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed" ftype="interval" compare="sim_size" delta='40000'/> 70 <output name="accepted_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed" ftype="interval" />
76 <output name="raw_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter" ftype="interval" compare="sim_size" delta='40000'/> 71 <output name="raw_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter" ftype="interval" />
77 <output name="rejected_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter" ftype="interval" compare="sim_size" delta='40000'/> 72 <output name="rejected_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter" ftype="interval" />
78 <output name="failed_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_failed_reference_points" ftype="interval" compare="sim_size" delta='40000'/> 73 <output name="failed_reference_points" file="cHi-C/chicQualityControl/new_referencepoints.bed_failed_reference_points" ftype="interval" />
79 <output name="report" file="cHi-C/chicQualityControl/new_referencepoints.bed_report" ftype="txt" compare="sim_size" delta='40000'/> 74 <output name="report" file="cHi-C/chicQualityControl/new_referencepoints.bed_report" ftype="txt" />
80 75
81 <output name="plot_histrogram" file="cHi-C/chicQualityControl/histogram.png" ftype="png" compare='sim_size' delta='40000'/> 76 <output name="plot_histrogram" file="cHi-C/chicQualityControl/histogram.png" ftype="png" compare='sim_size' />
82 <output name="plot_sparsity" file="cHi-C/chicQualityControl/sparsity.png" ftype="png" compare="sim_size" delta='40000'/> 77 <output name="plot_sparsity" file="cHi-C/chicQualityControl/sparsity.png" ftype="png" compare="sim_size" />
83 78
84 </test> 79 </test>
85 </tests> 80 </tests>
86 <help><![CDATA[ 81 <help><![CDATA[
87 82
97 `$ chicQualityControl -m matrix1.h5 matrix2.h5 -rp referencePointsFile.txt --range 20000 40000 --sparsity 0.01 -o referencePointFile_QC_passed.txt` 92 `$ chicQualityControl -m matrix1.h5 matrix2.h5 -rp referencePointsFile.txt --range 20000 40000 --sparsity 0.01 -o referencePointFile_QC_passed.txt`
98 93
99 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 94 For more information about HiCExplorer please consider our documentation on readthedocs.io_
100 95
101 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 96 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
102 ]]></help> 97 ]]> </help>
103 <expand macro="citations" /> 98 <expand macro="citations" />
104 </tool> 99 </tool>