Mercurial > repos > bgruening > hicexplorer_hicplotsvl

comparison hicPlotSVL.xml @ 5:3f75bfd8812b 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 14:15:06 +0000
parents 681c0871ed1d
children eb745ee3bbd3
comparison
equal deleted inserted replaced
4:6e83e0a1a1b6 5:3f75bfd8812b
1 <tool id="hicexplorer_hicplotsvl" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicplotsvl" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>plots the relation of short vs long range contacts</description> 2 <description>plots the relation of short vs long range contacts</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicPlotSVL</token> 4 <token name="@BINARY@">hicPlotSVL</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
37 37
38 && mv plot.$image_file_format plot 38 && mv plot.$image_file_format plot
39 ]]> 39 ]]>
40 </command> 40 </command>
41 <inputs> 41 <inputs>
42 <expand macro='matrix_h5_cooler_multiple_macro'/> 42 <expand macro='matrix_h5_cooler_multiple_macro' />
43 <param argument="--distance" optional='true' type="integer" label="Short range distance" 43 <param argument="--distance" optional='true' type="integer" label="Short range distance" help="Distance which should be considered as short range. Default 2MB." value='2000000' />
44 help="Distance which should be considered as short range. Default 2MB." value='2000000'/>
45 <expand macro="chromosome_list" /> 44 <expand macro="chromosome_list" />
46 <param argument="--colorList" optional='true' type="text" label="Colorlist" help="Colorlist for the boxplots." /> 45 <param argument="--colorList" optional='true' type="text" label="Colorlist" help="Colorlist for the boxplots." />
47 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> 46 <expand macro="dpi" />
48 <param name="image_file_format" type="select" label="Image output format"> 47 <param name="image_file_format" type="select" label="Image output format">
49 <option value="png" selected="True">png</option> 48 <option value="png" selected="True">png</option>
50 <option value="svg">svg</option> 49 <option value="svg">svg</option>
51 <option value="pdf">pdf</option> 50 <option value="pdf">pdf</option>
52 </param> 51 </param>
56 <change_format> 55 <change_format>
57 <when input="image_file_format" value="svg" format="svg" /> 56 <when input="image_file_format" value="svg" format="svg" />
58 <when input="image_file_format" value="pdf" format="pdf" /> 57 <when input="image_file_format" value="pdf" format="pdf" />
59 </change_format> 58 </change_format>
60 </data> 59 </data>
61 <data name='output_p_values' from_work_dir='p_values.txt' format='txt' label='P values svl'/> 60 <data name='output_p_values' from_work_dir='p_values.txt' format='txt' label='P values svl' />
62 <data name='output_ratios' from_work_dir='ratios.txt' format='txt' label='Ratios svl'/> 61 <data name='output_ratios' from_work_dir='ratios.txt' format='txt' label='Ratios svl' />
63 62
64 </outputs> 63 </outputs>
65 <tests> 64 <tests>
66 <test> 65 <test>
67 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/> 66 <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" />
68 <param name="distance" value="2000000"/> 67 <param name="distance" value="2000000" />
69 <param name="dpi" value="10"/> 68 <param name="dpi" value="10" />
70 <param name="color" value="y m c"/> 69 <param name="color" value="y m c" />
71 <repeat name="chromosome_list"> 70 <repeat name="chromosome_list">
72 <param name="chromosomes" value="chr2L"/> 71 <param name="chromosomes" value="chr2L" />
73 </repeat> 72 </repeat>
74 <repeat name="chromosome_list"> 73 <repeat name="chromosome_list">
75 <param name="chromosomes" value="chr3L"/> 74 <param name="chromosomes" value="chr3L" />
76 </repeat> 75 </repeat>
77 <repeat name="chromosome_list"> 76 <repeat name="chromosome_list">
78 <param name="chromosomes" value="chr4"/> 77 <param name="chromosomes" value="chr4" />
79 </repeat> 78 </repeat>
80 79
81 <param name="image_file_format" value="png" /> 80 <param name="image_file_format" value="png" />
82 81
83 <output name="output_plot" file="hicPlotSVL/plot.png" ftype="png" compare="sim_size"/> 82 <output name="output_plot" file="hicPlotSVL/plot.png" ftype="png" compare="sim_size" />
84 <output name="output_p_values" file="hicPlotSVL/p_values.txt" ftype="txt" compare="sim_size"/> 83 <output name="output_p_values" file="hicPlotSVL/p_values.txt" ftype="txt" />
85 <output name="output_ratios" file="hicPlotSVL/ratios.txt" ftype="txt" compare="sim_size"/> 84 <output name="output_ratios" file="hicPlotSVL/ratios.txt" ftype="txt" />
86 85
87 </test> 86 </test>
88 </tests> 87 </tests>
89 <help><![CDATA[ 88 <help><![CDATA[
90 89
168 167
169 For more information about HiCExplorer please consider our documentation on readthedocs.io_. 168 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
170 169
171 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 170 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
172 171
173 ]]></help> 172 ]]> </help>
174 <expand macro="citations" /> 173 <expand macro="citations" />
175 </tool> 174 </tool>