Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

comparison hicPlotViewpoint.xml @ 18:a1e583dc6579 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
author iuc
date Mon, 01 Jul 2024 18:58:42 +0000
parents d488967c1625
children
comparison
equal deleted inserted replaced
17:b06a8bf0b798 18:a1e583dc6579
1 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>plot interactions around a viewpoint</description> 2 <description>plot interactions around a viewpoint</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicPlotViewpoint</token> 4 <token name="@BINARY@">hicPlotViewpoint</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
16 #if $interactionOutFileName: 16 #if $interactionOutFileName:
17 $interactionOutFileName interactions 17 $interactionOutFileName interactions
18 #end if 18 #end if
19 --outFileName plot.$image_file_format 19 --outFileName plot.$image_file_format
20 --region $region 20 --region $region
21 --referencePoint $referencePoint 21 --referencePoint '$referencePoint'
22 && mv plot.$image_file_format plot 22 && mv plot.$image_file_format plot
23 23
24 #if $interactionOutFileName: 24 #if $interactionOutFileName:
25 && mkdir interaction 25 && mkdir interaction
26 #for $counter, $matrix in enumerate($m.split(' ')): 26 #for $counter, $matrix in enumerate($m.split(' ')):
28 #end for 28 #end for
29 #end if 29 #end if
30 ]]> 30 ]]>
31 </command> 31 </command>
32 <inputs> 32 <inputs>
33 <expand macro='matrix_h5_cooler_multiple_macro' /> 33 <expand macro="matrix_h5_cooler_multiple_macro" />
34 <expand macro="region" /> 34 <expand macro="region" />
35 <param name="referencePoint" type="text" label="Reference point" help="The format is chr:referencePoint or chr:regionStart-regionEnd."> 35 <param name="referencePoint" type="text" label="Reference point" help="The format is chr:referencePoint or chr:regionStart-regionEnd.">
36 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator> 36 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator>
37 </param> 37 </param>
38 <param argument="--interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false" label="Create bedgraph file with interactions" /> 38 <param argument="--interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false" label="Create bedgraph file with interactions" />
52 <filter>interactionOutFileName</filter> 52 <filter>interactionOutFileName</filter>
53 <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true" /> 53 <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true" />
54 </data> 54 </data>
55 </outputs> 55 </outputs>
56 <tests> 56 <tests>
57 <test> 57 <test expect_num_outputs="1">
58 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" /> 58 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" />
59 <param name="image_file_format" value="png" /> 59 <param name="image_file_format" value="png" />
60 <param name='region' value='X:3000000-3500000' /> 60 <param name="region" value="X:3000000-3500000" />
61 <param name='referencePoint' value='X:3200000' /> 61 <param name="referencePoint" value="X:3200000" />
62 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size" /> 62 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size" />
63 </test> 63 </test>
64 <test> 64 <test expect_num_outputs="2">
65 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" /> 65 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool" />
66 <param name="image_file_format" value="png" /> 66 <param name="image_file_format" value="png" />
67 <param name='region' value='X:3000000-3500000' /> 67 <param name="region" value="X:3000000-3500000" />
68 <param name='referencePoint' value='X:3200000-3300000' /> 68 <param name="referencePoint" value="X:3200000-3300000" />
69 <param name='interactionOutFileName' value='True' /> 69 <param name="interactionOutFileName" value="True" />
70 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size" /> 70 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size" />
71 <output name="interactionFile"> 71 <output name="interactionFile">
72 <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" /> 72 <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" />
73 </output> 73 </output>
74 </test> 74 </test>