Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

comparison hicPlotViewpoint.xml @ 10:e8a131f0840f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
author iuc
date Mon, 16 Dec 2019 22:44:11 +0000
parents 4a352a9fae50
children 4b4d91356d93
comparison
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9:4a352a9fae50 10:e8a131f0840f
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 9
10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple): 10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
11 ln -s '$m' ${counter}_matrix && 11 ln -s '$m' ${counter}_matrix.$m.ext &&
12 #end for 12 #end for
13 #set $m = '" "'.join([ '%s_matrix' % $counter 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 hicPlotViewpoint --matrix "$m" 15 @BINARY@ --matrix $m
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 && ls -lah 23
24 #if $interactionOutFileName: 24 #if $interactionOutFileName:
25 #for $counter, $m in enumerate($matrix_h5_cooler_multiple): 25 && mkdir interaction
26 && mv interactions_${counter}_matrix.bedgraph ${counter}_interactions.bedgraph 26 #for $counter, $matrix in enumerate($m.split(' ')):
27 && mv interactions_${matrix}.bedgraph interaction/${counter}_interactions.bedgraph
27 #end for 28 #end for
28 #end if 29 #end if
29 ]]> 30 ]]>
30 </command> 31 </command>
31 <inputs> 32 <inputs>
50 <when input="image_file_format" value="svg" format="svg" /> 51 <when input="image_file_format" value="svg" format="svg" />
51 </change_format> 52 </change_format>
52 </data> 53 </data>
53 54
54 <data format="bedgraph" name="interactionFile" > 55 <data format="bedgraph" name="interactionFile" >
55 <discover_datasets pattern='(?P&lt;designation&gt;.+)\_interactions\.bedgraph' directory="." visible="true"/>
56 <filter>interactionOutFileName</filter> 56 <filter>interactionOutFileName</filter>
57 <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true"/>
57 </data> 58 </data>
58 59
59 </outputs> 60 </outputs>
60 <tests> 61 <tests>
61 <test> 62 <test>
62 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 63 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/>
63 <param name="image_file_format" value="png" /> 64 <param name="image_file_format" value="png" />
64 <param name='region' value='X:3000000-3500000' /> 65 <param name='region' value='X:3000000-3500000' />
65 <param name='referencePoint' value='X:3200000' /> 66 <param name='referencePoint' value='X:3200000' />
66 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/> 67 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
67 </test> 68 </test>
68 <test> 69 <test>
69 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 70 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/>
70 <param name="image_file_format" value="png" /> 71 <param name="image_file_format" value="png" />
71 <param name='region' value='X:3000000-3500000' /> 72 <param name='region' value='X:3000000-3500000' />
72 <param name='referencePoint' value='X:3200000-3300000' /> 73 <param name='referencePoint' value='X:3200000-3300000' />
73 <param name='interactionOutFileName' value='True' /> 74 <param name='interactionOutFileName' value='True' />
74 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/> 75 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
75 <output name="interactionFile"> 76 <output name="interactionFile">
76 <discovered_dataset designation="0" file="li_32-33mb_interactions.bedgraph" /> 77 <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" />
77 </output> 78 </output>
78 </test> 79 </test>
79 </tests> 80 </tests>
80 <help><![CDATA[ 81 <help><![CDATA[
81 Plot Viewpoint 82 Plot Viewpoint