Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

comparison hicPlotViewpoint.xml @ 5:67bd57e960a3 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
author iuc
date Sat, 09 Jun 2018 15:34:08 -0400
parents c4f273c3c73f
children 5e9c304c424c
comparison
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4:c4f273c3c73f 5:67bd57e960a3
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 hicPlotViewpoint --matrix '$matrix_h5_cooler' 10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
11 ln -s '$m' ${counter}_matrix &&
12 #end for
13 #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
14
15 hicPlotViewpoint --matrix "$m"
11 #if $interactionOutFileName: 16 #if $interactionOutFileName:
12 $interactionOutFileName interactions.bedgraph 17 $interactionOutFileName interactions
13 #end if 18 #end if
14 --outFileName plot.$image_file_format 19 --outFileName plot.$image_file_format
15 --region $region 20 --region $region
16 --referencePoint $referencePoint 21 --referencePoint $referencePoint
17 && mv plot.$image_file_format plot 22 && mv plot.$image_file_format plot
23 && ls -lah
24 #if $interactionOutFileName:
25 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
26 && mv interactions_${counter}_matrix.bedgraph ${counter}_interactions.bedgraph
27 #end for
28 #end if
18 ]]> 29 ]]>
19 </command> 30 </command>
20 <inputs> 31 <inputs>
21 <expand macro='matrix_h5_cooler_macro' /> 32 <expand macro='matrix_h5_cooler_multiple_macro' />
22 <expand macro="region" /> 33 <expand macro="region" />
23 <param name="referencePoint" type="text" label="Reference point" 34 <param name="referencePoint" type="text" label="Reference point"
24 help="The format is chr:referencePoint or chr:regionStart-regionEnd."/> 35 help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
25 36
26 <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false" 37 <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false"
31 </param> 42 </param>
32 43
33 </inputs> 44 </inputs>
34 <outputs> 45 <outputs>
35 46
36 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot"> 47 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
37 <change_format> 48 <change_format>
38 <when input="image_file_format" value="png" format="png" /> 49 <when input="image_file_format" value="png" format="png" />
39 <when input="image_file_format" value="svg" format="svg" /> 50 <when input="image_file_format" value="svg" format="svg" />
40 </change_format> 51 </change_format>
41 </data> 52 </data>
42 <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph' label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Bedgraph"> 53
54 <data format="bedgraph" name="interactionFile" >
55 <discover_datasets pattern='(?P&lt;designation&gt;.+)\_interactions\.bedgraph' directory="." visible="true"/>
43 <filter>interactionOutFileName</filter> 56 <filter>interactionOutFileName</filter>
44 </data> 57 </data>
45 58
46 </outputs> 59 </outputs>
47 <tests> 60 <tests>
48 <test> 61 <test>
49 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/> 62 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
50 <param name="image_file_format" value="png" /> 63 <param name="image_file_format" value="png" />
51 <param name='region' value='X:3000000-3500000' /> 64 <param name='region' value='X:3000000-3500000' />
52 <param name='referencePoint' value='X:3200000' /> 65 <param name='referencePoint' value='X:3200000' />
53 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/> 66 <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
54 </test> 67 </test>
55 <test> 68 <test>
56 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/> 69 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
57 <param name="image_file_format" value="png" /> 70 <param name="image_file_format" value="png" />
58 <param name='region' value='X:3000000-3500000' /> 71 <param name='region' value='X:3000000-3500000' />
59 <param name='referencePoint' value='X:3200000-3300000' /> 72 <param name='referencePoint' value='X:3200000-3300000' />
60 <param name='interactionOutFileName' value='True' /> 73 <param name='interactionOutFileName' value='True' />
61 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/> 74 <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
62 <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/> 75 <output name="interactionFile">
63 76 <discovered_dataset designation="0" file="li_32-33mb_interactions.bedgraph" />
77 </output>
64 </test> 78 </test>
65 </tests> 79 </tests>
66 <help><![CDATA[ 80 <help><![CDATA[
67 Plot Viewpoint 81 Plot Viewpoint
68 ============== 82 ==============