Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint
comparison hicPlotViewpoint.xml @ 15:58de3c7c8e89 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 11:08:32 +0000 |
| parents | b637a1e3cb14 |
| children | 8d203e74869b |
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| 14:7cdc1a2de16e | 15:58de3c7c8e89 |
|---|---|
| 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> |