Mercurial > repos > bgruening > hicexplorer_hiccorrelate
diff macros.xml @ 20:2b4d6a8dab36 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author | iuc |
---|---|
date | Wed, 18 Oct 2023 10:30:15 +0000 |
parents | bab2fa7355d9 |
children | 2786a931cad2 |
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--- a/macros.xml Tue Jan 10 19:03:49 2023 +0000 +++ b/macros.xml Wed Oct 18 10:30:15 2023 +0000 @@ -1,7 +1,7 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@TOOL_VERSION@">3.6</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">3.7.2</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@USE_RANGE@"> #if $use_range.select_use_range == "yes_use_range": --range $use_range.range_min:$use_range.range_max @@ -37,7 +37,8 @@ <xml name="citations"> <citations> - <citation type="doi">10.5281/zenodo.1133705</citation> + <citation type="doi">10.1093/nar/gkaa220</citation> + <citation type="doi">10.1093/nar/gky504</citation> <yield /> </citations> </xml> @@ -348,6 +349,10 @@ <xml name='matrix_h5_cooler_multiple_macro'> <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" /> </xml> + + <xml name='matrix_cooler_multiple_macro'> + <param name='matrix_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Hi-C matrix" /> + </xml> <xml name='convertFormat_single_macro'> <conditional name="inputFormat_conditional"> <param name="inputFormat_selector" type="select" label="Choose input file type"> @@ -356,6 +361,8 @@ <option value="optionHic">hic</option> <option value="optionHomer">Homer</option> <option value="optionHicpro">HiCPro</option> + <option value="option2Dtext">2D-text</option> + </param> <when value="optionCool"> <expand macro='matrix_h5_cooler_macro' /> @@ -377,9 +384,17 @@ <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' /> </when> <when value="optionHicpro"> - <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' /> + <param name='matrixHicpro' type='data' format='txt' label='.hicpro matrix' /> <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' /> </when> + <when value="option2Dtext"> + <param name='matrix2Dtext' type='data' format='txt' label='A 2D text matrix' /> + + <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> + <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> + </param> + <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' /> + </when> </conditional> </xml> @@ -390,6 +405,9 @@ <option value="optionH5">h5</option> <option value="optionHomer">Homer</option> <option value="optionHicpro">HiCPro</option> + <option value="option2Dtext">2D-text</option> + + </param> <when value="optionCool"> <expand macro='matrix_h5_cooler_multiple_macro' /> @@ -408,6 +426,14 @@ <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' /> <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' /> </when> + <when value="option2Dtext"> + <param name='matrix2Dtext' type='data' format='txt' multiple="true" label='A 2D text matrix' /> + + <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> + <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> + </param> + <param name='chromosomeSizes' type='data' format='txt' label='Chromosome sizes file' /> + </when> </conditional> </xml> <xml name='convertFormat_single_output_macro'> @@ -418,6 +444,8 @@ <option value="h5">h5</option> <option value="homer">Homer</option> <option value="ginteractions">ginteractions</option> + <option value="hicpro">hicpro</option> + </param> <when value="cool"> <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' /> @@ -426,6 +454,7 @@ <when value='h5' /> <when value='homer' /> <when value='ginteractions' /> + <when value='hicpro' /> </conditional> </xml> <token name="@REFERENCES@">