Mercurial > repos > bgruening > hicexplorer_hicsummatrices
diff macros.xml @ 15:f5d54dc64697 draft
"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
| author | bgruening |
|---|---|
| date | Mon, 16 Dec 2019 13:12:48 +0000 |
| parents | 34ea556ba897 |
| children | 3a7698050cb6 |
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--- a/macros.xml Mon Dec 09 10:37:59 2019 +0000 +++ b/macros.xml Mon Dec 16 13:12:48 2019 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">3.3.1</token> + <token name="@WRAPPER_VERSION@">2.1.4</token> <token name="@USE_RANGE@"> #if $use_range.select_use_range == "yes_use_range": --range $range_min:$range_max @@ -15,25 +15,6 @@ <version_command>@BINARY@ --version</version_command> </xml> - <token name="@CHROMOSOME_LIST@"> - #if $chromosome_list: - #set $chromosomes = [] - #for $chrom in $chromosome_list: - #silent $chromosomes.append("'%s'" % $chrom.chromosomes) - #end for - #set $chromosome_string = ' '.join($chromosomes) - --chromosomes $chromosome_string - #end if - </token> - - <xml name="chromosome_list"> - <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included."> - <param argument="--chromosomes" type="text" value="" > - <validator type="empty_field" /> - </param> - </repeat> - </xml> - <xml name="citations"> <citations> <citation type="doi">10.5281/zenodo.1133705</citation> @@ -133,7 +114,6 @@ <option value="brg">brg</option> <option value="jet">jet</option> <option value="afmhot">afmhot</option> - <option value="plasma">plasma</option> <option value="Accent_r">Accent reversed</option> <option value="Spectral_r">Spectral reversed</option> <option value="Set1_r">Set1 reversed</option> @@ -203,10 +183,10 @@ <option value="brg_r">brg reversed</option> <option value="jet_r">jet reversed</option> <option value="afmhot_r">afmhot reversed</option> - <option value="plasma_r">plasma reversed</option> </param> </xml> + <xml name="multiple_input_matrices"> <repeat name="input_files" title="Hi-C Matrix files" min="2"> <param name="matrix" type="data" format="h5,cool" @@ -222,22 +202,19 @@ #set $matrices = [] #set $mlabels = [] #for $counter, $i in enumerate($input_files): - ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; - #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext)) + ln -s $i.matrix #echo str($counter)+'_matrix'#; + #silent $matrices.append( '%s_matrix' % $counter ) #if str($i.mlabel.value) != "": - #set $mlabels += ['\'%s\'' % ($i.mlabel.value)] + #set $mlabels += ['"%s"' % ($i.mlabel.value)] #else - #set $mlabels += ['\'%s\'' % ($i.matrix.name)] + #set $mlabels += ['"%s"' % ($i.matrix.name)] #end if #end for #set $mlabels = ' '.join($mlabels) #set $matrices = ' '.join($matrices) </token> - <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token> - <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token> - <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token> <xml name="region"> <param name="region" type="text" label="Region of the genome to limit the operation" @@ -353,96 +330,6 @@ <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" label="Matricies to compute on" multiple="true"/> </xml> - - - - <xml name='convertFormat_single_macro'> - <conditional name="inputFormat_conditional"> - <param name="inputFormat_selector" type="select" label="Choose input file type"> - <option value="optionCool" selected="True">cool</option> - <option value="optionH5">h5</option> - <!-- <option value="optionHic">hic</option> --> - <option value="optionHomer">Homer</option> - <option value="optionHicpro">HiCPro</option> - </param> - <when value="optionCool"> - <expand macro='matrix_h5_cooler_macro' /> - <param name='correctionName' type='text' label='Correction factors column name'/> - <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/> - <param name='chromosome' type='text' label='Load only one chromosome'/> - <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/> - - </when> - <when value="optionH5"> - <expand macro='matrix_h5_cooler_macro' /> - </when> - <!-- <when value="optionHic"> - <param name='matrixHic' type='data' format='binary' label='.hic matrix'/> - <param name='resolutions' type='text' label='List of resolutions'/> - </when> --> - - <when value="optionHomer"> - <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='bedHicpro' type='data' format='bed' label='HicPro bed file'/> - </when> - </conditional> - </xml> - - <xml name='convertFormat_multiple_macro'> - <conditional name="inputFormat_conditional"> - <param name="inputFormat_selector" type="select" label="Choose input file type"> - <option value="optionCool" selected="True">cool</option> - <option value="optionH5">h5</option> - <option value="optionHomer">Homer</option> - <option value="optionHicpro">HiCPro</option> - </param> - <when value="optionCool"> - <expand macro='matrix_h5_cooler_multiple_macro' /> - <param name='correctionName' type='text' label='Correction factors column name'/> - <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/> - <param name='chromosome' type='text' label='Load only one chromosome'/> - <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/> - - </when> - <when value="optionH5"> - <expand macro='matrix_h5_cooler_multiple_macro' /> - </when> - - <when value="optionHomer"> - <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' multiple="true"/> - </when> - - <when value="optionHicpro"> - <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/> - <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/> - </when> - </conditional> - </xml> - <xml name='convertFormat_single_output_macro'> - <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> --> - - <conditional name="outputFormat_conditional"> - <param name="outputFormat_selector" type="select" label="Choose output file type"> - <option value="cool" selected="True">cool</option> - <option value="h5">h5</option> - <option value="homer">Homer</option> - <option value="ginteractions">ginteractions</option> - - </param> - <when value="cool"> - <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count'/> - <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column'/> - </when> - <when value='h5'/> - <when value='homer'/> - <when value='ginteractions'/> - - </conditional> - </xml> <token name="@REFERENCES@"> .. class:: infomark