--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicConvertFormat.xml	Mon Dec 16 15:28:54 2019 -0500
@@ -0,0 +1,375 @@
+<tool id="hicexplorer_hicconvertformat" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>Convert between different file formats</description>
+    <macros>
+        <token name="@BINARY@">hicConvertFormat</token>
+        <token name="@SINGLE_INPUT@">
+            #if $xml_path.inputFormat_selector == 'optionCool':
+                --matrices 'matrix.cool'
+                --inputFormat cool
+                #if $xml_path.correctionName:
+                    --correction_name '$xml_path.correctionName'
+                #end if
+
+                #if $xml_path.correctionDivision:
+                    --correction_division
+                #end if
+
+                #if $xml_path.chromosome:
+                    #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($xml_path.chromosome).split(' ') ])
+
+                    --chromosome $chromosome
+                #end if
+
+                #if $xml_path.loadRawValues:
+                    --load_raw_values
+                #end if
+            #end if
+            #if $xml_path.inputFormat_selector == 'optionH5':
+                --matrices "matrix.h5"
+                --inputFormat h5
+
+            #end if 
+            #if $xml_path.inputFormat_selector == 'optionHomer':
+                --matrices "matrix.homer"
+                --inputFormat homer
+
+            #end if 
+            #if $xml_path.inputFormat_selector == 'optionHicpro':
+                --matrices "matrix.hicpro"
+                --bedFileHicpro "matrix.bed"
+                --inputFormat hicpro
+            #end if 
+            #if $xml_path.inputFormat_selector == 'optionHic':
+                --matrices "matrix.hic"
+                #if $xml_path.resolutions:
+                    #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ])
+
+                    --resolutions $resolutions
+                #end if
+                --inputFormat hic
+            #end if 
+        </token>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+
+        ## single to single case
+        
+
+        #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
+            #set xml_path = $outputSingleMultiple_conditional.inputFormat_conditional
+        
+            #if $xml_path.inputFormat_selector == 'optionCool':
+                ln -s "$xml_path.matrix_h5_cooler" "matrix.cool" &&
+
+            #end if
+            #if $xml_path.inputFormat_selector == 'optionH5':
+                ln -s "$xml_path.matrix_h5_cooler" "matrix.h5" &&
+
+            #end if
+            #if $xml_path.inputFormat_selector == 'optionHomer':
+               ln -s "$xml_path.matrixHomer" "matrix.homer" && 
+
+            #end if
+
+            #if $xml_path.inputFormat_selector == 'optionHicpro':
+                ln -s "$xml_path.matrixHicpro" "matrix.hicpro" && 
+                ln -s "$xml_path.bedHicpro" "matrix.bed" &&
+            #end if
+
+            #if $xml_path.inputFormat_selector == 'optionHic':
+                ln -s "$xml_path.matrixHic" "matrix.hic" &&
+            #end if
+
+
+
+            @BINARY@ 
+            @SINGLE_INPUT@
+            
+            
+            --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector
+            --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector'
+
+            #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
+                && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
+
+            #else:
+                && mv "matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" matrix_out
+            #end if
+        #end if
+
+        
+        ### Set up links to matrices to have correct ending
+        #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
+            #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
+                #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional
+                #if $xml_path.inputFormat_selector == 'optionCool':
+                    ln -s "$xml_path.matrix_h5_cooler" "matrix.cool" &&
+                #end if
+
+                #if $xml_path.inputFormat_selector == 'optionH5':
+                    ln -s "$xml_path.matrix_h5_cooler" "matrix.h5" &&
+
+                #end if
+
+                #if $xml_path.inputFormat_selector == 'optionHomer':
+                    ln -s "$xml_path.matrix_h5_cooler" "matrix.homer" &&
+
+                #end if
+
+                #if $xml_path.inputFormat_selector == 'optionHicpro':
+                    ln -s "$xml_path.matrix_h5_cooler" "matrix.hicpro" &&
+                    ln -s "$xml_path.bedHicpro" "matrix.bed" &&
+
+                #end if
+                #if $xml_path.inputFormat_selector == 'optionHic':
+                    ln -s "$xml_path.matrix_h5_cooler" "matrix.hic" &&
+
+                #end if
+            #else:
+                #set xml_manyToOne = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional
+                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionCool':
+                    #for $counter, $m in enumerate($xml_manyToOne.matrix_h5_cooler_multiple):
+                        ln -s '$m' "${counter}_matrix.cool" &&
+                    #end for
+                    #set $m = ' '.join([ '"%s_matrix"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix_h5_cooler_multiple) ])
+
+                #end if
+                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionH5':
+                    #for $counter, $m in enumerate($xml_manyToOne.matrix_h5_cooler_multiple):
+                        ln -s '$m' "${counter}_matrix.h5" &&
+                    #end for
+                    #set $m = ' '.join([ '"%s_matrix"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix_h5_cooler_multiple) ])
+                #end if
+                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer':
+                    #for $counter, $m in enumerate($xml_manyToOne.matrixHomer):
+                        ln -s '$m' "${counter}_matrix.homer" &&
+                    #end for
+                    #set $m = ' '.join([ '"%s_matrix.homer"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHomer) ])
+                #end if
+                 #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
+                    #for $counter, $m in enumerate($xml_manyToOne.matrixHicpro):
+                        ln -s '$m' "${counter}_matrix.hicpro" &&
+                    #end for
+                    #set $m = ' '.join([ '"%s_matrix.hicpro"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHicpro) ])
+                    
+                    #for $counter, $bed in enumerate($xml_manyToOne.bedHicpro):
+                        ln -s '$bed' "${counter}_matrix.bed" &&
+                    #end for
+                    #set $bed = ' '.join([ '"%s_matrix.bed"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.bedHicpro) ])
+                    --bedFileHicpro '$bed'
+                #end if
+            #end if
+
+
+        @BINARY@ 
+            --outputFormat mcool
+
+            #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
+                #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutions).split(" ") ])
+
+                --resolutions $resolutions
+                 #if $xml_path.inputFormat_selector == 'optionCool':
+                    --matrices "matrix.cool"
+                    --inputFormat cool
+                #end if
+                #if $xml_path.inputFormat_selector == 'optionH5':
+                    --matrices "matrix.h5"
+                    --inputFormat h5
+
+                #end if 
+                #if $xml_path.inputFormat_selector == 'optionHomer':
+                    --matrices "matrix.homer"
+                    --inputFormat homer
+
+                #end if 
+                #if $xml_path.inputFormat_selector == 'optionHicpro':
+                    --matrices "matrix.hicpro"
+                    --bedFileHicpro "matrix.bed"
+                    --inputFormat hicpro
+                #end if 
+                #if $xml_path.inputFormat_selector == 'optionHic':
+                    --matrices "matrix.hic"
+                    --inputFormat hic
+                #end if 
+            #end if
+
+            #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'manyToOne_option':
+                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionCool':
+                    --inputFormat cool
+                #end if
+
+                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionH5':
+                    --inputFormat h5
+                #end if
+
+
+                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer':
+                    --inputFormat homer
+                #end if
+
+                #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro':
+                    --inputFormat hicpro
+                    --bedFileHicpro '$bed'
+                #end if
+
+                --matrices $m
+            #end if
+            --outFileName matrix.mcool
+            && mv matrix.mcool matrix_out
+
+        #end if
+
+
+]]>
+    </command>
+    <inputs>
+
+        <conditional name="outputSingleMultiple_conditional">
+            <param name="outputSingleMultiple_selector" type="select" label="Choose output matrix type">
+                <option value="singleMatrix" selected="True">single matrix</option>
+                <option value="multipleMatrix">multiple matrix</option>
+            </param>            
+            <when value='singleMatrix'>
+                <expand macro='convertFormat_single_macro' />
+                <expand macro='convertFormat_single_output_macro' />
+            </when>
+            <when value='multipleMatrix'>
+                <conditional name="resolutionOrManyToOne_conditional">
+                    <param name="resolutionOrManyToOne_selector" type="select" label="Choose input file type">
+                        <option value='resolution_option' >Create out of one matrix a multi matrix with diffrerent resolutions</option>
+                        <option value='manyToOne_option'>Create out of n matrices one multi matrix </option>
+                    </param>
+                    <when value='resolution_option'>
+                        <param name='resolutions' type='text' label='To be stored resolutions'/>
+                        <expand macro='convertFormat_single_macro' />
+                    </when>
+                    <when value='manyToOne_option'>
+                        <expand macro='convertFormat_multiple_macro' />
+                    </when>
+                </conditional>
+                <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>
+        </conditional>
+    </inputs>
+    <outputs>
+
+        <data name='output_converted_matrix' from_work_dir='matrix_out' format='cool' label='Converted matrix'>
+            <filter>outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix'</filter>
+            <change_format>
+                <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="h5" format="h5" />
+                <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="homer" format="zip" />
+                <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="ginteractions" format="tsv" />
+            </change_format>
+        </data>
+        <data name='output_converted_matrix_multi' from_work_dir='matrix_out' format='mcool' label='Converted matrix mcool'>
+            <filter>outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name='outputSingleMultiple_conditional'>
+                <param name='outputSingleMultiple_selector' value='singleMatrix'/>
+                <conditional name='inputFormat_conditional'>
+                    <param name='inputFormat_selector' value='optionCool'/>
+                    <param name='matrix_h5_cooler' value='small_test_matrix.cool'/>
+                </conditional>
+                
+                <conditional name='outputFormat_conditional'>
+                    <param name='outputFormat_selector' value='h5'/>
+                </conditional>
+            </conditional>
+            <output name="output_converted_matrix" ftype="h5">
+                <assert_contents>
+                    <has_h5_keys keys='intervals,matrix,nan_bins'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <conditional name='outputSingleMultiple_conditional'>
+                <param name='outputSingleMultiple_selector' value='singleMatrix'/>
+                <conditional name='inputFormat_conditional'>
+                    <param name='inputFormat_selector' value='optionH5'/>
+                    <param name='matrix_h5_cooler' value='small_test_matrix.h5'/>
+                </conditional>
+                
+                <conditional name='outputFormat_conditional'>
+                    <param name='outputFormat_selector' value='cool'/>
+                </conditional>
+            </conditional>
+            <output name="output_converted_matrix" ftype="cool">
+                <assert_contents>
+                    <has_h5_keys keys='bins,chroms,indexes,pixels'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <conditional name='outputSingleMultiple_conditional'>
+                <param name='outputSingleMultiple_selector' value='singleMatrix'/>
+                <conditional name='inputFormat_conditional'>
+                    <param name='inputFormat_selector' value='optionCool'/>
+                    <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool'/>
+                </conditional>
+                
+                <conditional name='outputFormat_conditional'>
+                    <param name='outputFormat_selector' value='homer'/>
+                </conditional>
+            </conditional>
+            <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.homer" ftype="zip" compare="sim_size" delta="40000"/>
+        </test>
+        <test>
+            <conditional name='outputSingleMultiple_conditional'>
+                <param name='outputSingleMultiple_selector' value='singleMatrix'/>
+                <conditional name='inputFormat_conditional'>
+                    <param name='inputFormat_selector' value='optionCool'/>
+                    <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool'/>
+                </conditional>
+                
+                <conditional name='outputFormat_conditional'>
+                    <param name='outputFormat_selector' value='ginteractions'/>
+                </conditional>
+            </conditional>
+            <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tsv" compare="sim_size" delta="40000"/>
+            
+        </test>
+        <test>
+            <conditional name='outputSingleMultiple_conditional'>
+                <param name='outputSingleMultiple_selector' value='multipleMatrix'/>
+                <conditional name='resolutionOrManyToOne_conditional'>
+                    <param name='resolutionOrManyToOne_selector' value='resolution_option'/>
+                    <param name='resolutions' value='5000 10000 20000'/>
+                    <conditional name='inputFormat_conditional'>
+                        <param name='inputFormat_selector' value='optionH5'/>
+                        <param name='matrix_h5_cooler' value='small_test_matrix.h5'/>
+                    </conditional>
+                </conditional>
+            </conditional>
+            <output name="output_converted_matrix" ftype="cool">
+                <assert_contents>
+                    <has_h5_keys keys='resolutions'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Converting between different Hi-C interaction formats
+=====================================================
+
+Conversion of Hi-C matrices of different file formats. We support the conversion of hic to cool format via hic2cool,
+and homer, HicPro, h5 and cool format to h5, cool, homer or ginteractions format. Moreover, hicConvertFormat accepts multiple input files
+from one format with different resolutions and creates a mcool file. Each original file is stored under the path e.g. ::/resolutions/10000.
+A batch computation is possible, the number of input files and output files needs to match, all input files need to be of the same format type and
+all output files too.
+For input and output of cooler files special options are available, for all other formats they will be ignored.
+HiCPro file format needs an additional bed file as input.
+
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]></help>
+    <expand macro="citations" />
+</tool>