Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 5:3bc1425f9000 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:26:27 -0500
parents 652fdcbff650
children 30d427846764
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4:652fdcbff650 5:3bc1425f9000
19 #end for 19 #end for
20 20
21 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile": 21 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
22 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile' 22 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
23 --minDistance $restrictionCutFileBinSize_conditional.minDistance 23 --minDistance $restrictionCutFileBinSize_conditional.minDistance
24 --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize 24 --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
25 #end if 25 #end if
26 26
27 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize": 27 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
28 --binSize $restrictionCutFileBinSize_conditional.binSize 28 --binSize $restrictionCutFileBinSize_conditional.binSize
29 #end if 29 #end if
35 35
36 #if $region: 36 #if $region:
37 --region '$region' 37 --region '$region'
38 #end if 38 #end if
39 39
40 --outFileName ./matrix.h5 40 #if $outputFormat == 'h5'
41 --outFileName matrix.h5
42 #elif $outputFormat == 'cool'
43 --outFileName matrix.cool
44 #end if
41 --outBam ./unsorted.bam 45 --outBam ./unsorted.bam
42 46
43 $keepSelfCircles 47 $keepSelfCircles
44 48
45 #if $minMappingQuality and $minMappingQuality is not None: 49 #if $minMappingQuality and $minMappingQuality is not None:
108 the dangling end is the same restriction sequence. This is used 112 the dangling end is the same restriction sequence. This is used
109 to discard reads that end/start with such sequence 113 to discard reads that end/start with such sequence
110 and that are considered un-ligated fragments or 114 and that are considered un-ligated fragments or
111 'dangling-ends'. If not given, such statistics will 115 'dangling-ends'. If not given, such statistics will
112 not be available."/> 116 not be available."/>
117 <param name='outputFormat' type='select' label="Output file format">
118 <option value='h5'>HiCExplorer format</option>
119 <option value="cool">cool</option>
120 </param>
113 </inputs> 121 </inputs>
114 <outputs> 122 <outputs>
115 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/> 123 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
116 <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/> 124 <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}">
125 <filter>outputFormat == 'h5'</filter>
126 </data>
127 <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool" label="${tool.name} MATRIX on ${on_string}">
128 <filter>outputFormat == 'cool'</filter>
129 </data>
117 <data name="qc" format="html" label="${tool.name} QC"/> 130 <data name="qc" format="html" label="${tool.name} QC"/>
118 </outputs> 131 </outputs>
119 <tests> 132 <tests>
120 <test> 133 <test>
121 <repeat name="samFiles"> 134 <repeat name="samFiles">
122 <param name="samFile" value="small_test_R1_unsorted.bam" ftype="sam" /> 135 <param name="samFile" value="small_test_R1_unsorted.sam"/>
123 </repeat> 136 </repeat>
124 <repeat name="samFiles"> 137 <repeat name="samFiles">
125 <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/> 138 <param name="samFile" value="small_test_R2_unsorted.sam"/>
126 </repeat> 139 </repeat>
127 <conditional name="restrictionCutFileBinSize_conditional"> 140 <conditional name="restrictionCutFileBinSize_conditional">
128 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/> 141 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
129 <param name="binSize" value="5000"/> 142 <param name="binSize" value="5000"/>
130 </conditional> 143 </conditional>
144 <param name='outputFormat' value='h5'/>
145
131 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/> 146 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
132 <output name="outFileName" file="small_test_matrix.h5" ftype="h5" compare="sim_size" delta="30000"/> 147 <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
133 </test> 148 </test>
134 </tests> 149 </tests>
135 <help><![CDATA[ 150 <help><![CDATA[
136 151
137 Creation of the contact matrix 152 Creation of the contact matrix
138 =============================== 153 ===============================
139 154
140 ``hicBuildMatrix`` creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files 155 ``hicBuildMatrix`` creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files
141 corresponding to the first and second mates of the paired-end H-C reads. The sam and bam files should 156 corresponding to the first and second mates of the paired-end H-C reads. The sam and bam files should
142 not be sorted by position. There are two main options to create the Hi-C contact matrix, either by 157 not be sorted by position. There are two main options to create the Hi-C contact matrix, either by
143 fixed bin size (eg. 10.000 bp) or by bins of variable restriction fragment size length. 158 fixed bin size (eg. 10.000 bp) or by bins of variable restriction fragment size length.
144 ``hicBuildMatrix`` generates a quality control output that can be used to analyze the quality of the Hi-C reads. 159 ``hicBuildMatrix`` generates a quality control output that can be used to analyze the quality of the Hi-C reads.
145 160
146 Input 161 Input
147 ----- 162 -----
199 - right pairs 214 - right pairs
200 215
201 .. image:: $PATH_TO_IMAGES/hicQC.png 216 .. image:: $PATH_TO_IMAGES/hicQC.png
202 :width: 70 % 217 :width: 70 %
203 218
219
204 | For more information about HiCExplorer please consider our documentation on readthedocs.io_. 220 | For more information about HiCExplorer please consider our documentation on readthedocs.io_.
205 221
206 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 222 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
207 223
208 224