| Previous changeset 4:d387dacb6867 (2017-12-16) Next changeset 6:34da5ed2507c (2018-01-02) |
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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 |
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modified:
hicSumMatrices.xml macros.xml test-data/hicPlotDistVsCounts_result2.png test-data/small_test_matrix_result_sorted.bam |
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added:
test-data/Li_chrX30-35_cool.png test-data/Li_et_al_2015.cool test-data/covariance_small_50kb.cool test-data/covariance_small_50kb.h5 test-data/li_32-33mb_interactions.bedgraph test-data/li_32mb_interactions.bedgraph test-data/li_viewpoint_32-33Mb.png test-data/li_viewpoint_32Mb.png test-data/obs_exp_small_50kb.cool test-data/obs_exp_small_50kb.h5 test-data/pca1.bedgraph test-data/pca1.bw test-data/pca2.bedgraph test-data/pca2.bw test-data/pearson_small_50kb.cool test-data/pearson_small_50kb.h5 test-data/small_matrix_50kb_pearson_pca1_plot.png test-data/small_matrix_50kb_pearson_pca1_plot.svg test-data/small_test_R1_unsorted.sam test-data/small_test_R2_unsorted.sam test-data/small_test_matrix_2.h5 |
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| diff -r d387dacb6867 -r b9f41afc3312 hicSumMatrices.xml --- a/hicSumMatrices.xml Sat Dec 16 16:35:53 2017 -0500 +++ b/hicSumMatrices.xml Sat Dec 30 09:36:36 2017 -0500 |
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| @@ -7,27 +7,42 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - #for $counter, $m in enumerate($matrices): - ln -s '$m' ${counter}.npz.h5 && + #for $counter, $m in enumerate($matrix_h5_cooler_multiple): + ln -s '$m' ${counter}_matrix && #end for + #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) - #set $m = '" "'.join([ '%s.npz.h5' % $counter for $counter, $matrix in enumerate($matrices) ]) hicSumMatrices --matrices "$m" - --outFileName ./out.npz.h5 + #if $outputFormat == 'h5' + --outFileName matrix.h5 + #elif $outputFormat == 'cool' + --outFileName matrix.cool + #end if ]]> </command> <inputs> - <param argument="--matrices" type="data" format="h5" multiple="True" - label="Matrices to combine" help="Needs to have the same shape"/> + <expand macro='matrix_h5_cooler_multiple_macro'/> + + <param name='outputFormat' type='select' label="Output file format"> + <option value='h5'>HiCExplorer format</option> + <option value="cool">cool</option> + </param> </inputs> <outputs> - <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/> + <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5"> + <filter>outputFormat == 'h5'</filter> + </data> + <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool"> + <filter>outputFormat == 'cool'</filter> + </data> </outputs> <tests> <test> - <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> - <output name="outFileName" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/> + <param name="matrix_h5_cooler_multiple" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> + <!-- <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> --> + <param name='outputFormat' value='h5'/> + <output name="outFileName_h5" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/> </test> </tests> <help><![CDATA[ @@ -36,10 +51,10 @@ ``hicSumMatrix`` is combining two (or more) contact matrices of the same size to one. This is useful if replicates of an Hi-C experiment should be merged into one contact matrix to -increase the power of the data. It is the nature of Hi-C that real contact cannot be distinguished - from noise, especially with a low contact count. The more contacts are given, the more likely it is - that a high number of contacts are real contact or contain at least a high amount. Therefore it is - a common way to merge replicates of Hi-C experiments to increase the validity of the experiment. +increase the power of the data. It is the nature of Hi-C that real contact cannot be distinguished +from noise, especially with a low contact count. The more contacts are given, the more likely it is +that a high number of contacts are real contact or contain at least a high amount. Therefore it is +a common way to merge replicates of Hi-C experiments to increase the validity of the experiment. Input ----- |
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| diff -r d387dacb6867 -r b9f41afc3312 macros.xml --- a/macros.xml Sat Dec 16 16:35:53 2017 -0500 +++ b/macros.xml Sat Dec 30 09:36:36 2017 -0500 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">1.8.1</token> + <token name="@WRAPPER_VERSION@">2.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> @@ -11,7 +11,7 @@ <xml name="citations"> <citations> - <citation type="doi">10.5281/zenodo.159780</citation> + <citation type="doi">10.5281/zenodo.1123667</citation> <yield /> </citations> </xml> @@ -166,7 +166,7 @@ <xml name="multiple_input_matrices"> <repeat name="input_files" title="HiC Matrix files" min="2"> - <param name="matrix" type="data" format="h5" + <param name="matrix" type="data" format="h5,cool" label="HiC Matrix file" help=""/> <param name="mlabel" type="text" size="30" optional="true" value="" @@ -179,8 +179,8 @@ #set $matrices = [] #set $mlabels = [] #for $counter, $i in enumerate($input_files): - ln -s $i.matrix #echo str($counter)+'.npz.h5'#; - #silent $matrices.append( '%s.npz.h5' % $counter ) + 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)] @@ -299,7 +299,15 @@ <xml name="pseudocount"> <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> </xml> - + <xml name='matrix_h5_cooler_macro'> + <param name='matrix_h5_cooler' type="data" format="h5,cool" + label="Matrix to compute on."/> + + </xml> + <xml name='matrix_h5_cooler_multiple_macro'> + <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" + label="Matrix to compute on." multiple="True"/> + </xml> <token name="@REFERENCES@"> .. class:: infomark @@ -525,7 +533,7 @@ </xml> <xml name="track_input_h5_macro"> - <param name="track_input_h5" type="data" format="h5" label="Track file h5 format"/> + <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/> </xml> <xml name="track_input_bed_macro"> <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/> |
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| diff -r d387dacb6867 -r b9f41afc3312 test-data/Li_et_al_2015.cool |
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| diff -r d387dacb6867 -r b9f41afc3312 test-data/covariance_small_50kb.cool |
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| diff -r d387dacb6867 -r b9f41afc3312 test-data/hicPlotDistVsCounts_result2.png |
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| diff -r d387dacb6867 -r b9f41afc3312 test-data/li_32-33mb_interactions.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/li_32-33mb_interactions.bedgraph Sat Dec 30 09:36:36 2017 -0500 |
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| b |
| diff -r d387dacb6867 -r b9f41afc3312 test-data/li_32mb_interactions.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/li_32mb_interactions.bedgraph Sat Dec 30 09:36:36 2017 -0500 |
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|
| b |
| diff -r d387dacb6867 -r b9f41afc3312 test-data/pca1.bw |
| b |
| Binary file test-data/pca1.bw has changed |
| b |
| diff -r d387dacb6867 -r b9f41afc3312 test-data/pca2.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pca2.bedgraph Sat Dec 30 09:36:36 2017 -0500 |
| b |
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:Z:22\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6008:2166\t0\tchr3R\t7743490\t41\t50M\t*\t0\t0\tGACGGTCAGTCCGAGAAGCATCTGGAGCCGATGGCCAGTTTCNNNNNGCG\t@@@FFDDDHAHFFFHIJIGIJEIGGGGGHGHIHIFGHJEHDI########\tAS:i:77\tXN:i:0\tXM:i:6\tXO:i:0\tXG:i:0\tNM:i:6\tMD:Z:16G25G0G0G0G0C3\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6164:2167\t0\tchrU\t1886379\t2\t14S36M\t*\t0\t0\tCGCATTTGAAAGCTAGCTTTCTAGTTTCACTTGTTTGTTTTTNNNNGTTT\tB@CFFFFFHHHHGJHIIIJJJJIJIIJJJJIJIIIJIGIJJJ########\tAS:i:60\tXS:i:56\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:28T0T0T0T4\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6028:2168\t16\tchr3L\t23880171\t0\t27S23M\t*\t0\t0\tAGGAANNNGGACACTATCGAAAAAGCTAGCTTGCAAAGTTCAAATGACCG\t?B800###IIHC<GGFCIHIJJJJJJIJJJJJIJJIIHHGHGFFFDB@@B\tAS:i:46\tXS:i:46\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:23\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6130:2172\t0\tchr3L\t20041224\t44\t50M\t*\t0\t0\tCGAGGAAGCTGCAAATGGTACGGAGCTGCTGGCTGAGGACGTGTTTGTTG\t@@@BDDDDDFDDF9ABGH<CFFHHHGIIIIGIDEG@F)?FG6B8BB;B@@\tAS:i:96\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:37T12\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6218:2174\t16\tchr2R\t19978961\t44\t50M\t*\t0\t0\tAGGAGCGTTCGTACAAGCGAAGCTCGCCGGAGGACGACAAGCTGAGGCGC\t3>9;AEEE?G@=@@@/A:=<BDDGIFC:AGIGFCGHBDDFHDDDDDD@@@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6240:2175\t16\tchr2L\t8736543\t42\t50M\t*\t0\t0\tTTAAGTGGACTTCGTTAATGTTTTAAATTTGAAGAATATTTTACGAGTTA\tHIGIHEHFBGIIFJJJIGGJJIJJIJJJJJIIIJIJJHHHHHDFFFFB@@\tAS:i:85\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:4A25C19\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6080:2181\t0\tchr2L\t22737721\t44\t1S49M\t*\t0\t0\tACTCAGTATATATTAAAAGTTTGTTTATACAATATCCTTTTAATAGGTAT\t<@@FFFDDHAHHHJJIEGICHHGFHHEIJJJIIJJJJJIJJGIJIII?FI\tAS:i:98\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:49\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6184:2183\t16\tchr2L\t1627623\t44\t50M\t*\t0\t0\tTTTAGTTATTGGGCTTTAAAAAAATCTAAATTCTGTCATGATTGATTCTG\tJJJJJJIGIIIIIIJIJJJJJJJJJJJJJJIIJIJIJHHHHHFFFFFBCC\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6206:2186\t16\tchr3R\t5530104\t44\t50M\t*\t0\t0\tCACGACGGGACGCCCTAACGGTATCGTGTGTAATTGCAGTTGCACAAGCA\t<@GHCBJIHBJIJJJJJHIJJJIJJJJIGJIIIIGIGHHHGGFDFFFC@@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6022:2190\t0\tchr3R\t17305312\t36\t40M10S\t*\t0\t0\tACTATAGAAATCTATTAAAAGTATTCCATGTAAGCTAGCTTCTCCACTGT\t?@@BDDDFG?HHHEHIIIIIIHHIIIIFIGIIIIIIIIIGDDHGFFHDGD\tAS:i:72\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:36T3\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6130:2190\t0\tchr2R\t13131924\t36\t36M14S\t*\t0\t0\tATATTGAATTCGAGTCAGAAAAAATAAAACGAAGCTAGCTTATCTGTCAT\tCCCFFDFFGGGHDHHGEIHIIJEIJJJJIJJGIJJJJJJJJJJJJIIIJJ\tAS:i:72\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:36\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6163:2192\t16\tchr2L\t7371337\t2\t26M24S\t*\t0\t0\tGGGTTCTCCACCAGCCGGCAAAAGCTAGCTTAAATTAACTTTTAGTTTTA\tFB)B;B=HD9JJJJIJJJJJJJJJJJJJJJJJJJJJHFHHGHFFFFFCCC\tAS:i:52\tXS:i:48\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:26\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6060:2193\t16\tchr3R\t9331177\t44\t50M\t*\t0\t0\tGCTTACTCCTTTGCAGCACTAGTACTAATTTTTTATTTTTTCGAATTTTC\tGGHFCHFGGIJJIGIIHGIIEFGDIJJJIJJJJJIJIHHHHHFFFFFCC@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6038:2194\t0\tchrYHet\t283249\t2\t17S33M\t*\t0\t0\tAGGCAGTAAGGCAGTAAGCTAGCTTGCTATGGTATTTTTCCTTAAGTTCC\t@@@DDDDDHHHHHIIGIDC<<EEHICG@?<C>11?ECG<CCDHAAAFFGE\tAS:i:66\tXS:i:60\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:33\tYT:Z:UU\n' |
| b |
| diff -r d387dacb6867 -r b9f41afc3312 test-data/small_test_R2_unsorted.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_test_R2_unsorted.sam Sat Dec 30 09:36:36 2017 -0500 |
| b |
| b'@@ -0,0 +1,1000 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| b |
| diff -r d387dacb6867 -r b9f41afc3312 test-data/small_test_matrix_2.h5 |
| b |
| Binary file test-data/small_test_matrix_2.h5 has changed |
| b |
| diff -r d387dacb6867 -r b9f41afc3312 test-data/small_test_matrix_result_sorted.bam |
| b |
| Binary file test-data/small_test_matrix_result_sorted.bam has changed |
