Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix
comparison hicCorrectMatrix.xml @ 3:68b69a6922e5 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
| author | iuc |
|---|---|
| date | Thu, 02 Nov 2017 10:49:38 -0400 |
| parents | c041d564e6cc |
| children | c4b8a323d565 |
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| 2:87757fbd117d | 3:68b69a6922e5 |
|---|---|
| 3 <macros> | 3 <macros> |
| 4 <token name="@BINARY@">hicCorrectMatrix</token> | 4 <token name="@BINARY@">hicCorrectMatrix</token> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
| 8 <command> | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 <![CDATA[ | 9 |
| 10 ln -s '$matrix' temp_matrix.npz.h5 && | 10 ln -s '$matrix' temp_matrix.npz.h5 && |
| 11 | 11 |
| 12 hicCorrectMatrix | 12 hicCorrectMatrix |
| 13 $mode.mode_selector | 13 $mode.mode_selector |
| 14 --matrix temp_matrix.npz.h5 | 14 --matrix temp_matrix.npz.h5 |
| 48 --outMatrixFile corrected_matrix.npz.h5 | 48 --outMatrixFile corrected_matrix.npz.h5 |
| 49 #if $mode.xMax: | 49 #if $mode.xMax: |
| 50 --xMax $mode.xMax | 50 --xMax $mode.xMax |
| 51 #end if | 51 #end if |
| 52 #if $mode.filterThreshold_low and $mode.filterThreshold_large: | 52 #if $mode.filterThreshold_low and $mode.filterThreshold_large: |
| 53 --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large | 53 --filterThreshold '$mode.filterThreshold_low' '$mode.filterThreshold_large' |
| 54 #end if | 54 #end if |
| 55 #else: | 55 #else: |
| 56 --plotName diagnostic_plot.png | 56 --plotName diagnostic_plot.png |
| 57 #if $mode.xMax: | 57 #if $mode.xMax: |
| 58 --xMax $mode.xMax | 58 --xMax $mode.xMax |
| 99 <expand macro="filterThreshold" /> | 99 <expand macro="filterThreshold" /> |
| 100 | 100 |
| 101 </when> | 101 </when> |
| 102 </conditional> | 102 </conditional> |
| 103 | 103 |
| 104 <repeat name="chromosomes" min="1" | 104 <repeat name="chromosomes" min="0" |
| 105 title="Include chromosomes" help="List of chromosomes to be included in the iterative correction. | 105 title="Include chromosomes" help="List of chromosomes to be included in the iterative correction. |
| 106 The order of the given chromosomes will be kept for the resulting corrected matrix"> | 106 The order of the given chromosomes will be kept for the resulting corrected matrix"> |
| 107 <param name="chromosome" type="text" value="" /> | 107 <param name="chromosome" type="text" value="" > |
| 108 <validator type="empty_field" /> | |
| 109 </param> | |
| 108 </repeat> | 110 </repeat> |
| 109 | 111 |
| 110 </inputs> | 112 </inputs> |
| 111 <outputs> | 113 <outputs> |
| 112 <data name="outFileName" from_work_dir="corrected_matrix.npz.h5" format="h5"> | 114 <data name="outFileName" from_work_dir="corrected_matrix.npz.h5" format="h5"> |
| 116 <filter>mode['mode_selector'] == "diagnostic_plot"</filter> | 118 <filter>mode['mode_selector'] == "diagnostic_plot"</filter> |
| 117 </data> | 119 </data> |
| 118 </outputs> | 120 </outputs> |
| 119 <tests> | 121 <tests> |
| 120 <test> | 122 <test> |
| 121 <param name="matrix" value="hicBuildMatrix_result1.h5" ftype="h5"/> | 123 <param name="matrix" value="small_test_matrix.h5" ftype="h5"/> |
| 122 <param name="mode_selector" value="correct"/> | 124 <param name="mode_selector" value="correct"/> |
| 123 <repeat name="chromosomes"> | 125 <repeat name="chromosomes"> |
| 124 <param name="chromosome" value="chrUextra"/> | 126 <param name="chromosome" value="chrUextra"/> |
| 125 </repeat> | 127 </repeat> |
| 126 <repeat name="chromosomes"> | 128 <repeat name="chromosomes"> |
| 127 <param name="chromosome" value="chr3LHet"/> | 129 <param name="chromosome" value="chr3LHet"/> |
| 128 </repeat> | 130 </repeat> |
| 129 <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/> | 131 <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/> |
| 130 </test> | 132 </test> |
| 131 <test> | 133 <test> |
| 132 <param name="matrix" ftype="h5" value="hicBuildMatrix_result1.h5"/> | 134 <param name="matrix" ftype="h5" value="small_test_matrix.h5"/> |
| 133 <param name="mode_selector" value="diagnostic_plot"/> | 135 <param name="mode_selector" value="diagnostic_plot"/> |
| 134 <repeat name="chromosomes"> | 136 <repeat name="chromosomes"> |
| 135 <param name="chromosome" value="chrUextra"/> | 137 <param name="chromosome" value="chrUextra"/> |
| 136 </repeat> | 138 </repeat> |
| 137 <repeat name="chromosomes"> | 139 <repeat name="chromosomes"> |
| 142 </tests> | 144 </tests> |
| 143 <help><![CDATA[ | 145 <help><![CDATA[ |
| 144 | 146 |
| 145 **What it does** | 147 **What it does** |
| 146 | 148 |
| 147 Runs Dekker's iterative correction over a hic matrix. | 149 Runs Dekker's iterative correction over a Hi-C matrix. |
| 148 | 150 |
| 151 correct: Run the iterative correction. | |
| 149 | 152 |
| 150 correct Run the iterative correction. | 153 diagnostic_plot: Plots a histogram of the coverage per bin together with the |
| 151 diagnostic_plot | 154 modified z-score based on the median absolute deviation |
| 152 Plots a histogram of the coverage per bin together with the | 155 method (see Boris Iglewicz and David Hoaglin 1993, Volume |
| 153 modified z-score based on the median absolute deviation | 156 16: How to Detect and Handle Outliers The ASQC Basic |
| 154 method (see Boris Iglewicz and David Hoaglin 1993, Volume | 157 References in Quality Control: Statistical Techniques, |
| 155 16: How to Detect and Handle Outliers The ASQC Basic | 158 Edward F. Mykytka, Ph.D., Editor. |
| 156 References in Quality Control: Statistical Techniques, | |
| 157 Edward F. Mykytka, Ph.D., Editor. | |
| 158 | |
| 159 | 159 |
| 160 ]]></help> | 160 ]]></help> |
| 161 <expand macro="citations" /> | 161 <expand macro="citations" /> |
| 162 </tool> | 162 </tool> |
| 163 | 163 |