Mercurial > repos > bgruening > deeptools
annotate bamFingerprint.xml @ 79:9f25cf7f11d9 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
| author | bgruening |
|---|---|
| date | Tue, 20 Oct 2015 14:41:43 -0400 |
| parents | 1dbd76a58d8b |
| children |
| rev | line source |
|---|---|
| 61 | 1 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0"> |
| 2 <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description> | |
| 3 <macros> | |
| 4 <token name="@BINARY@">bamFingerprint</token> | |
| 5 <import>deepTools_macros.xml</import> | |
| 6 </macros> | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
7 <expand macro="requirements" /> |
| 61 | 8 <command> |
| 9 <![CDATA[ | |
| 10 @multiple_input_bams@ | |
| 11 | |
| 12 bamFingerprint | |
| 13 | |
| 14 @THREADS@ | |
| 15 | |
| 16 --bamfiles #echo " ".join($files) | |
| 17 --labels #echo " ".join($labels) | |
| 18 | |
| 19 --fragmentLength $fragmentLength | |
| 20 | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
21 --plotFile $outFileName |
| 61 | 22 |
| 23 #if $output.showOutputSettings == "yes" | |
| 24 --plotFileFormat $output.outFileFormat | |
| 25 #if $output.saveRawCounts: | |
| 26 --outRawCounts '$outFileRawCounts' | |
| 27 #end if | |
| 28 #else | |
| 29 --plotFileFormat 'png' | |
| 30 #end if | |
| 31 | |
| 32 #if str($region).strip() != '': | |
| 33 --region '$region' | |
| 34 #end if | |
| 35 | |
| 36 #if $advancedOpt.showAdvancedOpt == "yes": | |
| 37 --binSize '$advancedOpt.binSize' | |
| 38 --numberOfSamples '$advancedOpt.numberOfSamples' | |
| 39 | |
| 40 $advancedOpt.doNotExtendPairedEnds | |
| 41 $advancedOpt.ignoreDuplicates | |
| 42 $advancedOpt.skipZeros | |
| 43 | |
| 44 #if $advancedOpt.minMappingQuality: | |
| 45 --minMappingQuality '$advancedOpt.minMappingQuality' | |
| 46 #end if | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
47 |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
48 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
49 --plotTitle '$advancedOpt.plotTitle' |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
50 #end if |
|
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
51 |
| 61 | 52 #end if |
| 53 ]]> | |
| 54 </command> | |
| 55 | |
| 56 <inputs> | |
| 57 <expand macro="multiple_input_bams" /> | |
| 58 <expand macro="fragmentLength" /> | |
| 59 <expand macro="region_limit_operation" /> | |
| 60 | |
| 61 <conditional name="advancedOpt"> | |
| 62 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | |
| 63 <option value="no" selected="true">no</option> | |
| 64 <option value="yes">yes</option> | |
| 65 </param> | |
| 66 <when value="no" /> | |
| 67 <when value="yes"> | |
| 68 <param name="binSize" type="integer" value="500" min="1" | |
| 69 label="Bin size in bp" | |
| 70 help="Length in base pairs for a window used to sample the genome."/> | |
| 71 <param name="numberOfSamples" type="integer" value="100000" min="1" | |
| 72 label="Number of samples" | |
| 73 help="Number of samples taken from the genome to compute the scaling factors. (--numberOfSamples)"/> | |
| 74 <expand macro="doNotExtendPairedEnds" /> | |
| 75 <expand macro="ignoreDuplicates" /> | |
| 76 <expand macro="minMappingQuality" /> | |
| 77 <expand macro="skipZeros" /> | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
78 <expand macro="plotTitle" /> |
| 61 | 79 </when> |
| 80 </conditional> | |
| 81 <conditional name="output"> | |
| 82 <param name="showOutputSettings" type="select" label="Show advanced output settings"> | |
| 83 <option value="no" selected="true">no</option> | |
| 84 <option value="yes">yes</option> | |
| 85 </param> | |
| 86 <when value="no" /> | |
| 87 <when value="yes"> | |
| 88 <expand macro="input_image_file_format" /> | |
|
65
9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
61
diff
changeset
|
89 <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/> |
| 61 | 90 </when> |
| 91 </conditional> | |
| 92 </inputs> | |
| 93 <outputs> | |
| 94 <expand macro="output_image_file_format" /> | |
| 95 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> | |
| 96 <filter> | |
| 97 (( | |
| 98 output['showOutputSettings'] == 'yes' and | |
| 99 output['saveRawCounts'] is True | |
| 100 )) | |
| 101 </filter> | |
| 102 </data> | |
| 103 </outputs> | |
| 104 <tests> | |
| 105 <test> | |
| 106 <repeat name="input_files"> | |
| 107 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" /> | |
| 108 </repeat> | |
| 109 <repeat name="input_files"> | |
| 110 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" /> | |
| 111 </repeat> | |
| 112 <param name="fragmentLength" value="200" /> | |
| 113 <param name="showAdvancedOpt" value="no" /> | |
| 114 <param name="showOutputSettings" value="no" /> | |
|
66
1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
galaxyp
parents:
65
diff
changeset
|
115 <output name="outFileName" file="bamFingerprint_result1.png" ftype="png" compare="sim_size" /> |
| 61 | 116 </test> |
| 117 </tests> | |
| 118 <help> | |
| 119 <![CDATA[ | |
| 120 **What it does** | |
| 121 | |
| 122 This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal) | |
| 123 and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3). | |
| 124 | |
| 125 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length. | |
| 126 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank) | |
| 127 and the cumulative sum of read counts are plotted. An ideal input (control sample) with perfect uniform distribution of reads | |
| 128 along the genome (i.e. without enrichments in open chromatin etc.) should | |
| 129 generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep | |
| 130 rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in | |
| 131 few bins which corresponds to high, narrow enrichments seen for transcription factors. | |
| 132 | |
| 133 | |
| 134 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png | |
| 135 | |
| 136 | |
| 137 You can find more details on the bamFingerprint wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint | |
| 138 | |
| 139 | |
| 140 **Output files**: | |
| 141 | |
| 142 - Diagnostic plot | |
| 143 - Data matrix of raw counts | |
| 144 | |
| 145 ----- | |
| 146 | |
| 147 @REFERENCES@ | |
| 148 ]]> | |
| 149 </help> | |
| 150 <expand macro="citations" /> | |
| 151 </tool> |