Mercurial > repos > devteam > bamtools_split
annotate bamtools-split.xml @ 2:fc222996ce9b draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Mon, 12 Oct 2015 11:57:54 -0400 |
| parents | 56a189070900 |
| children | 10dcc8027778 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bamSplit" name="Split" version="0.0.1" force_history_refresh="True"> |
| 2 <description>BAM datasets on variety of attributes</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> | |
| 5 </requirements> | |
| 6 <command> | |
| 7 | |
| 8 echo "BAM" > $report && | |
| 9 | |
| 10 #for $bam_count, $input_bam in enumerate( $input_bams ): | |
| 11 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" && | |
| 12 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && | |
| 13 #end for | |
| 14 | |
| 15 bamtools | |
| 16 split | |
| 17 | |
| 18 #if str ( $analysis_type.analysis_type_selector ) == "-tag" : | |
| 19 | |
| 20 ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}" | |
| 21 | |
| 22 #else | |
| 23 | |
| 24 ${analysis_type.analysis_type_selector} | |
| 25 | |
| 26 #end if | |
| 27 | |
| 28 -stub split_bam | |
| 29 | |
| 30 #for $bam_count, $input_bam in enumerate( $input_bams ): | |
| 31 -in "localbam_${bam_count}.bam" | |
| 32 #end for | |
| 33 | |
| 34 </command> | |
| 35 | |
| 36 <inputs> | |
| 37 <repeat name="input_bams" title="BAM dataset(s) to filter" min="1"> | |
| 38 <param name="input_bam" type="data" format="bam" label="BAM dataset" /> | |
| 39 </repeat> | |
| 40 <conditional name="analysis_type"> | |
| 41 <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option"> | |
| 42 <option value="-mapped">Mapping status (-mapped)</option> | |
| 43 <option value="-paired">Pairing status (-paired)</option> | |
| 44 <option value="-reference">Reference name (-reference)</option> | |
| 45 <option value="-tag">Specific tag (-tag)</option> | |
| 46 </param> | |
|
2
fc222996ce9b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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47 <when value="-mapped" /> |
|
fc222996ce9b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
48 <when value="-paired" /> |
|
fc222996ce9b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
49 <when value="-reference" /> |
| 0 | 50 <when value="-tag"> |
| 51 <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> | |
| 52 </when> | |
| 53 </conditional> | |
| 54 </inputs> | |
| 55 | |
| 56 <outputs> | |
| 57 <data format="txt" name="report" label="BAMSplitter Run" hidden="true"> | |
| 58 <discover_datasets pattern="split_bam\.(?P<designation>.+)\.bam" ext="bam" visible="true"/> | |
| 59 </data> | |
| 60 </outputs> | |
| 61 <tests> | |
| 62 <test> | |
| 63 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> | |
| 64 <param name="analysis_type_selector" value="-mapped"/> | |
| 65 <output name="report"> | |
| 66 <assert_contents> | |
| 67 <has_line line="BAM" /> | |
| 68 </assert_contents> | |
| 69 <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> | |
| 70 </output> | |
| 71 | |
| 72 </test> | |
| 73 </tests> | |
| 74 <help> | |
| 75 **What is does** | |
| 76 | |
| 77 BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). | |
| 78 | |
| 79 ----- | |
| 80 | |
| 81 .. class:: warningmark | |
| 82 | |
| 83 **DANGER: Multiple Outputs** | |
| 84 | |
| 85 As described below, splitting a BAM dataset(s) on reference name or a tag value can produce very large numbers of outputs. Read below and know what you are doing. | |
| 86 | |
| 87 ----- | |
| 88 | |
| 89 **How it works** | |
| 90 | |
| 91 The following options can be specified via "**Split BAM dataset(s) by**" dropdown:: | |
| 92 | |
| 93 Mapping status (-mapped) split mapped/unmapped and generate two output files | |
| 94 named (MAPPED) and (UNMAPPED) containing mapped and unmapped | |
| 95 reads, respectively. | |
| 96 | |
| 97 Pairing status (-paired) split single-end/paired-end alignments and generate two output files | |
| 98 named (SINGLE_END) and (PAIRED_END) containing paired and unpaired | |
| 99 reads, respectively. | |
| 100 | |
| 101 Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with | |
| 102 very large number of reference sequences (scaffolds) it can generate | |
| 103 thousands (if not millions) of output datasets. | |
| 104 | |
| 105 Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this | |
| 106 option from the menu will allow you to enter the tag name. As was the | |
| 107 case with the reference splitting above, this option can produce very | |
| 108 large number of outputs if a tag has a large number of unique values. | |
| 109 | |
| 110 ----- | |
| 111 | |
| 112 .. class:: infomark | |
| 113 | |
| 114 **More information** | |
| 115 | |
| 116 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki | |
| 117 | |
| 118 </help> | |
| 119 <citations> | |
| 120 <citation type="doi">10.1093/bioinformatics/btr174</citation> | |
| 121 </citations> | |
| 122 </tool> |