Mercurial > repos > devteam > bamtools_split
annotate bamtools-split.xml @ 3:10dcc8027778 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
| author | devteam |
|---|---|
| date | Mon, 09 Nov 2015 12:04:47 -0500 |
| parents | fc222996ce9b |
| children | 64ed37303c15 |
| rev | line source |
|---|---|
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="bamSplit" name="Split" version="0.0.2" force_history_refresh="True"> |
| 0 | 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 && | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 |
| 0 | 10 #for $bam_count, $input_bam in enumerate( $input_bams ): |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 ln -s "${input_bam}" "localbam_${bam_count}.bam" && |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && |
| 0 | 13 #end for |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 |
| 0 | 15 bamtools |
| 16 split | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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17 |
| 0 | 18 #if str ( $analysis_type.analysis_type_selector ) == "-tag" : |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 |
| 0 | 20 ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}" |
| 21 | |
| 22 #else | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 |
| 0 | 24 ${analysis_type.analysis_type_selector} |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 |
| 0 | 26 #end if |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 |
| 0 | 28 -stub split_bam |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 |
| 0 | 30 #for $bam_count, $input_bam in enumerate( $input_bams ): |
| 31 -in "localbam_${bam_count}.bam" | |
| 32 #end for | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 |
| 0 | 34 </command> |
| 35 | |
| 36 <inputs> | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> |
| 0 | 38 <conditional name="analysis_type"> |
| 39 <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option"> | |
| 40 <option value="-mapped">Mapping status (-mapped)</option> | |
| 41 <option value="-paired">Pairing status (-paired)</option> | |
| 42 <option value="-reference">Reference name (-reference)</option> | |
| 43 <option value="-tag">Specific tag (-tag)</option> | |
| 44 </param> | |
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fc222996ce9b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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45 <when value="-mapped" /> |
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fc222996ce9b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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46 <when value="-paired" /> |
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fc222996ce9b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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47 <when value="-reference" /> |
| 0 | 48 <when value="-tag"> |
| 49 <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> | |
| 50 </when> | |
| 51 </conditional> | |
| 52 </inputs> | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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changeset
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53 |
| 0 | 54 <outputs> |
| 55 <data format="txt" name="report" label="BAMSplitter Run" hidden="true"> | |
| 56 <discover_datasets pattern="split_bam\.(?P<designation>.+)\.bam" ext="bam" visible="true"/> | |
| 57 </data> | |
| 58 </outputs> | |
| 59 <tests> | |
| 60 <test> | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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changeset
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61 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> |
| 0 | 62 <param name="analysis_type_selector" value="-mapped"/> |
| 63 <output name="report"> | |
| 64 <assert_contents> | |
| 65 <has_line line="BAM" /> | |
| 66 </assert_contents> | |
| 67 <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> | |
| 68 </output> | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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changeset
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69 |
| 0 | 70 </test> |
| 71 </tests> | |
| 72 <help> | |
| 73 **What is does** | |
| 74 | |
| 75 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). | |
| 76 | |
| 77 ----- | |
| 78 | |
| 79 .. class:: warningmark | |
| 80 | |
| 81 **DANGER: Multiple Outputs** | |
| 82 | |
| 83 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. | |
| 84 | |
| 85 ----- | |
| 86 | |
| 87 **How it works** | |
| 88 | |
| 89 The following options can be specified via "**Split BAM dataset(s) by**" dropdown:: | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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90 |
| 0 | 91 Mapping status (-mapped) split mapped/unmapped and generate two output files |
| 92 named (MAPPED) and (UNMAPPED) containing mapped and unmapped | |
| 93 reads, respectively. | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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94 |
| 0 | 95 Pairing status (-paired) split single-end/paired-end alignments and generate two output files |
| 96 named (SINGLE_END) and (PAIRED_END) containing paired and unpaired | |
| 97 reads, respectively. | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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98 |
| 0 | 99 Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with |
| 100 very large number of reference sequences (scaffolds) it can generate | |
| 101 thousands (if not millions) of output datasets. | |
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10dcc8027778
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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changeset
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102 |
| 0 | 103 Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this |
| 104 option from the menu will allow you to enter the tag name. As was the | |
| 105 case with the reference splitting above, this option can produce very | |
| 106 large number of outputs if a tag has a large number of unique values. | |
| 107 | |
| 108 ----- | |
| 109 | |
| 110 .. class:: infomark | |
| 111 | |
| 112 **More information** | |
| 113 | |
| 114 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki | |
| 115 | |
| 116 </help> | |
| 117 <citations> | |
| 118 <citation type="doi">10.1093/bioinformatics/btr174</citation> | |
| 119 </citations> | |
| 120 </tool> |