Mercurial > repos > devteam > bamtools_split
annotate bamtools_split.xml @ 3:9676127a1ed2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
author | iuc |
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date | Wed, 04 Dec 2019 07:47:03 -0500 |
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children | 0a7b0989fa09 |
rev | line source |
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3
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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1 <tool id="bamtools_split" name="Split" version="2.4.0"> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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2 <description>BAM datasets on variety of attributes</description> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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3 <requirements> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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4 <requirement type="package" version="2.4.0">bamtools</requirement> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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5 </requirements> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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6 <command> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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7 <![CDATA[ |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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8 echo "BAM" > $report && |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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9 #for $bam_count, $input_bam in enumerate( $input_bams ): |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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10 ln -s "${input_bam}" "localbam_${bam_count}.bam" && |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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11 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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12 #end for |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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13 bamtools |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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14 split |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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15 #if str ( $analysis_type.analysis_type_selector ) == "-tag" : |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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16 ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}" |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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17 #else |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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18 ${analysis_type.analysis_type_selector} |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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19 #end if |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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20 -stub split_bam |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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21 #for $bam_count, $input_bam in enumerate( $input_bams ): |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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22 -in "localbam_${bam_count}.bam" |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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23 #end for |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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24 ]]> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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25 </command> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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26 <inputs> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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27 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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28 <conditional name="analysis_type"> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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29 <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option"> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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30 <option value="-mapped">Mapping status (-mapped)</option> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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31 <option value="-paired">Pairing status (-paired)</option> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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32 <option value="-reference">Reference name (-reference)</option> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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33 <option value="-tag">Specific tag (-tag)</option> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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34 </param> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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35 <when value="-mapped" /> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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36 <when value="-paired" /> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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37 <when value="-reference" /> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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38 <when value="-tag"> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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39 <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
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40 </when> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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41 </conditional> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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42 </inputs> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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43 <outputs> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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44 <data format="txt" name="report" label="BAMSplitter Run" hidden="true"> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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45 <discover_datasets pattern="split_bam\.(?P<designation>.+)\.bam" ext="bam" visible="true"/> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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46 </data> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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47 </outputs> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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48 <tests> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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49 <test> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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50 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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51 <param name="analysis_type_selector" value="-mapped"/> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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52 <output name="report"> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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53 <assert_contents> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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54 <has_line line="BAM" /> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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55 </assert_contents> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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56 <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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57 </output> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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58 </test> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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59 <test> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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60 <param name="input_bams" ftype="bam" value="bamtools-input2.bam"/> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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61 <param name="analysis_type_selector" value="-reference"/> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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62 <param name="output_type" value="dataset_collection"/> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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63 <output name="report"> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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64 <assert_contents> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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65 <has_line line="BAM" /> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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66 </assert_contents> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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67 <discovered_dataset designation="REF_chr1" file="bamtools_input2.chr1" ftype="bam"/> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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68 </output> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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69 </test> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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70 </tests> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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71 <help> |
9676127a1ed2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
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72 **What is does** |
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73 |
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74 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). |
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75 |
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76 ----- |
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77 |
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78 .. class:: warningmark |
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79 |
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80 **DANGER: Multiple Outputs** |
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81 |
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82 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. |
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83 |
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84 ----- |
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85 |
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86 **How it works** |
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87 |
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88 The following options can be specified via "**Split BAM dataset(s) by**" dropdown:: |
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89 |
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90 Mapping status (-mapped) split mapped/unmapped and generate two output files |
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91 named (MAPPED) and (UNMAPPED) containing mapped and unmapped |
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92 reads, respectively. |
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93 |
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94 Pairing status (-paired) split single-end/paired-end alignments and generate two output files |
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95 named (SINGLE_END) and (PAIRED_END) containing paired and unpaired |
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96 reads, respectively. |
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97 |
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98 Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with |
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99 very large number of reference sequences (scaffolds) it can generate |
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100 thousands (if not millions) of output datasets. |
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101 |
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102 Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this |
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103 option from the menu will allow you to enter the tag name. As was the |
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104 case with the reference splitting above, this option can produce very |
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105 large number of outputs if a tag has a large number of unique values. |
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106 |
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107 ----- |
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108 |
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109 .. class:: infomark |
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110 |
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111 **More information** |
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112 |
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113 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki |
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114 |
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115 </help> |
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116 <citations> |
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117 <citation type="doi">10.1093/bioinformatics/btr174</citation> |
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118 </citations> |
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119 </tool> |