Mercurial > repos > devteam > bamtools_filter
annotate bamtools-filter.xml @ 11:6fae66d050a7 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
author | devteam |
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date | Thu, 25 May 2017 11:49:21 -0400 |
parents | 4089f1be1a71 |
children | ce5482dfe8bd |
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11
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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1 <tool id="bamFilter" name="Filter" version="2.4.1"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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2 <description>BAM datasets on a variety of attributes</description> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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3 <requirements> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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4 <requirement type="package" version="2.4.0">bamtools</requirement> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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5 </requirements> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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6 <command> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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7 <![CDATA[ |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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8 cp '$script_file' '$out_file2' && |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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9 ln -s '${input_bam}' localbam.bam && |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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10 ln -s '${input_bam.metadata.bam_index}' localbam.bam.bai && |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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11 bamtools filter -script '$script_file' -in localbam.bam -out '$out_file1' |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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12 ]]> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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13 </command> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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14 <configfiles> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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15 <configfile name="script_file"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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16 <![CDATA[ |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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17 <% import json %> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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18 #set $config = dict() |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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19 #if $conditions: |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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20 #set $config[ 'filters' ] = [] |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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21 #for $i, $condition in enumerate( $conditions, start=1 ): |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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22 #set $filter = dict( id=str( $i ) ) |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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23 #for $j, $s in enumerate( $condition.filters, start=1 ): |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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24 #set $filter[ $str( s[ 'bam_property' ][ 'bam_property_selector' ] ) ] = $str( s[ 'bam_property' ][ 'bam_property_value' ] ) |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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25 #end for |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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26 $(config[ 'filters' ].append( $filter )) |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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27 #end for |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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28 #if str( $rule_configuration.rules_selector ) == "true": |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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29 #set $config[ 'rule' ] = $rule_configuration.rules |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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30 #end if |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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31 #end if |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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32 $json.dumps( $config, indent=4 ) |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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33 ]]> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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34 </configfile> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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35 </configfiles> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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36 <inputs> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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37 <param name="input_bam" type="data" format="bam" label="BAM dataset(s) to filter" /> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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38 <repeat name="conditions" title="Condition" min="1"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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39 <repeat name="filters" title="Filter" min="1"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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40 <conditional name="bam_property"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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41 <param name="bam_property_selector" type="select" label="Select BAM property to filter on"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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42 <option value="alignmentFlag"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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43 <option value="cigar"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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44 <option value="insertSize"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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45 <option value="isDuplicate"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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46 <option value="isFailedQC"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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47 <option value="isFirstMate"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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48 <option value="isMapped"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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49 <option value="isMateMapped"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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50 <option value="isMateReverseStrand"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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51 <option value="isPaired"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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52 <option value="isPrimaryAlignment"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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53 <option value="isProperPair"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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54 <option value="isReverseStrand"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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55 <option value="isSecondMate"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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56 <option selected="True" value="mapQuality"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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57 <option value="matePosition"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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58 <option value="mateReference"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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59 <option value="name"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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60 <option value="position"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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61 <option value="queryBases"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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62 <option value="reference"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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63 <option value="tag"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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64 </param> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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65 <!-- would be fanstastic to have AND and OR constructs in when statements --> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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66 <when value="alignmentFlag"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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67 <param name="bam_property_value" type="integer" value="3" label="Filter on this alignment flag" help="Default (3) is for a paired read mapped in a proper pair"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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68 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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69 <when value="cigar"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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70 <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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71 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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72 <when value="insertSize"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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73 <param name="bam_property_value" type="text" value=">=250" label="Filter on insert size" help="You can use >, <, =, and ! (not) in your expression. E.g., to select pairs with insert size above 250 nt use ">=250""> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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74 <sanitizer invalid_char=""> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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75 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/><add value="-"/></valid> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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76 </sanitizer> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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77 </param> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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78 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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79 <when value="isDuplicate"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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80 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" /> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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81 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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82 <when value="isFailedQC"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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83 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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84 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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85 <when value="isFirstMate"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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86 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select first mate in a read pair" help="Checked = is first mate, Empty = is NOT first mate"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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87 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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88 <when value="isMapped"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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89 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Selected mapped reads" help="Checked = Mapped, Empty = NOT mapped"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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90 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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91 <when value="isMateMapped"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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92 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mapped mate" help="Checked = Mate IS mapped Empty = Mate is NOT mapped"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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93 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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94 <when value="isMateReverseStrand"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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95 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mate on the reverse strand" help="Checked = Mate IS on reverse strand, Empty = Mate is NOT on the reverse strand"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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96 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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97 <when value="isPaired"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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98 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select paired reads" help="Checked = Read IS paired, Empty = Read is NOT paired"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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99 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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100 <when value="isPrimaryAlignment"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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101 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select BAM records for primary alignments" help="Checked = Alignment IS primary, Empty = Alignment is NOT primary"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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102 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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103 <when value="isProperPair"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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104 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select properly paired reads" help="Checked = Read IS in proper pair, Empty = Read is NOT in the proper pair"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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105 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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106 <when value="isReverseStrand"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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107 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads in the reverse strand only" help="Checked = Read IS on the reverse strand, Empty = Read is NOT on the reverse strand"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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108 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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109 <when value="isSecondMate"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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110 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select second mate in a read pair" help="Checked = Read IS second mate, Empty = Read is NOT second mate"/> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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111 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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112 <when value="mapQuality"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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113 <param name="bam_property_value" type="text" value="20" label="Filter on read mapping quality (phred scale)" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mapping quality of at least 30 use ">=30""> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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114 <sanitizer invalid_char=""> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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115 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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116 </sanitizer> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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117 </param> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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118 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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119 <when value="matePosition"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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120 <param name="bam_property_value" type="text" value="1000000" label="Filter on the position of the mate" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mate (second end) mapping after position 1,000,000 use ">1000000""> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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121 <sanitizer invalid_char=""> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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122 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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123 </sanitizer> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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124 </param> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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125 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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126 <when value="mateReference"> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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127 <param name="bam_property_value" type="text" value="chr22" label="Filter on reference name for the mate" help="You can use = and ! (not) in your expression. E.g., to select reads with mates mapping to chrM use "chr22""> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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128 <sanitizer invalid_char=""> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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129 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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130 </sanitizer> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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131 </param> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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132 </when> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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133 <when value="name"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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134 <param name="bam_property_value" type="text" label="Filter on read name" help="You can use = and ! (not) in your expression."> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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135 <sanitizer invalid_char=""> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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136 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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137 </sanitizer> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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138 </param> |
6fae66d050a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 53f2eeca99efda354323295a0ebfb5e7f21f2fd4
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139 </when> |
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140 <when value="position"> |
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141 <param name="bam_property_value" type="text" value="500000" label="Filter on the position of the read" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads mapping after position 5,000 use ">5000""> |
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142 <sanitizer invalid_char=""> |
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143 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> |
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144 </sanitizer> |
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145 </param> |
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146 </when> |
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147 <when value="queryBases"> |
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148 <param name="bam_property_value" type="text" value="ttagggttagg" label="Filter on a sequence motif" help="You can use ! (not) in your expression"> |
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149 <sanitizer invalid_char=""> |
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150 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> |
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151 </sanitizer> |
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152 </param> |
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153 </when> |
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154 <when value="reference"> |
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155 <param name="bam_property_value" type="text" value="chr22" label="Filter on the reference name for the read" help="You can use ! (not) in your expression"> |
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156 <sanitizer invalid_char=""> |
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157 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> |
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158 </sanitizer> |
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159 </param> |
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160 </when> |
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161 <when value="tag"> |
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162 <param name="bam_property_value" type="text" value="NM:>1" label="Filter on a particular tag" help="You can use >, <, =, and ! (not). Tag name and its value must be separated by ":". E.g., to obtain reads with at least one mismatch use "NM:>1""> |
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163 <sanitizer invalid_char=""> |
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164 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value=":!="/></valid> |
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165 </sanitizer> |
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166 </param> |
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167 </when> |
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168 </conditional> |
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169 </repeat> |
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170 </repeat> |
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171 <conditional name="rule_configuration"> |
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172 <param name="rules_selector" type="boolean" truevalue="true" falsevalue="false" label="Would you like to set rules?" help="Allows complex logical constructs. See Example 4 below." /> |
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173 <when value="false"/> |
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174 <when value="true"> |
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175 <param name="rules" type="text" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." > |
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176 <sanitizer invalid_char=""> |
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177 <valid initial="string.printable"/> |
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178 </sanitizer> |
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179 </param> |
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180 </when> |
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181 </conditional> |
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182 </inputs> |
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183 <outputs> |
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184 <data format="txt" name="out_file2" label="${tool.name} on ${on_string}: JSON filter rules" /> |
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185 <data name="out_file1" format="bam" label="${tool.name} on ${on_string}: Filtered BAM" /> |
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186 </outputs> |
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187 <tests> |
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188 <test> |
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189 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> |
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190 <param name="bam_property_selector" value="mapQuality"/> |
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191 <param name="bam_property_value" value=">20"/> |
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192 <output name="out_file1" ftype="bam" file="bamtools-test1.bam" /> |
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193 </test> |
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194 </tests> |
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195 <help> |
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196 **What is does** |
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197 |
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198 BAMTools filter is a very powerful utility to perform complex filtering of BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). |
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199 |
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200 ----- |
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201 |
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202 **How it works** |
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203 |
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204 The tool use logic relies on the three concepts: (1) input BAM, (2) groups, and (3) filters. |
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205 |
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206 *Input BAM(s)* |
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207 |
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208 The input BAM is self-explanatory. This is the dataset you will be filtering. The tool can accept just one or multiple BAM files. To filter on multiple BAMs just add them by clicking **Add new BAM dataset(s) to filter** |
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209 |
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210 *Conditions and Filters* |
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211 |
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212 Conditions for filtering BAM files can be arranged in **Groups and Filters**. While it can be confusing at first this is what gives ultimate power to this tools. So try to look at the examples we are supplying below. |
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214 ----- |
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216 **Example 1. Using a single filter** |
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218 When filtering on a single condition there is no need to worry about filters and conditions. Just choose a filter from the **Select BAM property to filter on:** dropdown and enter a value (or click a checkbox for binary filters). |
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219 For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below: |
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220 |
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221 .. image:: single-filter.png |
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225 **Example 2. Using multiple filters** |
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226 |
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227 Now suppose one needs to extract reads that (1) have mapping quality of at least 20, (2) contain at least 1 mismatch, and (3) are mapping onto forward strand only. |
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228 To do so we will use three filters as shown below (multiple filters are added to the interface by clicking on the **Add new Filter** button): |
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229 |
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230 .. image:: multiple-filters.png |
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231 |
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232 In this case (you can see that the three filters are grouped within a single Condition - **Condition 1**) the filter too use logical **AND** to perform filtering. |
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233 In other words only reads that (1) have mapping quality of at least 20 **AND** (2) contain at least 1 mismatch **AND** are mapping onto forward strand will be returned in this example. |
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237 **Example 3. Complex filtering with multiple conditions** |
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238 |
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239 Suppose now you would like to select **either** reads that (**1**) have (*1.1*) no mismatches and (*1.2*) are on the forward strand **OR** (**2**) reads that have (*2.1*) |
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240 at least one mismatch and (*2.2*) are on the reverse strand. In this scenario we have to set up two conditions: (**1**) and (**2**) each with two filters: *1.1* and *1.2* as well as *2.1* and *2.2*. |
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241 The following screenshot expalins how this can be done: |
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242 |
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243 .. image:: complex-filters.png |
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244 |
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247 **Example 4. Even more complex filtering with Rules** |
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248 |
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249 In the above example we have used two conditions (Condition 1 and Condition 2). Using multiple conditions allows to combine them and a variety of ways to enable even more powerful filtering. |
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250 For example, suppose get all reads that (**1**) do NOT map to mitochondria and either (**2**) have mapping quality over 20, or (**3**) are in properly mapped pairs. The logical rule to enable such |
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251 filtering will look like this:: |
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253 !(1) & (2 | 3) |
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255 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy: |
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257 .. image:: rule.png |
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259 There are three conditions here, each with a single filter. A text entry area that can be opened by clicking on the **Would you like to set rules?** checkbox enables you to enter a rule. |
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260 Here numbers correspond to numbers of conditions as they are shown in the interface. E.g., 1 corresponds to condition 1, 2 to condition 2 and so on... In human language this means:: |
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261 |
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262 NOT condition 1 AND (condition 2 OR condition 3) |
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264 ----- |
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266 **JSON script file** |
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267 |
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268 This tool produces two outputs. One of the them is a BAM file containing filtered reads. The other is a JSONified script. It can help you to see how your instructions are sent to BAMTools. |
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269 For instance, the example 4 looks like this in the JSON form:: |
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271 { |
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272 "filters": |
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273 [ |
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274 { "id": "1", |
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275 "tag":"NM:=0", |
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276 "isReverseStrand":"false" |
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277 }, |
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278 { "id": "2", |
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279 "tag":"NM:>0", |
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280 "isReverseStrand":"true" |
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281 } |
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282 ] |
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283 } |
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284 |
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286 ----- |
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288 **More information** |
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289 |
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290 .. class:: infomark |
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291 |
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292 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki |
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295 </help> |
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296 <citations> |
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297 <citation type="doi">10.1093/bioinformatics/btr174</citation> |
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298 </citations> |
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299 </tool> |