Mercurial > repos > iuc > bamutil_diff

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Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
author iuc
date Fri, 02 Apr 2021 20:20:54 +0000
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c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
1 <tool id="bamutil_diff" name="BamUtil diff" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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2 <description>two coordinate sorted SAM/BAM files</description>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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3 <macros>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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4 <import>macros.xml</import>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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5 </macros>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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6 <expand macro="requirements" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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7 <expand macro="edam"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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9 bam diff
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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10 --in1 '$in1'
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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11 --in2 '$in2'
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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12 #if $fields.choice == 'all':
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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13 --all
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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14 #elif $fields.choice == 'select':
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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15 $fields.flag
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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16 $fields.mapQual
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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17 $fields.mate
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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18 $fields.isize
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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19 $fields.seq
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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20 $fields.baseQual
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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21 $fields.noCigar
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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22 $fields.noPos
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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23 #if $fields.samtags.tagchoice == 'everyTag':
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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24 --everyTag
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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25 #elif $fields.samtags.tagchoice == 'specify':
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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26 --tags '$fields.samtags.tags'
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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27 #end if
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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28 #end if
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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29 --posDiff $posDiff
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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30 --recPoolSize -1
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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31 $onlyDiffs
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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32 --params
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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33 --noPhoneHome
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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34 --out $output_as
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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35 ]]></command>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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36 <inputs>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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37 <param argument="--in1" type="data" format="sam,bam" label="Input BAM 1"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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38 <param argument="--in2" type="data" format="sam,bam" label="Input BAM 2"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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39 <param argument="--posDiff" type="integer" value="100000" min="0" label="max base pair difference between possibly matching records"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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40 <param argument="--onlyDiffs" type="boolean" truevalue="--onlyDiffs" falsevalue="" checked="false" label="only print the fields that differ"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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41 <conditional name="fields">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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42 <param name="choice" type="select" label="BAM fields to diff">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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43 <option value="default" selected="true">Read Name, Flag Fragment bit, Position, Cigar</option>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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44 <option value="all">Diff all the SAM/BAM fields</option>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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45 <option value="select">Select SAM/BAM fields to diff</option>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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46 </param>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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47 <when value="default"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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48 <when value="all"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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49 <when value="select">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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50 <param argument="--flag" type="boolean" truevalue="--flag" falsevalue="" checked="false" label="diff the flags."/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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51 <param argument="--mapQual" type="boolean" truevalue="--mapQual" falsevalue="" checked="false" label="diff the mapping qualities."/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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52 <param argument="--mate" type="boolean" truevalue="--mate" falsevalue="" checked="false" label="diff the mate chrom/pos."/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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53 <param argument="--isize" type="boolean" truevalue="--isize" falsevalue="" checked="false" label="diff the insert sizes."/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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54 <param argument="--seq" type="boolean" truevalue="--seq" falsevalue="" checked="false" label="diff the sequence bases."/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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55 <param argument="--baseQual" type="boolean" truevalue="--baseQual" falsevalue="" checked="false" label="diff the base qualities."/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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56 <param argument="--noCigar" type="boolean" truevalue="--noCigar" falsevalue="" checked="false" label="do not diff the the cigars."/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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57 <param argument="--noPos" type="boolean" truevalue="--noPos" falsevalue="" checked="false" label="do not diff the positions."/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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58 <conditional name="samtags">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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59 <param name="tagchoice" type="select" label="Tags to diff">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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60 <option value="none">Do not diff tags</option>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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61 <option value="everyTag">Diff every tag</option>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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62 <option value="specify">Specify tags to diff</option>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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63 </param>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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64 <when value="none"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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65 <when value="everyTag"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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66 <when value="specify">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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67 <param argument="--tags" type="text" label="diff the specified Tags formatted as Tag:Type,Tag:Type,Tag:Type...">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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68 <validator type="regex" message="SAM 2-char Tag:type">^([A-Za-z][A-Za-z0-9]:[AifZHB])(,[A-Za-z][A-Za-z0-9]:[AifZHB])*$</validator>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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69 </param>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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70 </when>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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71 </conditional>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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72 </when>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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73 </conditional>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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74 <param name="output_as" type="select" label="Output format">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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75 <option value="diff.txt">ASCII text diff file</option>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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76 <option value="diff.bam">BAM files: diff, only_in_file1, only_in_file2</option>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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77 <option value="diff.sam">SAM files: diff, only_in_file1, only_in_file2</option>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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78 </param>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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79 </inputs>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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80 <outputs>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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81 <data name="diff_bam" format="bam" from_work_dir="diff.bam" label="${tool.name} on ${on_string}: diff.bam">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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82 <filter>output_as == 'diff.bam'</filter>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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83 </data>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
84 <data name="diff_only1_bam" format="bam" from_work_dir="diff_only1_*.bam" label="${tool.name} on ${on_string} only in: ${in1.element_identifier}">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
85 <filter>output_as == 'diff.bam'</filter>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
86 </data>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
87 <data name="diff_only2_bam" format="bam" from_work_dir="diff_only2_*.bam" label="${tool.name} on ${on_string} only in: ${in2.element_identifier}">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
88 <filter>output_as == 'diff.bam'</filter>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
89 </data>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
90 <data name="diff_sam" format="sam" from_work_dir="diff.sam" label="${tool.name} on ${on_string}: diff.sam">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
91 <filter>output_as == 'diff.sam'</filter>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
92 </data>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
93 <data name="diff_only1_sam" format="sam" from_work_dir="diff_only1_*.sam" label="${tool.name} on ${on_string} only in: ${in1.element_identifier}">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
94 <filter>output_as == 'diff.sam'</filter>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
95 </data>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
96 <data name="diff_only2_sam" format="sam" from_work_dir="diff_only2_*.sam" label="${tool.name} on ${on_string} only in: ${in2.element_identifier}">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
97 <filter>output_as == 'diff.sam'</filter>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
98 </data>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
99 <data name="diff_txt" format="txt" from_work_dir="diff.txt" label="${tool.name} on ${on_string}: diff.txt">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
100 <filter>output_as == 'diff.txt'</filter>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
101 </data>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
102 </outputs>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
103 <tests>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
104 <!-- Test-1 -->
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
105 <test expect_num_outputs="1">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
106 <param name="in1" ftype="sam" value="in1.sam"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
107 <param name="in2" ftype="sam" value="in2.sam"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
108 <param name="posDiff" value="100000"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
109 <param name="onlyDiffs" value="true"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
110 <conditional name="fields">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
111 <param name="choice" value="default"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
112 </conditional>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
113 <param name="output_as" value="diff.txt"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
114 <output name="diff_txt">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
115 <assert_contents>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
116 <has_text text="NB500964:249:HHLFNBGX7:3:21407:1974:9687" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
117 <has_text_matching expression="&lt;\t1a3\t74M74N1M" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
118 <has_text_matching expression="&gt;\ta3\t74M66N1M" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
119 </assert_contents>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
120 </output>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
121 </test>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
122
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
123 <!-- Test-2 -->
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
124 <test expect_num_outputs="3">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
125 <param name="in1" ftype="sam" value="in1.sam"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
126 <param name="in2" ftype="sam" value="in2.sam"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
127 <param name="posDiff" value="100000"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
128 <param name="onlyDiffs" value="true"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
129 <conditional name="fields">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
130 <param name="choice" value="select"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
131 <param name="flag" value="true"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
132 <param name="seq" value="true"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
133 <conditional name="samtags">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
134 <param name="tagchoice" value="specify"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
135 <param name="tags" value="AS:i,MD:Z"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
136 </conditional>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
137 </conditional>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
138 <param name="output_as" value="diff.sam"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
139 <output name="diff_sam">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
140 <assert_contents>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
141 <has_text text="NB500964:249:HHLFNBGX7:4:12608:21020:10228" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
142 <not_has_text text="NB500964:249:HHLFNBGX7:4:11510:10074:3541" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
143 <not_has_text text="NB500964:249:HHLFNBGX7:1:12312:5087:3846" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
144 </assert_contents>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
145 </output>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
146 <output name="diff_only1_sam">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
147 <assert_contents>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
148 <has_text text="NB500964:249:HHLFNBGX7:1:12312:5087:3846" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
149 <not_has_text text="NB500964:249:HHLFNBGX7:4:11510:10074:3541" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
150 <has_text text="TGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCACCG" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
151 <has_text text="AS:i:0" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
152 <has_text text="MD:Z:75" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
153 </assert_contents>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
154 </output>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
155 <output name="diff_only2_sam">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
156 <assert_contents>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
157 <has_text text="NB500964:249:HHLFNBGX7:4:11510:10074:3541" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
158 <not_has_text text="NB500964:249:HHLFNBGX7:1:12312:5087:3846" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
159 <has_text text="ATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCA" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
160 <has_text text="AS:i:0" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
161 <has_text text="MD:Z:75" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
162 </assert_contents>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
163 </output>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
164 </test>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
165 <!-- Test-3 -->
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
166 <test expect_num_outputs="1">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
167 <param name="in1" ftype="sam" value="in1.sam"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
168 <param name="in2" ftype="sam" value="in3.sam"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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169 <param name="posDiff" value="100000"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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170 <param name="onlyDiffs" value="true"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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171 <conditional name="fields">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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172 <param name="choice" value="default"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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173 </conditional>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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174 <param name="output_as" value="diff.txt"/>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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175 <output name="diff_txt">
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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176 <assert_contents>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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177 <not_has_text text="NB500964:249:HHLFNBGX7:3:21407:1974:9687" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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178 </assert_contents>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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179 </output>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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180 </test>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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181 </tests>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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182 <help><![CDATA[
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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183 **bamUtil diff**
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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184
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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185 The diff option on the bamUtil executable prints the difference between two coordinate sorted SAM/BAM files. This can be used to compare the outputs of running a SAM/BAM through different tools/versions of tools.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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186 The diff tool compares records that have the same Read Name and Fragment (from the flag). If a matching ReadName & Fragment is not found, the record is considered to be different.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
187 diff assumes the files are coordinate sorted and uses this assumption for determining how long to store a record before determining that the other file does not contain a matching ReadName/Fragment. If the files are not coordinate sorted, this logic does not work.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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188 By default, just the chromosome/position and cigar are compared for each record.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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189 Note: The headers are not compared.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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190
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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191 Options are available to compare::
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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192
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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193 - all fields
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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194 - flags
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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195 - mapping quality
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
196 - mate chromosome/position
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
197 - insert size
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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198 - sequence
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
199 - base quality
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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200 - specified tags
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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201 - all tags
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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202 - turn off position comparison
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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203 - turn off cigar comparison
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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204
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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205 **Inputs**
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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206 Two BAM or SAM alignment files
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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207
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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208 **Outputs**
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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209 Choice of 2 Output Formats:
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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210
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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211 ::
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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212
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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213 **Diff Format**
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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214 There are 2 types of differences.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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215 ReadName/Fragment combo is in one file, but not in the other file within the window set by recPoolSize & posDiff
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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216 ReadName/Fragment combo is in both files, but at least one of the specified fields to diff is different
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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217 Each difference output consists of 2 or 3 lines. If the record only appears in one of the files, the diff is 2 lines, if it appears in both files, the diff is 3 lines.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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218 The first line of the difference output is just the read name.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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219 The 2nd and 3rd line (if present) begin with either a '<' or a '>'. If the record is from the first file (--in1), it begins with a '<'. If the record is from the 2nd file (--in2), it begins with a '>'.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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220 The 2nd line is the flag followed by the diff'd fields from one of the records.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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diff changeset
221 The 3rd line (if a matching record was found) is the flag followed by the diff'd fields from the matching record.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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222 The diff'd record lines are tab separated, and are in the following order if --onlyDiffs is not specified::
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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223
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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224 - '<' or '>'
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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225 - flag
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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226 - chrom:pos (chromosome name ':' 1 based position) - if --noPos is not specified
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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227 - cigar - if --noCigar is not specified
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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228 - mapping quality - if --mapq or --all is specified
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
229 - mate chrom:pos (chromosome name ':' 1 based position) - if --mate or --all is specified
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
230 - insert size - if --isize or --all is specified
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
231 - sequence - if --seq or --all is specified
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
232 - base quality - if --baseQual or --all is specified
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
233 - tag:type:value - for each tag:type specified in --tags or for every tag if --all or --everyTag specified
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
234
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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diff changeset
235
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
236 **BAM Format**
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
237 In SAM/BAM format there will be 3 output files::
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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238
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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239 1. the specified name with record diffs
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
240 2. specified name with _only_<in1>.sam/bam with records only in the in1 file
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
241 3. specified name with _only_<in2>.sam/bam with records only in the in2 file
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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242
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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diff changeset
243 Records that are identical in the two files are not written in any of these output files.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
244 When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags::
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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245
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
246 - ZF - Flag
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
247 - ZP - Chromosome:1-based Position
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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248 - ZC - Cigar
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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diff changeset
249 - ZM - Mapping Quality
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
parents:
diff changeset
250 - ZN - Chromosome:1-based Mate Position
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
251 - ZI - Insert Size
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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252 - ZS - Sequence
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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diff changeset
253 - ZQ - Base Quality
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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254 - ZT - Tags
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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255
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
iuc
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256 If --onlyDiffs is not specified, all fields that were compared will be printed in the tags. If --onlyDiffs is specified, then only the differing compared fields will be printed in the tags.
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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257
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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258
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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259
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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260
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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261 https://genome.sph.umich.edu/wiki/BamUtil:_diff
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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262
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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263 ]]></help>
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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264 <expand macro="citations" />
c28c4c132459 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"
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265 </tool>