Mercurial > repos > jjohnson > bamutil_diff

annotate bamutil_diff.xml @ 0:2cafa8420c04 draft default tip

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
author jjohnson
date Fri, 26 Mar 2021 13:16:53 +0000
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1 <tool id="bamutil_diff" name="BamUtil diff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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2 <description>two coordinate sorted SAM/BAM files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 bam diff
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9 --in1 '$in1'
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10 --in2 '$in2'
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11 #if $fields.choice == 'all':
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12 --all
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13 #elif $fields.choice == 'select':
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14 $fields.flag
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15 $fields.mapQual
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16 $fields.mate
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17 $fields.isize
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18 $fields.seq
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19 $fields.baseQual
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20 $fields.noCigar
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21 $fields.noPos
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22 #if $fields.samtags.tagchoice == 'everyTag':
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23 --everyTag
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24 #elif $fields.samtags.tagchoice == 'specify':
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25 --tags '$fields.samtags.tags'
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26 #end if
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27 #end if
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28 --posDiff $posDiff
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29 --recPoolSize -1
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30 $onlyDiffs
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31 --params
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32 --noPhoneHome
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33 --out $output_as
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34 ]]></command>
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35 <inputs>
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36 <param argument="--in1" type="data" format="sam,bam" label="Input BAM 1"/>
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37 <param argument="--in2" type="data" format="sam,bam" label="Input BAM 2"/>
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38 <param argument="--posDiff" type="integer" value="100000" min="0" label="max base pair difference between possibly matching records"/>
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39 <param argument="--onlyDiffs" type="boolean" truevalue="--onlyDiffs" falsevalue="" checked="false" label="only print the fields that differ"/>
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40 <conditional name="fields">
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41 <param name="choice" type="select" label="BAM fields to diff">
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42 <option value="default" selected="true">Read Name, Flag Fragment bit, Position, Cigar</option>
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43 <option value="all">Diff all the SAM/BAM fields</option>
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44 <option value="select">Select SAM/BAM fields to diff</option>
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45 </param>
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46 <when value="default"/>
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47 <when value="all"/>
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48 <when value="select">
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49 <param argument="--flag" type="boolean" truevalue="--flag" falsevalue="" checked="false" label="diff the flags."/>
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50 <param argument="--mapQual" type="boolean" truevalue="--mapQual" falsevalue="" checked="false" label="diff the mapping qualities."/>
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51 <param argument="--mate" type="boolean" truevalue="--mate" falsevalue="" checked="false" label="diff the mate chrom/pos."/>
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52 <param argument="--isize" type="boolean" truevalue="--isize" falsevalue="" checked="false" label="diff the insert sizes."/>
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53 <param argument="--seq" type="boolean" truevalue="--seq" falsevalue="" checked="false" label="diff the sequence bases."/>
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54 <param argument="--baseQual" type="boolean" truevalue="--baseQual" falsevalue="" checked="false" label="diff the base qualities."/>
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55 <param argument="--noCigar" type="boolean" truevalue="--noCigar" falsevalue="" checked="false" label="do not diff the the cigars."/>
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56 <param argument="--noPos" type="boolean" truevalue="--noPos" falsevalue="" checked="false" label="do not diff the positions."/>
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57 <conditional name="samtags">
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58 <param name="tagchoice" type="select" label="Tags to diff">
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59 <option value="none">Do not diff tags</option>
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60 <option value="everyTag">Diff every tag</option>
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61 <option value="specify">Specify tags to diff</option>
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62 </param>
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63 <when value="none"/>
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64 <when value="everyTag"/>
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65 <when value="specify">
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66 <param argument="--tags" type="text" label="diff the specified Tags formatted as Tag:Type,Tag:Type,Tag:Type...">
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67 <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>
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68 </param>
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69 </when>
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70 </conditional>
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71 </when>
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72 </conditional>
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73 <param name="output_as" type="select" label="Output format">
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74 <option value="diff.txt">ASCII text diff file</option>
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75 <option value="diff.bam">BAM files: diff, only_in_file1, only_in_file2</option>
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76 <option value="diff.sam">SAM files: diff, only_in_file1, only_in_file2</option>
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77 </param>
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78 </inputs>
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79 <outputs>
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80 <data name="diff_bam" format="bam" from_work_dir="diff.bam" label="${tool.name} on ${on_string}: diff.bam">
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81 <filter>output_as == 'diff.bam'</filter>
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82 </data>
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83 <data name="diff_only1_bam" format="bam" from_work_dir="diff_only1_*.bam" label="${tool.name} on ${on_string} only in: ${in1.element_identifier}">
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84 <filter>output_as == 'diff.bam'</filter>
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85 </data>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
86 <data name="diff_only2_bam" format="bam" from_work_dir="diff_only2_*.bam" label="${tool.name} on ${on_string} only in: ${in2.element_identifier}">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
87 <filter>output_as == 'diff.bam'</filter>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
88 </data>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
89 <data name="diff_sam" format="sam" from_work_dir="diff.sam" label="${tool.name} on ${on_string}: diff.sam">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
90 <filter>output_as == 'diff.sam'</filter>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
91 </data>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
92 <data name="diff_only1_sam" format="sam" from_work_dir="diff_only1_*.sam" label="${tool.name} on ${on_string} only in: ${in1.element_identifier}">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
93 <filter>output_as == 'diff.sam'</filter>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
94 </data>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
95 <data name="diff_only2_sam" format="sam" from_work_dir="diff_only2_*.sam" label="${tool.name} on ${on_string} only in: ${in2.element_identifier}">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
96 <filter>output_as == 'diff.sam'</filter>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
97 </data>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
98 <data name="diff_txt" format="txt" from_work_dir="diff.txt" label="${tool.name} on ${on_string}: diff.txt">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
99 <filter>output_as == 'diff.txt'</filter>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
100 </data>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
101 </outputs>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
102 <tests>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
103 <!-- Test-1 -->
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
104 <test>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
105 <param name="in1" ftype="sam" value="in1.sam"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
106 <param name="in2" ftype="sam" value="in2.sam"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
107 <param name="posDiff" value="100000"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
108 <param name="onlyDiffs" value="true"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
109 <conditional name="fields">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
110 <param name="choice" value="default"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
111 </conditional>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
112 <param name="output_as" value="diff.txt"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
113 <output name="diff_txt" file="diff.txt"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
114 <output name="diff_txt">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
115 <assert_contents>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
116 <has_text text="NB500964:249:HHLFNBGX7:3:21407:1974:9687" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
117 <has_text_matching expression="&lt;\t1a3\t74M74N1M" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
118 <has_text_matching expression="&gt;\ta3\t74M66N1M" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
119 </assert_contents>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
120 </output>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
121 </test>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
122
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
123 <!-- Test-2 -->
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
124 <test>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
125 <param name="in1" ftype="sam" value="in1.sam"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
126 <param name="in2" ftype="sam" value="in2.sam"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
127 <param name="posDiff" value="100000"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
128 <param name="onlyDiffs" value="true"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
129 <conditional name="fields">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
130 <param name="choice" value="select"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
131 <param name="flag" value="true"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
132 <param name="seq" value="true"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
133 <conditional name="samtags">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
134 <param name="tagchoice" value="specify"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
135 <param name="tags" value="AS:i,MD:Z"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
136 </conditional>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
137 </conditional>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
138 <param name="output_as" value="diff.sam"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
139 <output name="diff_sam">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
140 <assert_contents>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
141 <has_text text="NB500964:249:HHLFNBGX7:4:12608:21020:10228" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
142 <not_has_text text="NB500964:249:HHLFNBGX7:4:11510:10074:3541" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
143 <not_has_text text="NB500964:249:HHLFNBGX7:1:12312:5087:3846" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
144 </assert_contents>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
145 </output>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
146 <output name="diff_only1_sam">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
147 <assert_contents>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
148 <has_text text="NB500964:249:HHLFNBGX7:1:12312:5087:3846" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
149 <not_has_text text="NB500964:249:HHLFNBGX7:4:11510:10074:3541" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
150 <has_text text="TGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCACCG" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
151 <has_text text="AS:i:0" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
152 <has_text text="MD:Z:75" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
153 </assert_contents>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
154 </output>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
155 <output name="diff_only2_sam">
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
156 <assert_contents>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
157 <has_text text="NB500964:249:HHLFNBGX7:4:11510:10074:3541" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
158 <not_has_text text="NB500964:249:HHLFNBGX7:1:12312:5087:3846" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
159 <has_text text="ATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCA" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
160 <has_text text="AS:i:0" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
161 <has_text text="MD:Z:75" />
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
162 </assert_contents>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
163 </output>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
164 </test>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
165 <!-- Test-3 -->
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jjohnson
parents:
diff changeset
166 <test>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
167 <param name="in1" ftype="sam" value="in1.sam"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
168 <param name="in2" ftype="sam" value="in3.sam"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
169 <param name="posDiff" value="100000"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
170 <param name="onlyDiffs" value="true"/>
2cafa8420c04 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
jjohnson
parents:
diff changeset
171 <conditional name="fields">
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172 <param name="choice" value="default"/>
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173 </conditional>
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174 <param name="output_as" value="diff.txt"/>
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175 <output name="diff_txt">
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176 <assert_contents>
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177 <not_has_text text="NB500964:249:HHLFNBGX7:3:21407:1974:9687" />
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178 </assert_contents>
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179 </output>
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180 </test>
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181 </tests>
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182 <help><![CDATA[
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183 **bamUtil diff**
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184
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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.
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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.
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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.
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188 By default, just the chromosome/position and cigar are compared for each record.
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189 Note: The headers are not compared.
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190
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191 Options are available to compare::
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192
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193 - all fields
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194 - flags
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195 - mapping quality
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196 - mate chromosome/position
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197 - insert size
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198 - sequence
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199 - base quality
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200 - specified tags
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201 - all tags
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202 - turn off position comparison
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203 - turn off cigar comparison
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204
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205 **Inputs**
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206 Two BAM or SAM alignment files
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207
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208 **Outputs**
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209 Choice of 2 Output Formats:
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210
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211 ::
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212
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213 **Diff Format**
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214 There are 2 types of differences.
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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
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216 ReadName/Fragment combo is in both files, but at least one of the specified fields to diff is different
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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.
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218 The first line of the difference output is just the read name.
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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 '>'.
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220 The 2nd line is the flag followed by the diff'd fields from one of the records.
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221 The 3rd line (if a matching record was found) is the flag followed by the diff'd fields from the matching record.
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222 The diff'd record lines are tab separated, and are in the following order if --onlyDiffs is not specified::
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223
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224 - '<' or '>'
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225 - flag
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226 - chrom:pos (chromosome name ':' 1 based position) - if --noPos is not specified
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227 - cigar - if --noCigar is not specified
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228 - mapping quality - if --mapq or --all is specified
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229 - mate chrom:pos (chromosome name ':' 1 based position) - if --mate or --all is specified
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230 - insert size - if --isize or --all is specified
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231 - sequence - if --seq or --all is specified
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232 - base quality - if --baseQual or --all is specified
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233 - tag:type:value - for each tag:type specified in --tags or for every tag if --all or --everyTag specified
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234
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235
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236 **BAM Format**
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237 In SAM/BAM format there will be 3 output files::
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238
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239 1. the specified name with record diffs
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240 2. specified name with _only_<in1>.sam/bam with records only in the in1 file
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241 3. specified name with _only_<in2>.sam/bam with records only in the in2 file
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242
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243 Records that are identical in the two files are not written in any of these output files.
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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::
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245
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246 - ZF - Flag
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247 - ZP - Chromosome:1-based Position
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248 - ZC - Cigar
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249 - ZM - Mapping Quality
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250 - ZN - Chromosome:1-based Mate Position
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251 - ZI - Insert Size
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252 - ZS - Sequence
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253 - ZQ - Base Quality
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254 - ZT - Tags
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255
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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.
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257
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258
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259
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260
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261 https://genome.sph.umich.edu/wiki/BamUtil:_diff
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262
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263 ]]></help>
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264 <expand macro="citations" />
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265 </tool>