Mercurial > repos > iuc > stacks_sstacks

annotate stacks_sstacks.xml @ 5:59d244e79b8e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author iuc
date Thu, 27 Apr 2017 04:14:04 -0400
parents 47d7750df155
children 45cc649c9f8a
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1 <tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.0">
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2 <description>match stacks to a catalog</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 <expand macro="stdio"/>
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8 <command><![CDATA[
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9 #import re
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11 mkdir stacks_inputs stacks_outputs
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13 &&
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15 #set $catalog = ""
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16 #for $input_file in $input_cat
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17 #set $filename = str($input_file.element_identifier)
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18 #if not filename.endswith('.tsv')
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19 #set $filename = $filename + ".tsv"
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20 #end if
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21 #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
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22 ln -s '${input_file}' 'stacks_inputs/$filename' &&
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24 #if $filename.endswith('.tags.tsv')
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25 #set catalog += " -c 'stacks_inputs/"+$filename[:-17] + "'"
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26 #end if
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27 #end if
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28 #end for
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30 #set $samples = ""
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31 #for $input_file in $input_tags
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32 #set $filename = str($input_file.element_identifier)
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33 #if not filename.endswith('.tsv')
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34 #set $filename = $filename + ".tsv"
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35 #end if
5
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36 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
59d244e79b8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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37 ln -s '${input_file}' 'stacks_inputs/$filename' &&
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38
5
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39 #if $filename.endswith('.tags.tsv')
59d244e79b8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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40 #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'"
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41 #end if
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42 #end if
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43 #end for
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44
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45 sstacks
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46
5
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47 ## Batch description
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48 -b 1
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49
0
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50 -p \${GALAXY_SLOTS:-1}
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51
5
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52 #if $popmap
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53 -P stacks_inputs -M '$popmap'
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54 #else
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55 $catalog
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56 $samples
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57 -o stacks_outputs
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58 #end if
0
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59
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60 $g
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61
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62 $check_haplo
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64 $gapped
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65
5
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66 2>&1 | tee sstacks.log
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67
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68 #if $popmap
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69 ## When using a popmap, stacks write to the input dir
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70 && mv stacks_inputs/*matches.tsv stacks_outputs/
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71 #end if
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73 &&
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75 stacks_summary.py --stacks-prog sstacks --res-dir stacks_outputs --logfile sstacks.log --summary stacks_outputs/summary.html
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76 ]]></command>
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78 <inputs>
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79 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />
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80 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" />
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81
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82 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />
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83
0
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84 <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
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85
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86 <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" />
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87
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88 <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" />
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89 </inputs>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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parents:
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90
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
91 <outputs>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
92 <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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93
5
59d244e79b8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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parents: 1
diff changeset
94 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
59d244e79b8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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95
0
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
96 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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97 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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98 </collection>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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99 </outputs>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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100
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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101 <tests>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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102 <test>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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103 <param name="input_cat">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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104 <collection type="list">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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105 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
106 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
107 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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108 </collection>
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109 </param>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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110 <param name="input_tags">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
111 <collection type="list">
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112 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
113 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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114 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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115 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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116 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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117 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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118 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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119 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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120 </collection>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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121 </param>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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122
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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123 <output name="output_log">
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124 <assert_contents>
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125 <has_text text="Outputing to file" />
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126 </assert_contents>
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127 </output>
5
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128 <output name="output_summary">
59d244e79b8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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129 <assert_contents>
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130 <has_text text="Stacks Statistics" />
59d244e79b8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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131 </assert_contents>
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132 </output>
0
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133
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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134 <output_collection name="matches">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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135 <element name="PopA_01.matches">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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136 <assert_contents>
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iuc
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137 <has_text text="generated on " />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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138 </assert_contents>
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139 </element>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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140 </output_collection>
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iuc
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diff changeset
141 </test>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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142
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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143 <test>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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144 <param name="input_cat">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
145 <collection type="list">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
146 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
147 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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diff changeset
148 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
149 </collection>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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150 </param>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
151 <param name="input_tags">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
152 <collection type="list">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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153 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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parents:
diff changeset
154 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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155 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
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156 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
157 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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parents:
diff changeset
158 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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parents:
diff changeset
159 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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parents:
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160 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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161 </collection>
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162 </param>
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163 <param name="gapped" value="true" />
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164 <param name="check_haplo" value="true" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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165
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parents:
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166 <output name="output_log">
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167 <assert_contents>
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168 <has_text text="Outputing to file" />
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169 </assert_contents>
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170 </output>
5
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iuc
parents: 1
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171 <output name="output_summary">
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parents: 1
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172 <assert_contents>
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parents: 1
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173 <has_text text="Stacks Statistics" />
59d244e79b8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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parents: 1
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174 </assert_contents>
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175 </output>
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176
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177 <output_collection name="matches">
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178 <element name="PopA_01.matches">
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179 <assert_contents>
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180 <has_text text="generated on " />
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181 </assert_contents>
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182 </element>
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183 </output_collection>
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184 </test>
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185
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186 <test>
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187 <param name="input_cat">
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188 <collection type="list">
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189 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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190 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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191 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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192 </collection>
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193 </param>
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194 <param name="input_tags">
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195 <collection type="list">
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196 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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197 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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198 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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199 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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200 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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201 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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202 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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203 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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204 </collection>
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205 </param>
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206
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207 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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208
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209 <output name="output_log">
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210 <assert_contents>
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211 <has_text text="Outputing to file" />
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212 </assert_contents>
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213 </output>
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214 <output name="output_summary">
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215 <assert_contents>
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216 <has_text text="Stacks Statistics" />
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217 </assert_contents>
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218 </output>
0
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219
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220 <output_collection name="matches">
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221 <element name="PopA_01.matches">
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222 <assert_contents>
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223 <has_text text="generated on " />
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224 </assert_contents>
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225 </element>
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226 </output_collection>
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227 </test>
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228 </tests>
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229
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230 <help>
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231 <![CDATA[
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232 .. class:: infomark
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233
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234 **What it does**
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235
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236 Sets of stacks constructed by the ustacks or pstacks programs can be searched against a catalog produced by cstacks. In the case of a genetic map, stacks from the progeny would be matched against the catalog to determine which progeny contain which parental alleles.
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237
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238 --------
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239
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240 **Input files**
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241
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242 Output from denovo_map, refmap or cstacks/ustacks/pstacks
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243
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244 **Output files**
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245
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246 - XXX.tags.tsv file:
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247
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248 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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249
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250 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
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251
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252
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253 - XXX.snps.tsv file:
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254
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255 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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256
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257 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
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258
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259
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260 - XXX.alleles.tsv file:
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261
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262 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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263
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264 - XXX.matches.tsv file:
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265
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266 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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267
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268 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.
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269
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270 @STACKS_INFOS@
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271 ]]>
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272 </help>
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273 <expand macro="citation" />
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274 </tool>