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annotate macros.xml @ 1:d110a4141898 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
author iuc
date Thu, 23 Jun 2022 17:28:50 +0000
parents a04e64efa43a
children b3c3217c0cbc
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a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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1 <macros>
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2 <token name="@TOOL_VERSION@">2.1.0</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <xml name="xrefs">
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5 <xrefs>
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6 <xref type="bio.tools">ragtag</xref>
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7 </xrefs>
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8 </xml>
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9 <xml name="requirements">
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">ragtag</requirement>
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12 </requirements>
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13 </xml>
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14 <xml name="citations">
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15 <citations>
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16 <citation type="doi">10.1186/s13059-019-1829-6</citation>
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17 </citations>
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18 </xml>
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19 <xml name="input_options">
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20 <param name="reference" type="data" format="fasta" label="Reference FASTA file"/>
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21 <param name="query" type="data" format="fasta" label="Query FASTA file" />
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22 </xml>
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23 <xml name="common_parameters">
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24 <param argument="-e" type="data" format="txt" optional="true" label="List of reference headers to ignore"
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25 help="Use this parameter to provide a single column file listing any reference.fa headers that should
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26 be ignored (e.g. chr0/chrUn or alt contigs)"/>
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27 <param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave uncorrected"
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28 help="use this parameter to provide a single column file listing any query.fa headers that shall not be broken"/>
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29 <param argument="-f" type="integer" min="0" value="1000" label="Minimum unique single length"
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30 help="If an alignment is not entirely unique, at least -f bp of the alignment must be unique to be considered
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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31 for scaffolding. By default, entirely unique alignments are considered regardless of their length, but
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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32 this can be disabled with --remove-small. Doing so ensures that only alignments at least -f bp in length
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33 are considered for correction"/>
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34 <param argument="--remove-small" type="boolean" truevalue="--remove-small"
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35 falsevalue="" checked="false" label="Remove unique alignments"
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36 help="Remove unique alignments shorter than the minimum unique alignment length" />
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37 <param argument="-q" type="integer" min="0" value="10" label="Minimum mappping quality"
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38 help="Mapping quality scores quantify the probability that a read is misplaced" />
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39 <param argument="-d" type="integer" min="0" value="100000" label="Maximum alignment merge distance"
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40 help="For each query sequence, syntenic alignments within -d bp of each other are merged into longer alignments"/>
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41 <conditional name="mapping_conditional">
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42 <param name="mapping_option" type="select" label="Aligner tool">
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43 <option value="nucmer">Nucmer</option>
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44 <!--Unimap is not included because according the minimap2 developers, minimap2 backports unimap features https://github.com/lh3/minimap2/releases/tag/v2.19
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45 <option value="unimap">Unimap</option>
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46 -->
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47 <option value="minimap2" selected="true">Minimap2</option>
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48 </param>
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49 <when value="nucmer">
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50 <param name="anchor_mode" type="select" label="Anchoring mode">
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51 <option value="--mum">Use anchor matches that are unique in both the reference and query (--mum)</option>
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52 <option value="--mumreference">Use anchor matches that are unique in in the reference but not necessarily unique in the query (--mumreference)</option>
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53 <option value="--maxmatch" selected="true">Use all anchor matches regardless of their uniqueness (--maxmatch)</option>
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54 </param>
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55 <param argument="-l" type="integer" min="0" value="100" label="Minimun length of a single match"/>
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56 <param argument="-c" type="integer" min="0" value="500" label="Minimum length of a cluster of matches"/>
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57 </when>
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58 <when value="minimap2">
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59 <param argument="--mm2-params" type="select"
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60 label="Select a profile of preset options"
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61 help="Each profile comes with the preconfigured settings mentioned in parentheses" >
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62 <option value="asm5">Asm5: the alignment will not extend to regions with 5% or higher sequence divergence (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100)</option>
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63 <option value="asm10">Asm10: up to 10% sequence divergence (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100)</option>
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64 <option value="asm20">Asm20: up to 20% sequence divergence (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100)</option>
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65 </param>
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66 </when>
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67 </conditional>
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68 </xml>
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69 <token name="@INPUTS@"><![CDATA[
1
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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70 reference.fa
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71 query.fa
0
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72 ]]></token>
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73 <token name="@COMMON_PARAMETERS@"><![CDATA[
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74 --aligner $mode_conditional.advanced_options.mapping_conditional.mapping_option
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75 #if $mode_conditional.advanced_options.mapping_conditional.mapping_option == 'nucmer'
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76 --nucmer-params '$nucmer_params'
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77 #else
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78 #if $mode_conditional.advanced_options.mapping_conditional.mm2_params == 'asm5'
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79 --mm2-params '-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100'
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80 #else if $mode_conditional.advanced_options.mapping_conditional.mm2_params == 'asm10'
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81 --mm2-params '-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100'
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82 #else
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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83 --mm2-params '-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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84 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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85 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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86 #if $mode_conditional.advanced_options.e
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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87 -e '${mode_conditional.advanced_options.e}'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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88 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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89 #if $mode_conditional.advanced_options.j
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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90 -j '${mode_conditional.advanced_options.j}'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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91 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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92 -f $mode_conditional.advanced_options.f
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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93 --remove-small $mode_conditional.advanced_options.remove_small
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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94 -q $mode_conditional.advanced_options.q
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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95 -d $mode_conditional.advanced_options.d
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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96 ]]></token>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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97 </macros>