annotate ragtag.xml @ 1:d110a4141898 draft

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 <tool id='ragtag' name='RagTag' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' profile='20.01'>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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2 <description>reference-guided scaffolding of draft genomes</description>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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3 <macros>
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4 <import>macros.xml</import>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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5 </macros>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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6 <expand macro='xrefs' />
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7 <expand macro='requirements' />
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8 <command detect_errors='exit_code'><![CDATA[
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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9 #if $mode_conditional.mode_option != 'merge'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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10 #if $mode_conditional.advanced_options.mapping_conditional.mapping_option == 'nucmer'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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11 #set $nucmer_params = '%s -l %s -c %s' % ($mode_conditional.advanced_options.mapping_conditional.anchor_mode,
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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12 $mode_conditional.advanced_options.mapping_conditional.l,
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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13 $mode_conditional.advanced_options.mapping_conditional.c)
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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14 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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15 #end if
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16 #if $mode_conditional.mode_option == 'merge'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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17 #set $input_files = list()
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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18 mkdir merge_files &&
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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19 #for $i, $j in enumerate($mode_conditional.scaffold_files)
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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20 #set $out_file = './merge_files/scaffold_%s.agp' % $i
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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21 ln -s '${j}' $out_file &&
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22 $input_files.append($out_file)
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23 #end for
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24 #set $merge_files = " ".join($input_files)
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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25 #end if
1
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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26
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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27 ## symlink reference because a .fai file is created
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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28 #if $mode_conditional.mode_option in ['correct', 'scaffold', 'patch']
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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29 ln -s '$mode_conditional.reference' reference.fa &&
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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30 ln -s '$mode_conditional.query' query.fa &&
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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31 #else
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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32 ln -s '$assembly_fasta' assembly.fa &&
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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33 #end if
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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34
0
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35 ragtag.py $mode_conditional.mode_option -u
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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36 #if $mode_conditional.mode_option == 'correct'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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37 @INPUTS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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38 @COMMON_PARAMETERS@
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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39 #if $mode_conditional.validation_conditional.validation_option == 'true'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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40 -R '${mode_conditional.validation_conditional.R}'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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41 -T $mode_conditional.validation_conditional.read_type
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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42 -v $mode_conditional.validation_conditional.v
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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43 #if $mode_conditional.validation_conditional.max_cov
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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44 --max-cov $mode_conditional.validation_conditional.max_cov
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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45 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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46 #if $mode_conditional.validation_conditional.min_cov
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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47 --min-cov $mode_conditional.validation_conditional.min_cov
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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48 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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49 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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50 -b $mode_conditional.advanced_options.b
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51 #if $mode_conditional.advanced_options.missasembly_break
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52 $mode_conditional.advanced_options.missasembly_break
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53 #end if
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54 #if $mode_conditional.advanced_options.gff
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55 --gff '${mode_conditional.advanced_options.gff}'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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56 #end if
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57 --read-aligner 'minimap2' ## it is the only allowed
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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58 #else if $mode_conditional.mode_option == 'scaffold'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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59 @INPUTS@
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60 @COMMON_PARAMETERS@
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61 -i $mode_conditional.advanced_options.i
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62 -a $mode_conditional.advanced_options.a
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63 -s $mode_conditional.advanced_options.s
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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64 #if $mode_conditional.advanced_options.gap_conditional.gap_option == 'true'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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65 -r
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66 -g '${mode_conditional.advanced_options.gap_conditional.g}'
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67 -m '${mode_conditional.advanced_options.gap_conditional.m}'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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68 #end if
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69 #if $mode_conditional.advanced_options.unplaced_conditional.unplaced_option == 'true'
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70 -C
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71 #if $mode_conditional.advanced_options.unplaced_conditional.J
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72 -J '${mode_conditional.advanced_options.unplaced_conditional.J}'
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73 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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74 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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75 #else if $mode_conditional.mode_option == 'patch'
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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76 @INPUTS@
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77 @COMMON_PARAMETERS@
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78 -s $mode_conditional.advanced_options.s
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79 -i $mode_conditional.advanced_options.i
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80 #if $mode_conditional.advanced_options.patching_mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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81 $mode_conditional.advanced_options.patching_mode
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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82 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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83 #else
1
d110a4141898 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
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84 assembly.fa
0
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85 #if $mode_conditional.scaffold_files
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86 $merge_files
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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87 #end if
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iuc
parents:
diff changeset
88 #if $mode_conditional.merging_options.j
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diff changeset
89 -j $mode_conditional.merging_options.j
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
90 #end if
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
91 -l $mode_conditional.merging_options.l
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
92 -e $mode_conditional.merging_options.e
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
93 --gap-func $mode_conditional.merging_options.function_merging
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
94 #if $mode_conditional.hic_options.b
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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diff changeset
95 -b $mode_conditional.hic_options.b
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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parents:
diff changeset
96 -r $mode_conditional.hic_options.r
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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parents:
diff changeset
97 -p $mode_conditional.hic_options.p
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diff changeset
98 #end if
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diff changeset
99 #end if
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iuc
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diff changeset
100 -o ./
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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101 #if $mode_conditional.mode_option != 'merge'
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102 -t \${GALAXY_SLOTS:-2}
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diff changeset
103 #end if
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diff changeset
104 #if $mode_conditional.mode_option == 'patch'
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105 && mv ragtag.patch.asm.paf.log ragtag.patch.log
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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106 #end if
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iuc
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diff changeset
107 ]]> </command>
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108 <inputs>
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109 <conditional name="mode_conditional">
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110 <param name="mode_option" type="select" label="Operation mode">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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111 <option value="correct">Correct: homology-based missasembly correction</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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112 <option value="scaffold">Scaffold: homology-based assebly scaffolding</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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113 <option value="patch">Patch: homology-based assembly patching</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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114 <option value="merge">Merge: scaffolding merging</option>
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115 </param>
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116 <when value="correct">
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diff changeset
117 <expand macro="input_options"/>
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118 <conditional name="validation_conditional">
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119 <param name="validation_option" type="select" label="Use validation reads">
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120 <option value="true">Enabled</option>
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121 <option value="false" selected="true">Disabled</option>
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diff changeset
122 </param>
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iuc
parents:
diff changeset
123 <when value="true">
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124 <param argument="-R" type="data" format="fastq,fastqsanger" label="Validation reads"
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125 help="Without validation, the module will break at any point of reference discordance as defined by the 'correction options'.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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126 With validation, RagTag maps reads to the query assembly and verifies putative break points if they are near regions of
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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127 exceptionally low or high coverage. The reads used for validation should come from the same genotype as the query
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diff changeset
128 assembly to ensure that coverage abnormalities don't arise from true biological variation" />
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129 <param name="read_type" type="select" label="Read type">
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130 <option value="sr">Illumina</option>
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131 <option value="ont">Nanopore</option>
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132 <option value="corr">Error corrected long-reads</option>
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133 </param>
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134 <param argument="-v" type="integer" min="0" value="10000" label="Coverage validation window size"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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135 help="This parameter specifies the window around the putative misassembly break point that RagTag examines
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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136 for exceptionally low or high read coverage. The larger this window size, the more likely
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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diff changeset
137 it is to find an unrelated coverage abnormality"/>
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138 <param argument="--max-cov" type="integer" min="0" value="" optional="true" label="Break sequences at regions at or above this coverage level"/>
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139 <param argument="--min-cov" type="integer" min="0" value="" optional="true" label="Break sequences at regions at or below this coverage level"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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140 </when>
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141 <when value="false"/>
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142 </conditional>
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143 <section name="advanced_options" title="Advanced options">
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144 <expand macro="common_parameters"/>
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145 <param argument="-b" type="integer" min="0" value="5000" label="Minimum break distance from contig ends"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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146 help="Breaks will not be made within -b bp of query sequence termini"/>
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147 <param name="missasembly_break" type="select" optional="true" label="Break misassebly option"
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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148 help="One can also direct RagTag to only break misassemblies between (--inter, query maps to >1 reference sequence) or within
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149 (--intra, query maps discordantly to 1 reference sequence) reference sequences">
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150 <option value="--inter">Only break misassemblies between reference sequences (--inter)</option>
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151 <option value="--intra">Only break missasemblies within reference sequences (--intra)</option>
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152 </param>
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153 <param argument="--gff" type="data" format="gff" optional="true" label="Don't break sequences within GFF intervals"
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154 help=" If one has annotations associated with the query assembly, provide them with the --gff option to ensure that the query assembly
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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155 is never broken within annotation intervals. "/>
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156 </section>
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157 <param name="output_correct" type="select" multiple="true" label="Output files">
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158 <option value="fasta" selected="true">The corrected query assembly in FASTA format</option>
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159 <option value="agp" selected="true">The AGP file defining the exact coordinates of query sequence breaks</option>
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160 <option value="paf">The description of the approximate mapping positions between two set of sequences in PAF format</option>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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161 <option value="log">Log file</option>
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162 </param>
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163 </when>
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164 <when value="scaffold">
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diff changeset
165 <expand macro="input_options"/>
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iuc
parents:
diff changeset
166 <section name="advanced_options" title="advanced options">
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iuc
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167 <expand macro="common_parameters"/>
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168 <param argument="-i" type="float" min="0" max="1" value="0.2" label="Minimum grouping confidence score"
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169 help="The grouping confidence score is the number of base pairs a contig covered in its assigned reference chromosome
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diff changeset
170 divided by the total number of covered base pairs in the entire reference genome"/>
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171 <param argument="-a" type="float" min="0" max="1" value="0" label="Minimum location confidence score"
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172 help="To create a metric associated with contig ordering confidence, Ragtag define a location confidence. First, the smallest
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173 and largest alignment positions, with respect to the reference, between a contig and its assigned reference chromosome are found.
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174 The location confidence is then calculated as the number of covered base pairs in this range divided by the total number of
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175 base pairs in the range"/>
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176 <param argument="-s" type="float" min="0" max="1" value="0" label="Minimum orientation confidence score"
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177 help="To calculate the orientation confidence, each base pair in each alignment between a contig and its assigned reference chromosome
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178 casts a vote for the orientation of its alignment. The orientation confidence is the number of votes for the assigned orientation of
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179 the contig divided by the total number of votes"/>
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180 <conditional name="gap_conditional">
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181 <param name="gap_option" type="select" label="Infer gap sizes" help="When disabled, all gaps are 100 bp (-r)">
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182 <option value="true" selected="true">Enabled</option>
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183 <option value="false">Disabled</option>
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184 </param>
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185 <when value="true">
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186 <param argument="-g" type="integer" min="0" value="100" label="Minimum infered gap size" />
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187 <param argument="-m" type="integer" min="0" value="100000" label="Maximum inferred gap size"/>
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188 </when>
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189 <when value="false"/>
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190 </conditional>
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191 <conditional name="unplaced_conditional">
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192 <param name="unplaced_option" type="select" label="Concatenate unplaced contigs and make 'chr0' (-C)">
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193 <option value="true">Enabled</option>
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194 <option value="false" selected="true">Disabled</option>
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195 </param>
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196 <when value="true">
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197 <param argument="-J" type="data" format="txt" optional="true" label="List of query headers to leave unplaceds and exclude form 'chr0'"/>
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198 </when>
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199 <when value="false"/>
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200 </conditional>
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201 </section>
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202 <param name="output_scaffold" type="select" multiple="true" label="Output files">
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203 <option value="fasta" selected="true">The scaffolds in FASTA format, defined by the ordering and orientations of the sequences containted in the AGP file</option>
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204 <option value="agp" selected="true">The ordering and orientations of query sequences in AGP format</option>
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205 <option value="paf">The description of the approximate mapping positions between two set of sequences in PAF format</option>
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206 <option value="confidence">Confidence score values</option>
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207 <option value="stats">Summary statistics for the scaffolding process</option>
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208 <option value="log">Log file</option>
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209 </param>
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210 </when>
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211 <when value="patch">
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diff changeset
212 <expand macro="input_options"/>
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213 <section name="advanced_options" title="advanced options">
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214 <expand macro="common_parameters"/>
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215 <param argument="-s" type="integer" min="0" value="50000" label="Minimum merged alignment length"
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216 help="After merging, alignments less than -s bp long will be removed"/>
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217 <param argument="-i" type="float" min="0" max="1" value="0.05" label="Maximum merged alignment distance"
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218 help="Maximum merged alignment distance from sequence terminus as fraction of the sequence length. Alignments must
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219 be within -i bp of a target sequence terminus or gap to be considered for patchin "/>
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220 <param name="patching_mode" type="select" optional="true" label="Patching mode">
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221 <option value="--fill-only">Only fill existing target gaps. Do not join target sequences</option>
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222 <option value="--join_only">Only join and patch target sequences. DO not fill existing gaps</option>
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223 </param>
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224 </section>
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225 <param name="output_patch" type="select" multiple="true" label="Output files">
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226 <option value="final_fasta" selected="true">The final FASTA file containing the patched assembly</option>
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227 <option value="final_agp" selected="true">The final AGP file defining how final FASTA is built</option>
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228 <option value="assembly_file" selected="true">Assembly alignment files</option>
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229 <option value="split_assembly">The split target assembly and the renamed query assembly combined into one FASTA file</option>
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230 <option value="split_description">An AGP file defining how the target assembly was split at gaps</option>
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231 <option value="target_gaps">The target assembly split at gaps</option>
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232 <option value="agp_renamed">An AGP file defining the new names for query sequences</option>
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233 <option value="fasta_renamed">A FASTA file with the original query sequence, but with new names</option>
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234 <option value="log">Log file</option>
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235 </param>
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236 </when>
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237 <when value="merge">
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238 <param name="assembly_fasta" type="data" format="fasta" label="Assembly FASTA file"/>
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239 <param name="scaffold_files" type="data" format="agp" multiple="true" optional="true" label="Scaffold AGP files"/>
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240 <section name="merging_options" title="Merging options">
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241 <param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave unplaced"/>
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242 <param argument="-l" type="integer" min="0" value="100000" label="Minimum assembly sequence length"
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243 help="Assembly sequences shorter than -l will also be left unplaced."/>
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244 <param argument="-e" type="float" min="0" value="0" label="Minimum edge weight"
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245 help="The edges in the merging graph represent scaffolding adjacencies. If an AGP file supports a particular adjacency,
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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246 its weight is added to the edge weight. Any edges with a weight lower than the minimum edge weigth will be removed from the graph"/>
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247 <param name="function_merging" type="select" label="Function for merging gap lengths"
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248 help="Scaffold gaps can differ between input AGP files. For example, a Hi-C derived AGP file might place 100 bp gaps between sequences
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249 while a reference-guided AGP file might infer gap sizes based on a reference genome. Use this parameter to specify how gap sizes
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250 should be computed from the supporting AGP files (--gap-func)">
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251 <option value="min" selected="true">Min</option>
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252 <option value="max">Max</option>
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253 <option value="mean">Mean</option>
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254 </param>
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255 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
256 <section name="hic_options" title="HI-C options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
257 <param argument="-b" type="data" format="bam" optional="true" label="Hi-C alignments" help="Sorted by read name"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
258 <param argument="-r" type="text" value="" optional="true" label="Restriction enzymes/sites or 'DNase'" help="List of restrction enzimes/sites or 'DNase', separated by comma. E.g. GATC,GACC">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
259 <sanitizer invalid_char="">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
260 <valid initial="string.letters,string.digits">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
261 <add value="," />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
262 <add value="[" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
263 <add value="]" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
264 </valid>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
265 </sanitizer>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
266 <validator type="regex">[0-9a-zA-Z,\]\[]+</validator>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
267 </param>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
268 <param argument="-p" type="float" min="0" max="1" value="1" optional="true" label="Portion of the sequence termini to consider for links"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
269 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
270 </when>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
271 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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diff changeset
272 </inputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
273 <outputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
274 <!--Correct mode outputs-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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diff changeset
275 <data format="paf" name="correct_paf" from_work_dir="ragtag.correct.asm.paf" label="${tool.name} on ${on_string}: PAF">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
276 <filter>mode_conditional["mode_option"] == "correct" and "paf" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
277 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
278 <data format="agp" name="correct_agp" from_work_dir="ragtag.correct.agp" label="${tool.name} on ${on_string}: AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
279 <filter>mode_conditional["mode_option"] == "correct" and "agp" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
280 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
281 <data format="fasta" name="correct_fasta" from_work_dir="ragtag.correct.fasta" label="${tool.name} on ${on_string}: FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
282 <filter>mode_conditional["mode_option"] == "correct" and "fasta" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
283 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
284 <data format="txt" name="correct_log" from_work_dir="ragtag.correct.asm.paf.log" label="${tool.name} on ${on_string}: log">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
285 <filter>mode_conditional["mode_option"] == "correct" and "log" in mode_conditional["output_correct"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
286 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
287 <!--Scaffold mode outputs-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
288 <data format="paf" name="scaffold_paf" from_work_dir="ragtag.scaffold.asm.paf" label="${tool.name} on ${on_string}: PAF">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
289 <filter>mode_conditional["mode_option"] == "scaffold" and "paf" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
290 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
291 <data format="agp" name="scaffold_agp" from_work_dir="ragtag.scaffold.agp" label="${tool.name} on ${on_string}: AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
292 <filter>mode_conditional["mode_option"] == "scaffold" and "agp" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
293 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
294 <data format="fasta" name="scaffold_fasta" from_work_dir="ragtag.scaffold.fasta" label="${tool.name} on ${on_string}: FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
295 <filter>mode_conditional["mode_option"] == "scaffold" and "fasta" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
296 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
297 <data format="txt" name="scaffold_log" from_work_dir="ragtag.scaffold.asm.paf.log" label="${tool.name} on ${on_string}: log">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
298 <filter>mode_conditional["mode_option"] == "scaffold" and "log" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
299 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
300 <data format="tabular" name="scaffold_stats" from_work_dir="ragtag.scaffold.stats" label="${tool.name} on ${on_string}: stats">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
301 <filter>mode_conditional["mode_option"] == "scaffold" and "stats" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
302 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
303 <data format="tabular" name="scaffold_confidence" from_work_dir="ragtag.scaffold.confidence.txt" label="${tool.name} on ${on_string}: confidence">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
304 <filter>mode_conditional["mode_option"] == "scaffold" and "confidence" in mode_conditional["output_scaffold"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
305 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
306 <!--Patch mode outputs-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
307 <data format="agp" name="patch_agp" from_work_dir="ragtag.patch.agp" label="${tool.name} on ${on_string}: final AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
308 <filter>mode_conditional["mode_option"] == "patch" and "final_agp" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
309 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
310 <data format="paf" name="patch_paf" from_work_dir="ragtag.patch.asm.paf" label="${tool.name} on ${on_string}: final PAF">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
311 <filter>mode_conditional["mode_option"] == "patch" and "assembly_file" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
312 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
313 <data format="txt" name="patch_log" from_work_dir="ragtag.patch.log" label="${tool.name} on ${on_string}: log">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
314 <filter>mode_conditional["mode_option"] == "patch" and "log" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
315 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
316 <data format="fasta" name="patch_comps_fasta" from_work_dir="ragtag.patch.comps.fasta" label="${tool.name} on ${on_string}: components FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
317 <filter>mode_conditional["mode_option"] == "patch" and "split_assembly" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
318 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
319 <data format="agp" name="patch_ctg_agp" from_work_dir="ragtag.patch.ctg.agp" label="${tool.name} on ${on_string}: contigs AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
320 <filter>mode_conditional["mode_option"] == "patch" and "split_description" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
321 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
322 <data format="fasta" name="patch_ctg_fasta" from_work_dir="ragtag.patch.ctg.fasta" label="${tool.name} on ${on_string}: contigs FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
323 <filter>mode_conditional["mode_option"] == "patch" and "target_gaps" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
324 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
325 <data format="fasta" name="patch_fasta" from_work_dir="ragtag.patch.fasta" label="${tool.name} on ${on_string}: final FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
326 <filter>mode_conditional["mode_option"] == "patch" and "final_fasta" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
327 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
328 <data format="agp" name="patch_rename_agp" from_work_dir="ragtag.patch.rename.agp" label="${tool.name} on ${on_string}: renamed AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
329 <filter>mode_conditional["mode_option"] == "patch" and "agp_renamed" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
330 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
331 <data format="fasta" name="patch_rename_fasta" from_work_dir="ragtag.patch.rename.fasta" label="${tool.name} on ${on_string}: renamed FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
332 <filter>mode_conditional["mode_option"] == "patch" and "fasta_renamed" in mode_conditional["output_patch"]</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
333 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
334 <!-- Merge mode outputs-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
335 <data format="agp" name="merge_agp" from_work_dir="ragtag.merge.agp" label="${tool.name} on ${on_string}: merged AGP">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
336 <filter>mode_conditional["mode_option"] == "merge"</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
337 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
338 <data format="fasta" name="merge_fasta" from_work_dir="ragtag.merge.fasta" label="${tool.name} on ${on_string}: merged FASTA">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
339 <filter>mode_conditional["mode_option"] == "merge"</filter>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
340 </data>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
341 </outputs>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
342 <tests>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
343 <test expect_num_outputs="4">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
344 <!--Test 01 correct mode minimap2-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
345 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
346 <param name="mode_option" value="correct"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
347 <param name="reference" value="genome.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
348 <param name="query" value="contigs.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
349 <param name="output_correct" value="fasta,agp,paf,log"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
350 <section name="advanced_options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
351 <param name="e" value="reference_headers_skip.txt"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
352 <param name="j" value="query_headers_skip.txt"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
353 <param name="f" value="1000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
354 <conditional name="mapping_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
355 <param name="mapping_option" value="minimap2"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
356 <param name="mm2_params" value="asm5"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
357 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
358 <param name="remove_small" value="false"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
359 <param name="q" value="10"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
360 <param name="d" value="100000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
361 <param name="b" value="5000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
362 <param name="missasembly_break" value="--inter"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
363 <param name="gff" value="annotation.gff"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
364 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
365 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
366 <output name="correct_paf" file="correct_paf_01.paf" ftype="paf"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
367 <output name="correct_agp" file="correct_agp_01.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
368 <output name="correct_fasta" file="correct_fasta_01.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
369 <output name="correct_log" file="correct_log_01.txt" ftype="txt" lines_diff="20"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
370 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
371 <!--Test 02 correct mode nucmer-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
372 <test expect_num_outputs="2">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
373 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
374 <param name="mode_option" value="correct"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
375 <param name="reference" value="genome.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
376 <param name="query" value="contigs.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
377 <param name="output_correct" value="fasta,agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
378 <section name="advanced_options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
379 <param name="f" value="1000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
380 <conditional name="mapping_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
381 <param name="mapping_option" value="nucmer"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
382 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
383 <param name="remove_small" value="true"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
384 <param name="q" value="10"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
385 <param name="d" value="100000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
386 <param name="b" value="5000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
387 <param name="missasembly_break" value="--inter"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
388 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
389 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
390 <output name="correct_fasta" file="correct_fasta_02.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
391 <output name="correct_agp" file="correct_agp_02.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
392
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
393 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
394 <!--Test 03 scaffold mode-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
395 <test expect_num_outputs="6">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
396 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
397 <param name="mode_option" value="scaffold"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
398 <param name="reference" value="genome.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
399 <param name="query" value="contigs.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
400 <param name="output_scaffold" value="fasta,agp,paf,confidence,log,stats"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
401 <section name="advanced_options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
402 <param name="f" value="1000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
403 <param name="remove_small" value="true"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
404 <param name="q" value="10"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
405 <param name="d" value="100000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
406 <param name="i" value="0.2"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
407 <param name="a" value="0"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
408 <param name="s" value="0"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
409 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
410 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
411 <output name="scaffold_paf" file="scaffold_paf_03.paf" ftype="paf"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
412 <output name="scaffold_agp" file="scaffold_apg.03.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
413 <output name="scaffold_fasta" file="scaffold_fasta_03.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
414 <output name="scaffold_log" file="scaffold_log_03.txt" ftype="txt" lines_diff="20"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
415 <output name="scaffold_stats" file="scaffold_stats_03.tabular" ftype="tabular"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
416 <output name="scaffold_confidence" file="scaffold_confidence_03.tabular" ftype="tabular"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
417 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
418 <!--Test 04 patch mode-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
419 <test expect_num_outputs="9">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
420 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
421 <param name="mode_option" value="patch"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
422 <param name="reference" value="genome.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
423 <param name="query" value="contigs.fna"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
424 <param name="output_patch" value="final_fasta,final_agp,assembly_file,split_assembly,split_description,target_gaps,agp_renamed,fasta_renamed,log"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
425 <section name="advanced_options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
426 <param name="s" value="50000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
427 <param name="i" value="0.05"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
428 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
429 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
430 <output name="patch_agp" file="patch_agp_04.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
431 <output name="patch_paf" file="patch_paf_04.paf" ftype="paf"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
432 <output name="patch_log" file="patch_log_04.txt" ftype="txt" lines_diff="20"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
433 <output name="patch_comps_fasta" ftype="fasta">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
434 <assert_contents>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
435 <has_size value="603691" delta="100" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
436 </assert_contents>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
437 </output>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
438 <output name="patch_ctg_fasta" file="patch_ctg_fasta_04.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
439 <output name="patch_ctg_agp" file="patch_ctg_fasta_04.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
440 <output name="patch_fasta" file="patch_fasta_04.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
441 <output name="patch_rename_agp" file="patch_rename_agp.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
442 <output name="patch_rename_fasta" file="patch_rename_fasta.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
443 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
444 <test expect_num_outputs="2">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
445 <!-- Test 05 merge mode-->
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
446 <conditional name="mode_conditional">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
447 <param name="mode_option" value="merge"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
448 <param name="assembly_fasta" value="correct_fasta_01.fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
449 <param name="scaffold_files" value="correct_agp_01.agp,correct_agp_02.agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
450 <section name="merging_options">
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
451 <param name="l" value="100000"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
452 <param name="e" value="0"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
453 <param name="function_merging" value="min"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
454 </section>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
455 </conditional>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
456 <output name="merge_agp" file="merge_agp_05.agp" ftype="agp"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
457 <output name="merge_fasta" file="merge_fasta_05.fasta" ftype="fasta"/>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
458 </test>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
459 </tests>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
460 <help><![CDATA[
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
461 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
462
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
463 **Purpose**
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
464
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
465 RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
466
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
467 - Homology-based misassembly correction
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
468 - Homology-based assembly scaffolding and patching
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
469 - Scaffold merging
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
470
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
471 ----
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
472
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
473 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
474
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
475 **Correct mode**
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
476
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
477 RagTag offers a correction module that uses a reference genome to identify and correct potential misassemblies in a query assembly.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
478 RagTag also provides the option to verify putative misassemblies by aligning reads (from the same genotype) to the query assembly
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
479 and observing read coverage near misassembly break points. In all cases, sequence is never added or subtracted. Query sequences
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
480 are only broken at points of putative misassembly.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
481
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
482 *Misassemblies vs true variation*
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
483
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
484 Reference-guided misassembly signatures are sometimes caused by true biological structural variation if the reference and query assemblies
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
485 represent distinct genotypes (or haplotypes). The read validation feature should help to avoid some of these misassembly false positives,
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
486 and the validation sensitivity can be tuned with command line parameters. However, it is ultimately up to the discretion of the user to decide
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
487 if misassembly correction is appropriate. One should validate all RagTag results with independent data (usually physical, optical, or genetic
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
488 maps), when possible.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
489
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
490 ----
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
491
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
492 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
493
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
494 **Scaffold mode**
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
495
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
496 Scaffolding is the process of ordering and orienting draft assembly (query) sequences into longer sequences. Gaps (stretches of "N" characters)
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
497 are placed between adjacent query sequences to indicate the presence of unknown sequence. RagTag uses whole-genome alignments to a reference
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
498 assembly to scaffold query sequences. RagTag does not alter input query sequence in any way and only orders and orients sequences, joining them with gaps.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
499
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
500 ----
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
501
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
502 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
503
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
504 **Patch mode**
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
505
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
506 This mode uses one genome assembly to *patch* another genome assembly. We define two types of patches:
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
507
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
parents:
diff changeset
508 - Fills are patches that fill assembly gaps. This process is like traditional gap-filling, though it uses an assembly instead of WGS sequencing reads.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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509 - Joins are patches that join distinct contigs. This is essentially scaffolding and gap-filling in a single step.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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510
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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511 ----
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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512
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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513 .. class:: infomark
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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514
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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515 **Merge mode**
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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516
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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517 Draft genome assemblies are often scaffolded multiple times using different approaches. For example, one might scaffold an assembly using different genome
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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518 maps (physical, linkage, Hi-C, etc.), different methods, or different method parameters. RagTag merge is a tool to merge and reconcile different scaffoldings
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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519 of the same assembly. In this way, one can leverage the advantages of multiple techniques to synergistically improve scaffolding.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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520
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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521 Most tools write scaffolding results in the AGP file format, which encodes adjacency and gap information in a plain text file. To run RagTag merge,
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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522 one must supply the assembly in FASTA format and at least two AGP files that define a scaffolding of the assembly. Each AGP file can optionally be
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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523 assigned a weight, allowing users to assign the relative influence of each AGP on the final result.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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524
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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525 If available, users can supply Hi-C alignments to the draft assembly to resolve conflicts in the merging graph. In this scenario, the input AGP
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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526 files are used to build the initial graph, but then Hi-C alignments are used to re-weight the graph before computing the scaffolding solution.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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527
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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528
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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529 **List of accepted restriction enzymes**
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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530
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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531 List of all accepted restriction enzymes and their restriction sites:
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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532
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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533 - HindIII: AAGCTT
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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534 - Sau3AI: GATC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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535 - MboI: GATC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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536 - DpnII: GATC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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537 - HinfI: GA[ATCG]TC
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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538 - DdeI: CT[ATCG]AG
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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539 - MseI: TTAA
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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540
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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541 For RagTag, use a comma separated list of enzymes or sites (or a mix). For example:
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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542
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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diff changeset
543 - Arima Hi-C v1.0: *Sau3AI,HinfI* or *GATC,GA[ATCG]TC*
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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diff changeset
544 - Arima Hi-C v2.0: *Sau3AI,HinfI,DdeI,MseI* or *GATC,GA[ATCG]TC,CT[ATCG]AG,TTAA*
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
iuc
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545
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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546 Note that for restriction sites, wildcards are represented with python regex syntax, not IUPAC ambiguity codes. e.g. '[ATCG]' instead of 'N'.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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547
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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548 Restriction enzymes are not necessarily the enzyme used for sample prep. Each is only a enzyme that cuts at the corresponding restriction site.
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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549
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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550 ]]> </help>
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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551 <expand macro="citations" />
a04e64efa43a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 4c4b2a548b4ce46da88810992459b3ac8581d035"
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552 </tool>