Mercurial > repos > iuc > mummer_delta_filter
annotate delta-filter.xml @ 4:e8fdceffea4c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
| author | iuc |
|---|---|
| date | Mon, 18 Mar 2024 12:41:50 +0000 |
| parents | fbca557a4847 |
| children |
| rev | line source |
|---|---|
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fbca557a4847
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
iuc
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1 <tool id="mummer_delta_filter" name="Delta-Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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2 <description>Filters alignment (delta) file from nucmer</description> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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3 <macros> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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4 <import>macros.xml</import> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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5 </macros> |
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3
fbca557a4847
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
iuc
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6 <expand macro="bio_tools"/> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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7 <expand macro="requirements" /> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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8 <command detect_errors="exit_code"> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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9 <![CDATA[ |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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10 delta-filter |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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11 $alignment |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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12 -i '$min_identity' |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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13 -l '$min_length' |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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14 $overlap |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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15 -u '$min_uniqueness' |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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16 -o '$max_overlap' |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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17 '$delta' > '$output' |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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18 ]]> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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19 </command> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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20 <inputs> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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21 <param name="delta" type="data" format="tabular" label="Match file from nucmer" /> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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22 <param name="alignment" type="select" label="Alignment Strategy" > |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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23 <option value="-m">Use default [Many-to-many alignment allowing for rearrangements] (-m)</option> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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24 <option value="-1">1-to-1 alignment allowing for rearrangements (-1)</option> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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25 <option value="-g">1-to-1 global alignment not allowing rearrangements (-g)</option> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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26 </param> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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27 <param name="min_identity" type="float" argument="-i" value="0" min="0" max="100" label="Minimum Identity" help="Set the minimum alignment identity. (-i)" /> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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28 <param name="min_length" type="integer" argument="-l" value="0" label="Minumum Legnth" help="Set the minimum alignment length. (-l)" /> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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29 <param name="overlap" type="select" label="Overlaps" |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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30 help=" Maps each position of each query/reference to its best hit in the reference/query, allowing for reference/query overlaps." > |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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31 <option value="-q">Reference overlaps (-q)</option> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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32 <option value="-r">Query overlaps (-r)</option> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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33 </param> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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34 <param name="min_uniqueness" type="float" argument="-u" value="0" min="0" max="100" label="Minimum Alignment Uniqueness" |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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35 help="Set the minimum alignment uniqueness, i.e. percent of the alignment matching to unique reference AND query sequence. (-u)" /> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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36 <param name="max_overlap" type="float" argument="-o" value="100" min="0" max="100" label="Maximum Alignment Overlap" |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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37 help="Set the maximum alignment overlap for overlap options as a percent of the alignment length. (-o)" /> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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38 </inputs> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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39 <outputs> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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40 <data name="output" format="tabular" from_work_dir="delta-filter.txt"/> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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41 </outputs> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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42 <tests> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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43 <test> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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44 <param name="delta" ftype="tabular" value="nucmer.txt" /> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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45 <output name="output" ftype="tabular" compare="diff" lines_diff="2" value="delta-filter.txt" /> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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46 </test> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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47 </tests> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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48 <help><![CDATA[ |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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49 This program filters the alignment file produced by nucmer, leaving only the desired alignments. Its primary function is the LIS algorithm which calculates the longest increasing subset of alignments. This allows for the calculation of a global set of alignments (i.e. 1-to-1 and mutually consistent order) with the 1-1 global option or locally consistent with 1-1 with rearrangements or many-to-many alignment. Reference sequences can be mapped to query sequences with the reference option of the Overlaps parameter, or queries to references with the Query option. This allows the user to exclude chance and repeat induced alignments, leaving only the "best" alignments between the two data sets. Filtering can also be performed on length, identity, and uniqueness. |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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50 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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51 An important distinction between the alignment options is that 1-1 global requires the alignments to be mutually consistent in their order, while the other options are not required to be mutually consistent and therefore tolerate translocations, inversions, etc. |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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52 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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53 In general cases, the many-to-many option is the best choice, however 1-1 alignment allowing for rearrangements can be handy for applications such as SNP finding which require a 1-to-1 mapping. |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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54 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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55 Finally, for mapping query contigs, or sequencing reads, to a reference genome, use the query option for the Overlaps parameter. |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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56 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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57 **Options**:: |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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58 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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59 -m Many-to-many alignment allowing for rearrangements |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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60 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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61 -1 1-to-1 alignment allowing for rearrangements |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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62 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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63 -g 1-to-1 global alignment not allowing rearrangements |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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64 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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65 -i Set the minimum alignment identity [0, 100], default 0 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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66 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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67 -l Set the minimum alignment length, default 0 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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68 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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69 -q Maps each position of each query to its best hit in the reference, allowing for reference |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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70 overlaps |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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71 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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72 -r Maps each position of each reference to its best hit in the query, allowing for query overlaps |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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73 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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74 -u Set the minimum alignment uniqueness, i.e. percent of the alignment matching to unique reference |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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75 AND query sequence [0,100], default 0 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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76 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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77 -o Set the maximum alignment overlap for -r and -q options as a percent of the alignment length |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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78 [0, 100], default 100 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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79 |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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changeset
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80 ]]></help> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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81 <expand macro="citation" /> |
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502018997bae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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82 </tool> |