Mercurial > repos > iuc > mummer_dnadiff

annotate dnadiff.xml @ 3:c78dffd707db draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:43:46 +0000
parents ea4257be5e04
children 1dba532ffe07
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ea4257be5e04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
iuc
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1 <tool id="mummer_dnadiff" name="DNAdiff" version="@MUMMER_VERSION@@WRAPPER_VERSION@">
0
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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2 <description>Evaluate similarities/differences between two sequences</description>
3
c78dffd707db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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3 <expand macro="bio_tools"/>
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e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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4 <macros>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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5 <import>macros.xml</import>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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6 </macros>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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7 <expand macro="requirements" />
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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8 <command detect_errors="exit_code">
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9 <![CDATA[
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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10 ln -s $reference_sequence reference.fa &&
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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11 ln -s $query_sequence query.fa &&
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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12 dnadiff
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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13 'reference.fa' 'query.fa'
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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14
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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15 ]]>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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16 </command>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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17 <inputs>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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18 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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19 <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" help="FastA or multi-FastA" />
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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20 <param name="report_only" type="select" label="Output only the general report file?" help="Select no to output all output files">
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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21 <option value="yes">YES</option>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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22 <option value="no">NO</option>
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23 </param>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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24 </inputs>
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25 <outputs>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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26 <data name="report" format="txt" from_work_dir="out.report" label="${tool.name} on ${on_string}: report" />
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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27 <data name="delta" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta">
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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28 <filter> report_only == 'no'</filter>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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29 </data>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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30 <data name="1delta" format="tabular" from_work_dir="out.1delta" label="${tool.name} on ${on_string}: 1delta" >
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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31 <filter> report_only == 'no' </filter>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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32 </data>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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33 <data name="mdelta" format="tabular" from_work_dir="out.mdelta" label="${tool.name} on ${on_string}: mdelta" >
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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34 <filter> report_only == 'no' </filter>
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35 </data>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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36 <data name="1coords" format="tabular" from_work_dir="out.1coords" label="${tool.name} on ${on_string}: 1coords" >
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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37 <filter> report_only == 'no' </filter>
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38 <actions>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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39 <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" />
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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40 </actions>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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41 </data>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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42 <data name="mcoords" format="tabular" from_work_dir="out.mcoords" label="${tool.name} on ${on_string}: mcoords" >
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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43 <filter> report_only == 'no' </filter>
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44 <actions>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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45 <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" />
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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46 </actions>
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47 </data>
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48 <data name="snps" format="tabular" from_work_dir="out.snps" label="${tool.name} on ${on_string}: snps" >
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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49 <filter> report_only == 'no' </filter>
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50 <actions>
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51 <action name="column_names" type="metadata" default="[P1], [REF SUB], [QUERY SUB], [P2], [BUFF], [DIST], [LEN REF], [LEN QUERY], [REF FRAME], [QUERY FRAME], [REF TAG], [QUERY TAG]" />
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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52 </actions>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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53 </data>
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54 <data name="rdiff" format="tabular" from_work_dir="out.rdiff" label="${tool.name} on ${on_string}: rdiff" >
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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55 <filter> report_only == 'no' </filter>
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56 <actions>
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57 <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length" />
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58 </actions>
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59 </data>
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60 <data name="qdiff" format="tabular" from_work_dir="out.qdiff" label="${tool.name} on ${on_string}: qdiff" >
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61 <filter> report_only == 'no' </filter>
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62 <actions>
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63 <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length" />
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64 </actions>
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65 </data>
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
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70 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta"/>
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71 <param name="input_type" value="sequence" />
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72 <param name="report_only" value="no" />
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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73 <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/>
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74 <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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75 <output name="1delta" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/>
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76 <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/>
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77 <output name="1coords" ftype="tabular" compare="diff" value="1coords.txt"/>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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78 <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/>
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79 <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/>
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80 <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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81 <output name="qdiff" ftype="tabular" compare="diff" value="qdiff.txt"/>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85 This script is a wrapper around nucmer that builds an alignment using default parameters, and runs many of nucmer's helper scripts to process the output and report alignment statistics, SNPs, breakpoints, etc. It is designed for evaluating the sequence and structural similarity of two highly similar sequence sets. E.g. comparing two different assemblies of the same organism, or comparing two strains of the same species.
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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86
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87 **Output files:**
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88 * report: Summary of alignments, differences and SNPs
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89 * delta: Standard nucmer alignment output
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90 * 1delta: 1-to-1 alignment from delta-filter -1
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91 * mdelta: M-to-M alignment from delta-filter -m
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92 * 1coords: 1-to-1 coordinates from show-coords -THrcl .1delta
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93 * mcoords: M-to-M coordinates from show-coords -THrcl .mdelta
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94 * snps: SNPs from show-snps -rlTHC .1delta
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95 * rdiff: Classified ref breakpoints from show-diff -rH .mdelta
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96 * qdiff: Classified qry breakpoints from show-diff -qH .mdelta
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97 ]]></help>
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98 <expand macro="citation" />
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99 </tool>