Mercurial > repos > iuc > mummer_dnadiff

annotate dnadiff.xml @ 7:25258d5914ed draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 980f7472892817697208792e4443fa579625b696
author iuc
date Tue, 04 Feb 2025 09:16:45 +0000
parents 1df1c3eb857f
children
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1dba532ffe07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
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1 <tool id="mummer_dnadiff" name="DNAdiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Evaluate similarities/differences between two sequences</description>
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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1dba532ffe07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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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 &&
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11 ln -s $query_sequence query.fa &&
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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12 dnadiff
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13 'reference.fa' 'query.fa'
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14
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
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19 <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" help="FastA or multi-FastA" />
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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20 <param name="report_only" type="select" label="Output only the general report file?" help="Select no to output all output files">
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21 <option value="yes">YES</option>
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22 <option value="no">NO</option>
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23 </param>
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24 </inputs>
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25 <outputs>
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26 <data name="report" format="txt" from_work_dir="out.report" label="${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 ${on_string}: delta">
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28 <filter> report_only == 'no'</filter>
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29 </data>
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30 <data name="delta1" format="tabular" from_work_dir="out.1delta" label="${tool.name} on ${on_string}: 1delta" >
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31 <filter> report_only == 'no' </filter>
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32 </data>
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33 <data name="mdelta" format="tabular" from_work_dir="out.mdelta" label="${tool.name} on ${on_string}: mdelta" >
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34 <filter> report_only == 'no' </filter>
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35 </data>
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36 <data name="coords1" format="tabular" from_work_dir="out.1coords" label="${tool.name} on ${on_string}: 1coords" >
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37 <filter> report_only == 'no' </filter>
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38 <actions>
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39 <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" />
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40 </actions>
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41 </data>
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42 <data name="mcoords" format="tabular" from_work_dir="out.mcoords" label="${tool.name} on ${on_string}: mcoords" >
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43 <filter> report_only == 'no' </filter>
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44 <actions>
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45 <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" />
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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46 </actions>
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47 </data>
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48 <data name="snps" format="tabular" from_work_dir="out.snps" label="${tool.name} on ${on_string}: snps" >
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49 <filter> report_only == 'no' </filter>
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50 <actions>
5
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51 <action name="column_names" type="metadata" default="[P1], [REF SUB], [QUERY SUB], [P2], [BUFF], [DIST], [LEN REF], [LEN QUERY], [REF FRAME], [QUERY FRAME], [REF TAG], [QUERY TAG]" />
0
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52 </actions>
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53 </data>
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54 <data name="rdiff" format="tabular" from_work_dir="out.rdiff" label="${tool.name} on ${on_string}: rdiff" >
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55 <filter> report_only == 'no' </filter>
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56 <actions>
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57 <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length" />
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58 </actions>
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59 </data>
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60 <data name="qdiff" format="tabular" from_work_dir="out.qdiff" label="${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 expect_num_outputs="9">
0
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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="report_only" value="no" />
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72 <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/>
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73 <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/>
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74 <output name="delta1" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/>
0
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75 <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/>
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76 <output name="coords1" ftype="tabular" compare="diff" value="1coords.txt"/>
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77 <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/>
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78 <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/>
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79 <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/>
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80 <output name="qdiff" ftype="tabular" compare="diff" value="qdiff.txt"/>
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84 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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85
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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86 **Output files:**
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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87 * report: Summary of alignments, differences and SNPs
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88 * delta: Standard nucmer alignment output
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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89 * 1delta: 1-to-1 alignment from delta-filter -1
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90 * mdelta: M-to-M alignment from delta-filter -m
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91 * 1coords: 1-to-1 coordinates from show-coords -THrcl .1delta
e2971ee76a9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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92 * mcoords: M-to-M coordinates from show-coords -THrcl .mdelta
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93 * snps: SNPs from show-snps -rlTHC .1delta
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94 * rdiff: Classified ref breakpoints from show-diff -rH .mdelta
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95 * qdiff: Classified qry breakpoints from show-diff -qH .mdelta
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96 ]]></help>
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97 <expand macro="citation" />
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98 </tool>