Mercurial > repos > iuc > mummer_dnadiff

comparison dnadiff.xml @ 5:1df1c3eb857f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit d3549bc73d5fdfdded1c3e63485f5eb98c479d52
author iuc
date Sat, 19 Oct 2024 20:56:55 +0000
parents 1dba532ffe07
children
comparison
equal deleted inserted replaced
4:1dba532ffe07 5:1df1c3eb857f
10 ln -s $reference_sequence reference.fa && 10 ln -s $reference_sequence reference.fa &&
11 ln -s $query_sequence query.fa && 11 ln -s $query_sequence query.fa &&
12 dnadiff 12 dnadiff
13 'reference.fa' 'query.fa' 13 'reference.fa' 'query.fa'
14 14
15 ]]> 15 ]]>
16 </command> 16 </command>
17 <inputs> 17 <inputs>
18 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" /> 18 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
19 <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" help="FastA or multi-FastA" /> 19 <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" help="FastA or multi-FastA" />
20 <param name="report_only" type="select" label="Output only the general report file?" help="Select no to output all output files"> 20 <param name="report_only" type="select" label="Output only the general report file?" help="Select no to output all output files">
46 </actions> 46 </actions>
47 </data> 47 </data>
48 <data name="snps" format="tabular" from_work_dir="out.snps" label="${tool.name} on ${on_string}: snps" > 48 <data name="snps" format="tabular" from_work_dir="out.snps" label="${tool.name} on ${on_string}: snps" >
49 <filter> report_only == 'no' </filter> 49 <filter> report_only == 'no' </filter>
50 <actions> 50 <actions>
51 <action name="column_names" type="metadata" default="[P1], [REF SUB], [QUERY SUB], [P2], [BUFF], [DIST], [LEN REF], [LEN QUERY], [REF FRAME], [QUERY FRAME], [REF TAG], [QUERY TAG]" /> 51 <action name="column_names" type="metadata" default="[P1], [REF SUB], [QUERY SUB], [P2], [BUFF], [DIST], [LEN REF], [LEN QUERY], [REF FRAME], [QUERY FRAME], [REF TAG], [QUERY TAG]" />
52 </actions> 52 </actions>
53 </data> 53 </data>
54 <data name="rdiff" format="tabular" from_work_dir="out.rdiff" label="${tool.name} on ${on_string}: rdiff" > 54 <data name="rdiff" format="tabular" from_work_dir="out.rdiff" label="${tool.name} on ${on_string}: rdiff" >
55 <filter> report_only == 'no' </filter> 55 <filter> report_only == 'no' </filter>
56 <actions> 56 <actions>
63 <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length" /> 63 <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length" />
64 </actions> 64 </actions>
65 </data> 65 </data>
66 </outputs> 66 </outputs>
67 <tests> 67 <tests>
68 <test> 68 <test expect_num_outputs="9">
69 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" /> 69 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
70 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta"/> 70 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta"/>
71 <param name="report_only" value="no" /> 71 <param name="report_only" value="no" />
72 <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/> 72 <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/>
73 <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/> 73 <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/>