Mercurial > repos > iuc > mummer_dnadiff

comparison dnadiff.xml @ 4:1dba532ffe07 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
author iuc
date Sat, 27 Nov 2021 09:52:11 +0000
parents c78dffd707db
children 1df1c3eb857f
comparison
equal deleted inserted replaced
3:c78dffd707db 4:1dba532ffe07
1 <tool id="mummer_dnadiff" name="DNAdiff" version="@MUMMER_VERSION@@WRAPPER_VERSION@"> 1 <tool id="mummer_dnadiff" name="DNAdiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Evaluate similarities/differences between two sequences</description> 2 <description>Evaluate similarities/differences between two sequences</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 ln -s $reference_sequence reference.fa && 10 ln -s $reference_sequence reference.fa &&
11 ln -s $query_sequence query.fa && 11 ln -s $query_sequence query.fa &&
25 <outputs> 25 <outputs>
26 <data name="report" format="txt" from_work_dir="out.report" label="${tool.name} on ${on_string}: report" /> 26 <data name="report" format="txt" from_work_dir="out.report" label="${tool.name} on ${on_string}: report" />
27 <data name="delta" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta"> 27 <data name="delta" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta">
28 <filter> report_only == 'no'</filter> 28 <filter> report_only == 'no'</filter>
29 </data> 29 </data>
30 <data name="1delta" format="tabular" from_work_dir="out.1delta" label="${tool.name} on ${on_string}: 1delta" > 30 <data name="delta1" format="tabular" from_work_dir="out.1delta" label="${tool.name} on ${on_string}: 1delta" >
31 <filter> report_only == 'no' </filter> 31 <filter> report_only == 'no' </filter>
32 </data> 32 </data>
33 <data name="mdelta" format="tabular" from_work_dir="out.mdelta" label="${tool.name} on ${on_string}: mdelta" > 33 <data name="mdelta" format="tabular" from_work_dir="out.mdelta" label="${tool.name} on ${on_string}: mdelta" >
34 <filter> report_only == 'no' </filter> 34 <filter> report_only == 'no' </filter>
35 </data> 35 </data>
36 <data name="1coords" format="tabular" from_work_dir="out.1coords" label="${tool.name} on ${on_string}: 1coords" > 36 <data name="coords1" format="tabular" from_work_dir="out.1coords" label="${tool.name} on ${on_string}: 1coords" >
37 <filter> report_only == 'no' </filter> 37 <filter> report_only == 'no' </filter>
38 <actions> 38 <actions>
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]" /> 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]" />
40 </actions> 40 </actions>
41 </data> 41 </data>
66 </outputs> 66 </outputs>
67 <tests> 67 <tests>
68 <test> 68 <test>
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="input_type" value="sequence" />
72 <param name="report_only" value="no" /> 71 <param name="report_only" value="no" />
73 <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"/>
74 <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"/>
75 <output name="1delta" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/> 74 <output name="delta1" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/>
76 <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/> 75 <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/>
77 <output name="1coords" ftype="tabular" compare="diff" value="1coords.txt"/> 76 <output name="coords1" ftype="tabular" compare="diff" value="1coords.txt"/>
78 <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/> 77 <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/>
79 <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/> 78 <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/>
80 <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/> 79 <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/>
81 <output name="qdiff" ftype="tabular" compare="diff" value="qdiff.txt"/> 80 <output name="qdiff" ftype="tabular" compare="diff" value="qdiff.txt"/>
82 </test> 81 </test>