Mercurial > repos > drosofff > msp_cap3

comparison cap3.xml @ 1:ddb463fdf57e draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_cap3 commit 70fadb7e8972b1db550d0e067584930ce1ec8673
author drosofff
date Sat, 31 Oct 2015 19:15:56 -0400
parents e2ae46b16b3b
children
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0:e2ae46b16b3b 1:ddb463fdf57e
1 <tool id="cap3" name="cap3" version="1.1.0"> 1 <tool id="cap3" name="cap3" version="1.2.0">
2 <description>Sequence Assembly tool</description> 2 <description>Sequence Assembly tool</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3">cap3</requirement> 4 <requirement type="package" version="3">cap3</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 cap3 "$inputSequences" > "$cap3stdout"; 7 cap3 "$inputSequences" -o $overlaplength -p $overlapidentity > "$cap3stdout";
8 mv "$inputSequences".cap.contigs $contigs; 8 mv "$inputSequences".cap.contigs $contigs;
9 mv "$inputSequences".cap.contigs.qual $contigsqual; 9 mv "$inputSequences".cap.contigs.qual $contigsqual;
10 mv "$inputSequences".cap.contigs.links $contigslink; 10 mv "$inputSequences".cap.contigs.links $contigslink;
11 mv "$inputSequences".cap.ace $ace; 11 mv "$inputSequences".cap.ace $ace;
12 mv "$inputSequences".cap.info $info; 12 mv "$inputSequences".cap.info $info;
15 15
16 </command> 16 </command>
17 17
18 <inputs> 18 <inputs>
19 <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" /> 19 <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" />
20 <param label="specify overlap length cutoff > 15 (40)" name="overlaplength" type="integer" size="3" value="40" help="-o option. must be > 15. 40 by default" />
21 <param label="specify overlap percent identity cutoff N > 65 (90)" name="overlapidentity" type="integer" size="3" value="90" help="-p option. must be > 65. 90 by default" />
20 </inputs> 22 </inputs>
21 23
22 <outputs> 24 <outputs>
23 <data format="fasta" name="contigsandsinglets" label="${tool.name} on ${on_string}: Contigs and singlets" from_work_dir="${inputSequences}.cap.contigs" /> 25 <data format="fasta" name="contigsandsinglets" label="${tool.name} on ${on_string}: Contigs and singlets" from_work_dir="${inputSequences}.cap.contigs" />
24 <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output" hidden="true"/> 26 <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output" hidden="true"/>
31 </outputs> 33 </outputs>
32 34
33 <tests> 35 <tests>
34 <test> 36 <test>
35 <param name="inputSequences" value="input.fa" ftype="fasta"/> 37 <param name="inputSequences" value="input.fa" ftype="fasta"/>
38 <param name="overlaplength" value="40" />
39 <param name="overlapidentity" value="90" />
36 <output name="contigsandsinglets" file="contigsandsinglets.fa"/> 40 <output name="contigsandsinglets" file="contigsandsinglets.fa"/>
37 <output name="cap3stdout" file="cap3stdout.txt"/> 41 <output name="cap3stdout" file="cap3stdout.txt"/>
38 <output name="contigs" file="contigs.fa"/> 42 <output name="contigs" file="contigs.fa"/>
39 <output name="contigsqual" file="contigsqual.txt"/> 43 <output name="contigsqual" file="contigsqual.txt"/>
40 <output name="contigslink" file="contigslink.txt"/> 44 <output name="contigslink" file="contigslink.txt"/>