Mercurial > repos > drosofff > msp_cap3
comparison cap3.xml @ 1:ddb463fdf57e draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_cap3 commit 70fadb7e8972b1db550d0e067584930ce1ec8673
author | drosofff |
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date | Sat, 31 Oct 2015 19:15:56 -0400 |
parents | e2ae46b16b3b |
children |
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0:e2ae46b16b3b | 1:ddb463fdf57e |
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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"/> |