Mercurial > repos > drosofff > msp_cap3

annotate cap3.xml @ 0:118834adb4ce draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Mon, 08 Jun 2015 07:55:57 -0400
parents
children 8fe1c798372d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
1 <tool id="cap3" name="cap3" version="1.0.1">
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
2 <description>Sequence Assembly tool</description>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
3 <requirements>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
4 <requirement type="package" version="3">cap3</requirement>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
5 </requirements>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
6 <command>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
7 cap3 "$inputSequences" > "$cap3stdout";
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
8 mv "$inputSequences".cap.contigs $contigs;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
9 mv "$inputSequences".cap.contigs.qual $contigsqual;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
10 mv "$inputSequences".cap.contigs.links $contigslink;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
11 mv "$inputSequences".cap.ace $ace;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
12 mv "$inputSequences".cap.info $info;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
13 mv "$inputSequences".cap.singlets $singlets;
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
14
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
15 </command>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
16
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
17 <inputs>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
18 <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" />
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
19 </inputs>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
20
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
21 <outputs>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
22 <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output"/>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
23 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" />
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
24 <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="True" />
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
25 <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="True" />
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
26 <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="True" />
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
27 <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="True" />
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
28 <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" hidden="True" />
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
29 </outputs>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
30
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
31 <help>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
32
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
33 </help>
118834adb4ce planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
34 </tool>