Mercurial > repos > drosofff > msp_cap3
changeset 0:118834adb4ce draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Mon, 08 Jun 2015 07:55:57 -0400 |
| parents | |
| children | 8fe1c798372d |
| files | cap3.xml tool_dependencies.xml |
| diffstat | 2 files changed, 40 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cap3.xml Mon Jun 08 07:55:57 2015 -0400 @@ -0,0 +1,34 @@ +<tool id="cap3" name="cap3" version="1.0.1"> +<description>Sequence Assembly tool</description> + <requirements> + <requirement type="package" version="3">cap3</requirement> + </requirements> +<command> +cap3 "$inputSequences" > "$cap3stdout"; + mv "$inputSequences".cap.contigs $contigs; + mv "$inputSequences".cap.contigs.qual $contigsqual; + mv "$inputSequences".cap.contigs.links $contigslink; + mv "$inputSequences".cap.ace $ace; + mv "$inputSequences".cap.info $info; + mv "$inputSequences".cap.singlets $singlets; + +</command> + + <inputs> + <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" /> + </inputs> + +<outputs> + <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output"/> + <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" /> + <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="True" /> + <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="True" /> + <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="True" /> + <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="True" /> + <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" hidden="True" /> +</outputs> + +<help> + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jun 08 07:55:57 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="cap3" version="3"> + <repository changeset_revision="a472ccd208e2" name="package_cap3_3" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>