Mercurial > repos > padge > clipkit
changeset 4:770695339600 draft default tip
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
author | padge |
---|---|
date | Mon, 11 Apr 2022 13:08:12 +0000 (2022-04-11) |
parents | 34f21474cdea |
children | |
files | clipkit.xml |
diffstat | 1 files changed, 32 insertions(+), 6 deletions(-) [+] |
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--- a/clipkit.xml Fri Mar 25 17:35:03 2022 +0000 +++ b/clipkit.xml Mon Apr 11 13:08:12 2022 +0000 @@ -41,39 +41,65 @@ <param name="complement" type="boolean" truevalue="--complement" falsevalue="" checked="False" label="create complement of the trimmed alignment" /> </inputs> <outputs> - <data name="trimmed_output" format="fasta" label="Trimmed alignment."/> + <data name="trimmed_output" format="fasta" label="Trimmed alignment."> + <!-- <filter>out_format_selector == 'fasta'</filter> --> + <change_format> + <when input="out_format_selector" value="fasta" format="fasta" /> + <when input="out_format_selector" value="clustal" format="clustal" /> + <when input="out_format_selector" value="maf" format="maf" /> + <when input="out_format_selector" value="mauve" format="xmfa" /> + <when input="out_format_selector" value="stockholm" format="stockholm" /> + <when input="out_format_selector" value="phylip" format="phylip" /> + <when input="out_format_selector" value="phylip_sequential" format="phylip" /> + <when input="out_format_selector" value="phylip_relaxed" format="phylip" /> + </change_format> + </data> <data name="log_output" format="txt" label="Clipkit log."/> <data name="complement_output" format="fasta" label="Clipkit complement."> <filter>complement</filter> + <change_format> + <when input="out_format_selector" value="fasta" format="fasta" /> + <when input="out_format_selector" value="clustal" format="clustal" /> + <when input="out_format_selector" value="maf" format="maf" /> + <when input="out_format_selector" value="mauve" format="xmfa" /> + <when input="out_format_selector" value="stockholm" format="stockholm" /> + <when input="out_format_selector" value="phylip" format="phylip" /> + <when input="out_format_selector" value="phylip_sequential" format="phylip" /> + <when input="out_format_selector" value="phylip_relaxed" format="phylip" /> + </change_format> </data> </outputs> <tests> <test> <param name="input1" value="simple.fa"/> <param name="mode_selector" value="smart-gap" /> + <param name="out_format_selector" value="fasta" /> <param name="gaps" value="0.9" /> - <output name="trimmed_output" file="simple.fa.clipkit"/> + <output name="trimmed_output" file="simple.fa.clipkit" ftype="fasta"/> <output name="log_output" file="simple.fa.clipkit.log"/> </test> <test> <param name="input1" value="simple.fa"/> <param name="mode_selector" value="gappy" /> + <param name="out_format_selector" value="fasta" /> <param name="gaps" value="0.2" /> - <output name="trimmed_output" file="gappy.simple.fa.clipkit"/> + <output name="trimmed_output" file="gappy.simple.fa.clipkit" ftype="fasta"/> </test> <test> <param name="input1" value="simple.fa"/> <param name="mode_selector" value="gappy" /> + <param name="out_format_selector" value="fasta" /> <param name="gaps" value="0.2" /> - <output name="trimmed_output" file="gappy.simple.fa.clipkit"/> + <output name="trimmed_output" file="gappy.simple.fa.clipkit" ftype="fasta"/> <output name="log_output" file="gappy.simple.fa.clipkit.log"/> </test> <test> <param name="input1" value="simple.fa"/> <param name="mode_selector" value="kpi" /> <param name="complement" value="true" /> + <param name="out_format_selector" value="fasta" /> <param name="gaps" value="0.9" /> - <output name="trimmed_output" file="kpi.simple.fa.clipkit"/> + <output name="trimmed_output" file="kpi.simple.fa.clipkit" ftype="fasta"/> <output name="complement_output" file="kpi.simple.fa.clipkit.complement"/> </test> <test> @@ -81,7 +107,7 @@ <param name="mode_selector" value="kpi-gappy" /> <param name="out_format_selector" value="phylip_relaxed" /> <param name="gaps" value="0.7" /> - <output name="trimmed_output" file="of.gaps.simple.phylip_relaxed"/> + <output name="trimmed_output" file="of.gaps.simple.phylip_relaxed" ftype="phylip"/> <output name="log_output" file="of.gaps.simple.phylip_relaxed.log"/> </test> </tests>