Mercurial > repos > rnateam > vienna_rna
changeset 1:b82c46050674 draft
Uploaded
author | rnateam |
---|---|
date | Wed, 04 Feb 2015 12:01:42 -0500 |
parents | 031ad3250176 |
children | 2c5a9f01ba08 |
files | rnacofold.xml rnafold.xml rnalfold.xml rnapaln.xml rnapdist.xml rnapkplex.xml rnaplex.xml rnaplfold.xml |
diffstat | 8 files changed, 22 insertions(+), 19 deletions(-) [+] |
line wrap: on
line diff
--- a/rnacofold.xml Tue Feb 03 04:59:51 2015 -0500 +++ b/rnacofold.xml Wed Feb 04 12:01:42 2015 -0500 @@ -53,13 +53,13 @@ </inputs> <outputs> <data format="txt" name="tabularFile"/> - <data format="txt" name="structure"> - <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" visible="true"/> - </data> - <data format="txt" name="dotplot"> + <collection name="sequence_outputs" type="list" label="rna_eps outputs"> + <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" /> + </collection> + <collection name="matrix_outputs" type="list" label="rna_eps outputs"> <filter>pf is True</filter> <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> - </data> + </collection> </outputs> <tests> </tests>
--- a/rnafold.xml Tue Feb 03 04:59:51 2015 -0500 +++ b/rnafold.xml Wed Feb 04 12:01:42 2015 -0500 @@ -68,13 +68,14 @@ </inputs> <outputs> <data format="tabular" name="tabular_file"/> - <data format="txt" name="structure"> - <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" visible="true"/> - </data> - <data format="txt" name="dotplot"> + <collection name="sequence_outputs" type="list" label="rna_eps outputs"> + <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" /> + </collection> + <collection name="matrix_outputs" type="list" label="rna_eps outputs"> <filter>measelect['pf'] is True</filter> <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> - </data> + </collection> + </outputs> <tests> </tests>
--- a/rnalfold.xml Tue Feb 03 04:59:51 2015 -0500 +++ b/rnalfold.xml Wed Feb 04 12:01:42 2015 -0500 @@ -33,7 +33,7 @@ ]]> </command> <inputs> - <param format="fasta" name="fasta_input" type="data" label="FASTA file"/> + <param format="fasta" name="fasta_input" type="data" label="FASTA file"/> <param name="span" type="integer" min="0" max="5000" value="150" label="base pair span" help="Maximal distance between two paired bases. (-L)"/> <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/> <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
--- a/rnapaln.xml Tue Feb 03 04:59:51 2015 -0500 +++ b/rnapaln.xml Wed Feb 04 12:01:42 2015 -0500 @@ -73,9 +73,9 @@ </inputs> <outputs> <data format="txt" name="output"/> - <data format="txt" name="dotplot"> + <collection name="matrix_outputs" type="list" label="rna_eps outputs"> <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> - </data> + </collection> </outputs> <tests> </tests>
--- a/rnapdist.xml Tue Feb 03 04:59:51 2015 -0500 +++ b/rnapdist.xml Wed Feb 04 12:01:42 2015 -0500 @@ -63,8 +63,9 @@ <outputs> <data format="txt" name="output"/> <data format="txt" name="dotplot"> + <collection name="matrix_outputs" type="list" label="rna_eps outputs"> <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> - </data> + </collection> </outputs> <tests> </tests>
--- a/rnapkplex.xml Tue Feb 03 04:59:51 2015 -0500 +++ b/rnapkplex.xml Wed Feb 04 12:01:42 2015 -0500 @@ -49,9 +49,9 @@ </inputs> <outputs> <data format="txt" name="output"/> - <data format="txt" name="dotplot"> - <discover_datasets pattern="(?P<designation>.+)\.ps" ext="eps" visible="true"/> - </data> + <collection name="matrix_outputs" type="list" label="rna_eps outputs"> + <discover_datasets pattern="(?P<designation>.+)\.ps" ext="eps" /> + </collection> </outputs> <tests> </tests>
--- a/rnaplex.xml Tue Feb 03 04:59:51 2015 -0500 +++ b/rnaplex.xml Wed Feb 04 12:01:42 2015 -0500 @@ -77,6 +77,7 @@ <param name="scaleAccessibility" size="8" type="float" value="1.0" label="scale all opening energy by a factor" help="--scale-accessibility"/> <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structures subject to constraints. Constraints have to be given in the input file" help="--constraint"/> + <conditional name="advancedOptions"> <param name="advancedSelector" type="select" label="advanced options"> <option value="basic">basic Options</option>
--- a/rnaplfold.xml Tue Feb 03 04:59:51 2015 -0500 +++ b/rnaplfold.xml Wed Feb 04 12:01:42 2015 -0500 @@ -72,9 +72,9 @@ </conditional> </inputs> <outputs> - <data format="txt" name="dotplot"> + <collection name="matrix_outputs" type="list" label="rna_eps outputs"> <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> - </data> + </collection> <data format="tar" name="outputf"/> </outputs> <tests>