Mercurial > repos > rnateam > rnashapes
changeset 1:2541c3e74dfa draft
Uploaded
| author | rnateam |
|---|---|
| date | Mon, 16 Feb 2015 13:57:02 -0500 |
| parents | 6d37d9c1e9bb |
| children | f33190f18ee6 |
| files | RNAShapes.xml test-data/rnashapes_input1.fa test-data/rnashapes_result1.txt |
| diffstat | 3 files changed, 44 insertions(+), 14 deletions(-) [+] |
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--- a/RNAShapes.xml Fri Feb 13 05:34:43 2015 -0500 +++ b/RNAShapes.xml Mon Feb 16 13:57:02 2015 -0500 @@ -42,16 +42,24 @@ <param name="param_num_samples" type="integer" value="1000" min="0" label="Number of Samples" help="(--numSamples) Sets the number of samples that are drawn to estimate shape probabilities."/> </macro> <macro name="macro_param_absolute_deviation"> - <param name="param_absolute_deviation" type="float" optional="True" label="Absolute Deviation" help="(--absoluteDeviation) This sets the energy range as an absolute value of the minimum free energy. Cannot be combined with --relativeDeviation."/> + <param name="param_absolute_deviation" type="float" optional="True" label="Absolute Deviation" help="(--absoluteDeviation) This sets the energy range as an absolute value of the minimum free energy. Cannot be combined with --relativeDeviation."> + <validator type="in_range" min="0"/> + </param> </macro> <macro name="macro_param_relative_deviation"> - <param name="param_relative_deviation" type="float" optional="True" label="Relative Deviation" help="(--relativeDeviation) This sets the energy range as percentage of the minimum free energy. Cannot be combined with --absoluteDeviation."/> + <param name="param_relative_deviation" type="float" optional="True" label="Relative Deviation" help="(--relativeDeviation) This sets the energy range as percentage of the minimum free energy. Cannot be combined with --absoluteDeviation."> + <validator type="in_range" min="0"/> + </param> </macro> <macro name="macro_param_window_size"> - <param name="param_window_size" type="integer" min="1" optional="True" label="Window Size" help="(--windowSize) Activates window mode and computes substrings of this size. See below for details."/> + <param name="param_window_size" type="integer" optional="True" label="Window Size" help="(--windowSize) Activates window mode and computes substrings of this size. See below for details."> + <validator type="in_range" min="1"/> + </param> </macro> <macro name="macro_param_window_increment"> - <param name="param_window_increment" type="integer" min="1" optional="True" label="Window Increment" help="(--windowIncrement) Increment Size. See below for details."/> + <param name="param_window_increment" type="integer" optional="True" label="Window Increment" help="(--windowIncrement) Increment Size. See below for details."> + <validator type="in_range" min="1"/> + </param> </macro> <macro name="macro_param_structure_probs"> <param name="param_structure_probs" type="boolean" truevalue="1" falsevalue="0" label="Structure Probabilities" help="(--structureProbs) In addition to free energy also the probability of structures is calculated."/> @@ -70,12 +78,11 @@ </stdio> <command> + <![CDATA[ RNAshapes --mode $param_cond_mode.param_mode - #if $param_cond_mode.param_mode == 'outside': - --dotplot $param_out_dotplot - #else: - > $param_out + #if $param_cond_mode.param_mode != 'outside': + > $param_out #end if #if $varExists('param_cond_mode.param_shape_level'): --shapeLevel $param_cond_mode.param_shape_level @@ -116,10 +123,11 @@ --grammar $param_grammar --allowLP $param_allow_lp $param_in + ]]> </command> <inputs> - <param name="param_in" type="data" format="fasta" optional="False" label="Input: fasta file" /> + <param name="param_in" type="data" format="fasta" optional="False" label="Input: Fasta file" /> <conditional name="param_cond_mode"> <param name="param_mode" type="select" label="Calculation Mode" help="(--mode) For a description of the different modes see below."> @@ -204,13 +212,22 @@ </inputs> <outputs> - <data name="param_out" format="text"> - <filter>(param_cond_mode['param_mode'] != 'outside')</filter> + <data name="param_out" format="txt"> + <filter>param_cond_mode['param_mode'] != "outside"</filter> </data> - <data name="param_out_dotplot" format="ps"> - <filter>(param_cond_mode['param_mode'] == 'outside')</filter> - </data> + <collection name="param_out_dotplot" type="list" label="rna_eps outputs"> + <filter>param_cond_mode['param_mode'] == "outside"</filter> + <discover_datasets pattern="(?P<designation>.*)\.ps" ext="rna_eps" visible="true"/> + </collection> </outputs> + <tests> + <test> + <param name="param_in" value="rnashapes_input1.fa"/> + <param name="param_mode" value="mfe"/> + <output name="param_out" file="rnashapes_result1.txt"/> + </test> + </tests> + <help> **What id does**
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnashapes_input1.fa Mon Feb 16 13:57:02 2015 -0500 @@ -0,0 +1,6 @@ +>Ovis_aries_chr25.trna231-GluCTC (36320672-36320744) Glu (CTC) 73 bp Sc: 35.06 +TCCTTGGCAGTCCAGCGGTTAGGGCTTCATGCTCTCCCTGTCAAAGGCCCAGGTTCAATC +CCTGGTCAAGGAG +>Ovis_aries_chr2.trna2838-GluCTC (38727567-38727495) Glu (CTC) 73 bp Sc: 37.98 +TCTCTGGTGGTCCAGTGGCTAAGACTCTGTGCTCTCAATACAGGGCACCCAGGCTCGATC +CCTGGTCAGGGAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnashapes_result1.txt Mon Feb 16 13:57:02 2015 -0500 @@ -0,0 +1,7 @@ +>Ovis_aries_chr25.trna231-GluCTC (36320672-36320744) Glu (CTC) 73 bp Sc: 35.06 + 1 TCCTTGGCAGTCCAGCGGTTAGGGCTTCATGCTCTCCCTGTCAAAGGCCCAGGTTCAATCCCTGGTCAAGGAG 73 +-23.80 ((((((........((((..(((((.....)))))..)))).......(((((.......))))).)))))). [[][]] + +>Ovis_aries_chr2.trna2838-GluCTC (38727567-38727495) Glu (CTC) 73 bp Sc: 37.98 + 1 TCTCTGGTGGTCCAGTGGCTAAGACTCTGTGCTCTCAATACAGGGCACCCAGGCTCGATCCCTGGTCAGGGAC 73 +-24.70 (((((((....((((.((....((.((((((((((......)))))))..))).))...))))))))))))). []