Mercurial > repos > iuc > sfold
changeset 0:6cce721f568c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
| author | iuc |
|---|---|
| date | Wed, 27 Nov 2024 13:22:29 +0000 |
| parents | |
| children | |
| files | macros.xml sfold.xml test-data/cons.ct test-data/mfe.ct test-data/seq.fasta |
| diffstat | 5 files changed, 507 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 27 13:22:29 2024 +0000 @@ -0,0 +1,13 @@ +<macros> + <token name="@TOOL_VERSION@">2.2.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> + <xml name="requirements"> + <requirement type="package" version="2.2">sfold</requirement> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/nar/gkh449</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sfold.xml Wed Nov 27 13:22:29 2024 +0000 @@ -0,0 +1,335 @@ +<tool id="sfold" name="Sfold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Prediction of RNA secondary structures through structure ensemble sampling</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <expand macro="requirements"/> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if not $non_commercial_use + >&2 echo "this tool is only available for non commercial use"; + exit 1; + #end if + mkdir -p 'output' && + sfold '$fasta' + -a $a + #if $f: + -f '$f' + #end if + #if str($l) != '': + -l $l + #end if + #if $m: + -m '$m' + #end if + -w $w + -i $i + ]]></command> + <inputs> + <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> + <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> + </param> + <param argument="fasta" type="data" format="fasta" label="FASTA input"/> + <param argument="-a" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Run clustering on the sampled ensemble?"/> + <param argument="-f" type="data" format="ct" optional="true" label="Constrain data" help="Constraint syntax follows what is used in mfold 3.1"/> + <param argument="-l" type="integer" min="0" optional="true" label="Maximum distance between paired bases"/> + <param argument="-m" type="data" format="ct" optional="true" label="MFE structure" help="If provided, Sfold clustering module will determine the cluster to which this structure belongs."/> + <param argument="-w" type="integer" value="20" label="Length of antisense oligos"/> + <param argument="-i" type="select" label="Module"> + <option value="0">None</option> + <option value="1">Sirna</option> + <option value="2">Soligo</option> + <option value="3">Both</option> + </param> + <param name="output_selector" type="select" multiple="true" optional="true" display="checkboxes" label="Output options"> + <option value="ct" selected="true">Output ct files</option> + <option value="bp" selected="true">Output bp files</option> + <option value="clusters">Output cluster files</option> + </param> + </inputs> + <outputs> + <collection name="sfold_out" type="list" label="${tool.name} on ${on_string}: sfold log files"> + <discover_datasets pattern="(?P<name>.+)\.out$" format="txt" directory="output/"/> + </collection> + <collection name="sfold_bp" type="list" label="${tool.name} on ${on_string}: sfold bp files"> + <discover_datasets pattern="(?P<name>.+)\.bp$" format="txt" directory="output/"/> + <filter>'bp' in output_selector</filter> + </collection> + <collection name="sfold_ct" type="list" label="${tool.name} on ${on_string}: sfold ct files"> + <discover_datasets pattern="(?P<name>.+)\.ct$" format="ct" directory="output/"/> + <filter>'ct' in output_selector</filter> + </collection> + <collection name="sfold_cluster_out" type="list" label="${tool.name} on ${on_string}: sfold cluster log files"> + <discover_datasets pattern="(?P<name>.+)\.out$" format="txt" directory="output/clusters"/> + <discover_datasets pattern="(?P<name>.+)\.list$" format="txt" directory="output/clusters"/> + <filter>'clusters' in output_selector</filter> + </collection> + <collection name="sfold_cluster_bp" type="list" label="${tool.name} on ${on_string}: sfold cluster bp files"> + <discover_datasets pattern="(?P<name>.+)\.bp$" format="txt" directory="output/clusters"/> + <filter>'clusters' in output_selector and 'bp' in output_selector</filter> + </collection> + <collection name="sfold_cluster_ct" type="list" label="${tool.name} on ${on_string}: sfold cluster ct files"> + <discover_datasets pattern="(?P<name>.+)\.ct$" format="ct" directory="output/clusters"/> + <filter>'clusters' in output_selector and 'ct' in output_selector</filter> + </collection> + </outputs> + <tests> + <test expect_num_outputs="6"> + <param name="non_commercial_use" value="true"/> + <param name="fasta" value="seq.fasta"/> + <param name="a" value="true"/> + <param name="f" value="cons.ct"/> + <param name="l" value="30"/> + <param name="m" value="mfe.ct"/> + <param name="w" value="20"/> + <param name="i" value="1"/> + <param name="output_selector" value="ct,bp,clusters"/> + <output_collection name="sfold_out" type="list"> + <element name="10structure"> + <assert_contents> + <has_n_lines n="770"/> + <has_text text="Structure 1 -28.90 0.74863E-01"/> + </assert_contents> + </element> + <element name="10structure_2"> + <assert_contents> + <has_n_lines n="10"/> + </assert_contents> + </element> + <element name="bp.dist.from.ecentroid"> + <assert_contents> + <has_n_lines n="1001"/> + <has_text text="1 5"/> + </assert_contents> + </element> + <element name="bp"> + <assert_contents> + <has_text text="Structure 1"/> + </assert_contents> + </element> + <element name="bprob"> + <assert_contents> + <has_n_lines n="4"/> + <has_text text=".16225072123690604808E+01L"/> + </assert_contents> + </element> + <element name="cdf"> + <assert_contents> + <has_n_lines n="101"/> + </assert_contents> + </element> + <element name="fe"> + <assert_contents> + <has_n_lines n="1000"/> + <has_text text="1 -28.70"/> + </assert_contents> + </element> + <element name="fe_init"> + <assert_contents> + <has_n_lines n="1002"/> + <has_text text="Ensemble free energy (based on initial energies):-RT ln(U)= -28.297589224477537 "/> + </assert_contents> + </element> + <element name="loopr"> + <assert_contents> + <has_n_lines n="76"/> + </assert_contents> + </element> + <element name="pdf"> + <assert_contents> + <has_n_lines n="21"/> + </assert_contents> + </element> + <element name="sample"> + <assert_contents> + <has_n_lines n="1"/> + <has_text text="Structure data in BP format removed to"/> + </assert_contents> + </element> + <element name="sample_1000"> + <assert_contents> + <has_text text="(i j k): helix formed by base pairs i-j, (i+1)-(j-1),...,(i+k-1)-(j-k+1)"/> + </assert_contents> + </element> + <element name="sclass"> + <assert_contents> + <has_text text="Sequence length = 76"/> + </assert_contents> + </element> + <element name="sfold"> + <assert_contents> + <has_n_lines n="42"/> + <has_text text="1 G"/> + </assert_contents> + </element> + <element name="smfe"> + <assert_contents> + <has_n_lines n="2"/> + <has_text text="Minimum free energy in the sample (SMFE)= -28.90 kcal/mol"/> + </assert_contents> + </element> + <element name="sstrand"> + <assert_contents> + <has_n_lines n="76"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="sfold_bp" type="list"> + <element name="ecentroid"> + <assert_contents> + <has_text text="1 72"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="sfold_ct" type="list"> + <element name="ecentroid"> + <assert_contents> + <has_n_lines n="78"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="sfold_cluster_out" type="list"> + <element name="c01.2dhist"> + <assert_contents> + <has_text text="1"/> + </assert_contents> + </element> + <element name="c01.bp.dist.from.ccentroid"> + <assert_contents> + <has_text text="1"/> + </assert_contents> + </element> + <element name="c01.bp"> + <assert_contents> + <has_text text="Structure 1"/> + </assert_contents> + </element> + <element name="c01.fe"> + <assert_contents> + <has_text text=" 1"/> + </assert_contents> + </element> + <element name="c02.2dhist"> + <assert_contents> + <has_text text="72"/> + </assert_contents> + </element> + <element name="c02.bp.dist.from.ccentroid"> + <assert_contents> + <has_text text="1"/> + </assert_contents> + </element> + <element name="c02.bp"> + <assert_contents> + <has_text text="Structure 1"/> + </assert_contents> + </element> + <element name="c02.fe"> + <assert_contents> + <has_text text="10"/> + </assert_contents> + </element> + <element name="ch.index"> + <assert_contents> + <has_n_lines n="19"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="sfold_cluster_bp" type="list"> + <element name="c01.ccentroid"> + <assert_contents> + <has_text text="1 72"/> + </assert_contents> + </element> + <element name="c02.ccentroid"> + <assert_contents> + <has_text text="Structure 1"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="sfold_cluster_ct" type="list"> + <element name="c01.ccentroid"> + <assert_contents> + <has_n_lines n="78"/> + <has_text text="Length: 76"/> + </assert_contents> + </element> + <element name="c02.ccentroid"> + <assert_contents> + <has_n_lines n="78"/> + <has_text text="Length: 76"/> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="4"> + <param name="non_commercial_use" value="true"/> + <param name="fasta" value="seq.fasta"/> + <param name="a" value="true"/> + <param name="f" value="cons.ct"/> + <param name="l" value="30"/> + <param name="m" value="mfe.ct"/> + <param name="w" value="20"/> + <param name="i" value="1"/> + <param name="output_selector" value="bp,clusters"/> + <output_collection name="sfold_cluster_bp" type="list"> + <element name="c01.ccentroid"> + <assert_contents> + <has_text text="1 72"/> + </assert_contents> + </element> + <element name="c02.ccentroid"> + <assert_contents> + <has_text text="Structure 1"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="sfold_bp" type="list"> + <element name="ecentroid"> + <assert_contents> + <has_text text="1 72"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ +Sfold is a software package for statistical folding and rational design of nucleic acids. + +It provides tools for predicting RNA secondary structures, designing antisense oligonucleotides, and analyzing RNA folding patterns. Sfold is widely used in academic research for studying +RNA structure and function. + +Input Format + +----------- + +The program requires one input file of RNA sequence in FASTA format. + +Sfold options + +------------ + +The program can run based on the clustering on the sampled ensemble or not. +It can also predict the secondary structure based on the constraint and MFE structure files. +The sfold has two different modules: + +* SiRNA : Target accessibility prediction and RNA duplex thermodynamics for rational siRNA design +* Solig: Target accessibility prediction and rational design of antisense oligonucleotides and nucleic acid probes + +The program can be run based on the above-mentioned modules, both of them or none of them. + +Output Files + +------------ + +The Sfold program generates 4 different types of output files. sfold.out and sclass.out in your output log files, save the general messages from standard output/error from which you can know if your Sfold run was successful. Most of the other +files contain a header section that defines the formats and meanings of the data in the output. + +------------ + +Important: The program usage is restricted to non-commercial and academic research. + ]]> + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cons.ct Wed Nov 27 13:22:29 2024 +0000 @@ -0,0 +1,78 @@ +76 dG = -27.58 [Initially -28.90] test +1 G 0 2 72 1 +2 G 1 3 71 2 +3 G 2 4 70 3 +4 G 3 5 69 4 +5 C 4 6 68 5 +6 U 5 7 67 6 +7 A 6 8 66 7 +8 U 7 9 0 8 +9 A 8 10 0 9 +10 G 9 11 25 10 +11 C 10 12 24 11 +12 U 11 13 23 12 +13 C 12 14 22 13 +14 A 13 15 0 14 +15 G 14 16 0 15 +16 C 15 17 0 16 +17 U 16 18 0 17 +18 G 17 19 0 18 +19 G 18 20 0 19 +20 G 19 21 0 20 +21 A 20 22 0 21 +22 G 21 23 13 22 +23 A 22 24 12 23 +24 G 23 25 11 24 +25 C 24 26 10 25 +26 G 25 27 0 26 +27 C 26 28 43 27 +28 U 27 29 42 28 +29 U 28 30 41 29 +30 G 29 31 40 30 +31 C 30 32 39 31 +32 A 31 33 38 32 +33 U 32 34 37 33 +34 G 33 35 0 34 +35 G 34 36 0 35 +36 C 35 37 0 36 +37 A 36 38 33 37 +38 U 37 39 32 38 +39 G 38 40 31 39 +40 C 39 41 30 40 +41 A 40 42 29 41 +42 A 41 43 28 42 +43 G 42 44 27 43 +44 A 43 45 0 44 +45 G 44 46 0 45 +46 G 45 47 0 46 +47 U 46 48 0 47 +48 C 47 49 0 48 +49 A 48 50 65 49 +50 G 49 51 64 50 +51 C 50 52 63 51 +52 G 51 53 62 52 +53 G 52 54 61 53 +54 U 53 55 0 54 +55 U 54 56 0 55 +56 C 55 57 0 56 +57 G 56 58 0 57 +58 A 57 59 0 58 +59 U 58 60 0 59 +60 C 59 61 0 60 +61 C 60 62 53 61 +62 C 61 63 52 62 +63 G 62 64 51 63 +64 C 63 65 50 64 +65 U 64 66 49 65 +66 U 65 67 7 66 +67 A 66 68 6 67 +68 G 67 69 5 68 +69 C 68 70 4 69 +70 U 69 71 3 70 +71 C 70 72 2 71 +72 C 71 73 1 72 +73 A 72 74 0 73 +74 C 73 75 0 74 +75 C 74 76 0 75 +76 A 75 0 0 76 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mfe.ct Wed Nov 27 13:22:29 2024 +0000 @@ -0,0 +1,78 @@ +76 dG = -27.58 [Initially -28.90] test +1 G 0 2 72 1 +2 G 1 3 71 2 +3 G 2 4 70 3 +4 G 3 5 69 4 +5 C 4 6 68 5 +6 U 5 7 67 6 +7 A 6 8 66 7 +8 U 7 9 0 8 +9 A 8 10 0 9 +10 G 9 11 25 10 +11 C 10 12 24 11 +12 U 11 13 23 12 +13 C 12 14 22 13 +14 A 13 15 0 14 +15 G 14 16 0 15 +16 C 15 17 0 16 +17 U 16 18 0 17 +18 G 17 19 0 18 +19 G 18 20 0 19 +20 G 19 21 0 20 +21 A 20 22 0 21 +22 G 21 23 13 22 +23 A 22 24 12 23 +24 G 23 25 11 24 +25 C 24 26 10 25 +26 G 25 27 0 26 +27 C 26 28 43 27 +28 U 27 29 42 28 +29 U 28 30 41 29 +30 G 29 31 40 30 +31 C 30 32 39 31 +32 A 31 33 38 32 +33 U 32 34 37 33 +34 G 33 35 0 34 +35 G 34 36 0 35 +36 C 35 37 0 36 +37 A 36 38 33 37 +38 U 37 39 32 38 +39 G 38 40 31 39 +40 C 39 41 30 40 +41 A 40 42 29 41 +42 A 41 43 28 42 +43 G 42 44 27 43 +44 A 43 45 0 44 +45 G 44 46 0 45 +46 G 45 47 0 46 +47 U 46 48 0 47 +48 C 47 49 0 48 +49 A 48 50 65 49 +50 G 49 51 64 50 +51 C 50 52 63 51 +52 G 51 53 62 52 +53 G 52 54 61 53 +54 U 53 55 0 54 +55 U 54 56 0 55 +56 C 55 57 0 56 +57 G 56 58 0 57 +58 A 57 59 0 58 +59 U 58 60 0 59 +60 C 59 61 0 60 +61 C 60 62 53 61 +62 C 61 63 52 62 +63 G 62 64 51 63 +64 C 63 65 50 64 +65 U 64 66 49 65 +66 U 65 67 7 66 +67 A 66 68 6 67 +68 G 67 69 5 68 +69 C 68 70 4 69 +70 U 69 71 3 70 +71 C 70 72 2 71 +72 C 71 73 1 72 +73 A 72 74 0 73 +74 C 73 75 0 74 +75 C 74 76 0 75 +76 A 75 0 0 76 +