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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb |
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added:
macros.xml sfold.xml test-data/cons.ct test-data/mfe.ct test-data/seq.fasta |
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| diff -r 000000000000 -r 6cce721f568c macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 27 13:22:29 2024 +0000 |
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| @@ -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> |
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| diff -r 000000000000 -r 6cce721f568c sfold.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sfold.xml Wed Nov 27 13:22:29 2024 +0000 |
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| b'@@ -0,0 +1,335 @@\n+<tool id="sfold" name="Sfold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>Prediction of RNA secondary structures through structure ensemble sampling</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <expand macro="requirements"/>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if not $non_commercial_use\n+ >&2 echo "this tool is only available for non commercial use";\n+ exit 1;\n+ #end if\n+ mkdir -p \'output\' &&\n+ sfold \'$fasta\'\n+ -a $a\n+ #if $f: \n+ -f \'$f\'\n+ #end if\n+ #if str($l) != \'\':\n+ -l $l\n+ #end if\n+ #if $m: \n+ -m \'$m\'\n+ #end if\n+ -w $w\n+ -i $i\n+ ]]></command>\n+ <inputs>\n+ <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">\n+ <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>\n+ </param>\n+ <param argument="fasta" type="data" format="fasta" label="FASTA input"/>\n+ <param argument="-a" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Run clustering on the sampled ensemble?"/>\n+ <param argument="-f" type="data" format="ct" optional="true" label="Constrain data" help="Constraint syntax follows what is used in mfold 3.1"/>\n+ <param argument="-l" type="integer" min="0" optional="true" label="Maximum distance between paired bases"/>\n+ <param argument="-m" type="data" format="ct" optional="true" label="MFE structure" help="If provided, Sfold clustering module will determine the cluster to which this structure belongs."/>\n+ <param argument="-w" type="integer" value="20" label="Length of antisense oligos"/>\n+ <param argument="-i" type="select" label="Module">\n+ <option value="0">None</option>\n+ <option value="1">Sirna</option>\n+ <option value="2">Soligo</option>\n+ <option value="3">Both</option>\n+ </param>\n+ <param name="output_selector" type="select" multiple="true" optional="true" display="checkboxes" label="Output options">\n+ <option value="ct" selected="true">Output ct files</option>\n+ <option value="bp" selected="true">Output bp files</option>\n+ <option value="clusters">Output cluster files</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <collection name="sfold_out" type="list" label="${tool.name} on ${on_string}: sfold log files">\n+ <discover_datasets pattern="(?P<name>.+)\\.out$" format="txt" directory="output/"/>\n+ </collection>\n+ <collection name="sfold_bp" type="list" label="${tool.name} on ${on_string}: sfold bp files">\n+ <discover_datasets pattern="(?P<name>.+)\\.bp$" format="txt" directory="output/"/>\n+ <filter>\'bp\' in output_selector</filter>\n+ </collection>\n+ <collection name="sfold_ct" type="list" label="${tool.name} on ${on_string}: sfold ct files">\n+ <discover_datasets pattern="(?P<name>.+)\\.ct$" format="ct" directory="output/"/>\n+ <filter>\'ct\' in output_selector</filter>\n+ </collection>\n+ <collection name="sfold_cluster_out" type="list" label="${tool.name} on ${on_string}: sfold cluster log files">\n+ <discover_datasets pattern="(?P<name>.+)\\.out$" format="txt" directory="output/clusters"/>\n+ <discover_datasets pattern="(?P<name>.+)\\.list$" format="txt" directory="output/clusters"/>\n+ <filter>\'clusters\' in output_selector</filter>\n+ </collection>\n+ <collection name="sfold_cluster_bp" type="list" label='..b'\n+ <element name="c01.ccentroid">\n+ <assert_contents>\n+ <has_text text="1 72"/>\n+ </assert_contents>\n+ </element>\n+ <element name="c02.ccentroid">\n+ <assert_contents>\n+ <has_text text="Structure 1"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output_collection name="sfold_cluster_ct" type="list">\n+ <element name="c01.ccentroid">\n+ <assert_contents>\n+ <has_n_lines n="78"/>\n+ <has_text text="Length: 76"/>\n+ </assert_contents>\n+ </element>\n+ <element name="c02.ccentroid">\n+ <assert_contents>\n+ <has_n_lines n="78"/>\n+ <has_text text="Length: 76"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n+ <test expect_num_outputs="4">\n+ <param name="non_commercial_use" value="true"/>\n+ <param name="fasta" value="seq.fasta"/>\n+ <param name="a" value="true"/>\n+ <param name="f" value="cons.ct"/>\n+ <param name="l" value="30"/>\n+ <param name="m" value="mfe.ct"/>\n+ <param name="w" value="20"/>\n+ <param name="i" value="1"/>\n+ <param name="output_selector" value="bp,clusters"/>\n+ <output_collection name="sfold_cluster_bp" type="list">\n+ <element name="c01.ccentroid">\n+ <assert_contents>\n+ <has_text text="1 72"/>\n+ </assert_contents>\n+ </element>\n+ <element name="c02.ccentroid">\n+ <assert_contents>\n+ <has_text text="Structure 1"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output_collection name="sfold_bp" type="list">\n+ <element name="ecentroid">\n+ <assert_contents>\n+ <has_text text="1 72"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection> \n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Sfold is a software package for statistical folding and rational design of nucleic acids.\n+\n+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\n+RNA structure and function.\n+\n+Input Format\n+\n+-----------\n+\n+The program requires one input file of RNA sequence in FASTA format.\n+\n+Sfold options\n+\n+------------\n+\n+The program can run based on the clustering on the sampled ensemble or not.\n+It can also predict the secondary structure based on the constraint and MFE structure files.\n+The sfold has two different modules:\n+\n+* SiRNA : Target accessibility prediction and RNA duplex thermodynamics for rational siRNA design\n+* Solig: Target accessibility prediction and rational design of antisense oligonucleotides and nucleic acid probes\n+\n+The program can be run based on the above-mentioned modules, both of them or none of them.\n+\n+Output Files\n+\n+------------\n+\n+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\n+files contain a header section that defines the formats and meanings of the data in the output.\n+\n+------------\n+\n+Important: The program usage is restricted to non-commercial and academic research.\n+ ]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 6cce721f568c test-data/cons.ct --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cons.ct Wed Nov 27 13:22:29 2024 +0000 |
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| @@ -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 + |
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| diff -r 000000000000 -r 6cce721f568c test-data/mfe.ct --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mfe.ct Wed Nov 27 13:22:29 2024 +0000 |
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| @@ -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 + |
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| diff -r 000000000000 -r 6cce721f568c test-data/seq.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seq.fasta Wed Nov 27 13:22:29 2024 +0000 |
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| @@ -0,0 +1,3 @@ +>gi|395400|emb|X66515|ECTRALA E.coli tRNA-Ala +GGGGCTATAGCTCAGCTGGGAGAGCGCTTGCATGGCATGCAAGAGGTCAGCGGTTCGATC +CCGCTTAGCTCCACCA \ No newline at end of file |