Mercurial > repos > devteam > fasta_nucleotide_changer

annotate fasta_nucleotide_changer.xml @ 6:5904fbde39ec draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author iuc
date Thu, 10 Aug 2023 06:50:30 +0000
parents 156cfcd126c3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
5904fbde39ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
parents: 5
diff changeset
1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.2+galaxy@VERSION_SUFFIX@" profile="22.05" name="RNA/DNA" >
2
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
2 <description>converter</description>
3
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
3 <macros>
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
4 <import>macros.xml</import>
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
5 </macros>
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
6 <expand macro="requirements" />
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
8 @CATS@ fasta_nucleotide_changer
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
9 -$mode
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
10 -v
5
156cfcd126c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
11 @GZIP@ > '$output'
3
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
12 ]]></command>
2
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
13 <inputs>
3
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
14 <expand macro="fasta_input" />
0
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
15
2
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
16 <param name="mode" type="select" label="Convert">
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
17 <option value="d">RNA to DNA (U to T)</option>
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
18 <option value="r">DNA to RNA (T to U)</option>
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
19 </param>
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
20 </inputs>
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
21 <outputs>
3
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
22 <data name="output" format_source="input" metadata_source="input" />
2
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
23 </outputs>
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
24 <tests>
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
25 <test>
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
26 <param name="input" value="fasta_nuc_changer1.fasta" />
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
27 <param name="mode" value="r" />
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
28 <output name="output" ftype="fasta" file="fasta_nuc_change1.out" />
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
29 </test>
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
30 <test>
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
31 <param name="input" value="fasta_nuc_changer2.fasta" />
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
32 <param name="mode" value="d" />
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
33 <output name="output" ftype="fasta" file="fasta_nuc_change2.out" />
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
34 </test>
1cabf6626797 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
35 </tests>
3
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
36 <help><![CDATA[
0
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
37 **What it does**
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
38
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
39 This tool converts RNA FASTA files to DNA (and vice-versa).
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
40
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
41 In **RNA-to-DNA** mode, U's are changed into T's.
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
42
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
43 In **DNA-to-RNA** mode, T's are changed into U's.
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
44
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
45 --------
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
46
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
47 **Example**
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
48
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
49 Input RNA FASTA file ( from Sanger's mirBase )::
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
50
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
51 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
52 UGAGGUAGUAGGUUGUAUAGUU
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
53 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
54 UCCCUGAGACCUCAAGUGUGA
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
55 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
56 UGGAAUGUAAAGAAGUAUGUA
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
57
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
58 Output DNA FASTA file (with RNA-to-DNA mode)::
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
59
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
60 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
61 TGAGGTAGTAGGTTGTATAGTT
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
62 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
63 TCCCTGAGACCTCAAGTGTGA
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
64 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
65 TGGAATGTAAAGAAGTATGTA
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
66
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
67
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
68 ------
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
69
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
70 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
71
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
3
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
73 ]]></help>
ea1b0d77314d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
74 <expand macro="citations" />
0
399fe8a8ce37 Uploaded tool tarball.
devteam
parents:
diff changeset
75 </tool>