Mercurial > repos > devteam > fastx_renamer

annotate fastx_renamer.xml @ 6:82efcd97d9dd 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/fastx_renamer commit 17bcf78f445b2e515122330caccb591d8de2a5b4
author iuc
date Wed, 23 Apr 2025 05:18:53 +0000
parents f0cd2c0de268
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
f0cd2c0de268 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
parents: 4
diff changeset
1 <tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" >
1
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
2 <description></description>
2
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
3 <macros>
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
4 <import>macros.xml</import>
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
5 </macros>
4
51b360968c30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 3
diff changeset
6 <expand macro="requirements">
51b360968c30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 3
diff changeset
7 <requirement type="package" version="1.0.8">bzip2</requirement>
51b360968c30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 3
diff changeset
8 </expand>
2
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
10 @CATS@ fastx_renamer
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
11 -n $TYPE
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
12 -v
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
13 @FQQUAL@
4
51b360968c30 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 3
diff changeset
14 @GZIP@ > '$output'
2
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
15 ]]></command>
0
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
16
1
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
17 <inputs>
2
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
18 <expand macro="fastx_input" />
0
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
19
1
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
20 <param name="TYPE" type="select" label="Rename sequence identifiers to">
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
21 <option value="SEQ">Nucleotides sequence</option>
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
22 <option value="COUNT">Numeric Counter</option>
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
23 </param>
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
24 </inputs>
0
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
25
1
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
26 <outputs>
2
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
27 <data name="output" format_source="input" metadata_source="input" />
1
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
28 </outputs>
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
29 <tests>
2
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
30 <test>
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
31 <param name="input" value="fastx_renamer-in1.fastq" />
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
32 <param name="TYPE" value="SEQ" />
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
33 <output name="output" file="fastx_renamer-out1.fastq" />
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
34 </test>
1
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
35 </tests>
2
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
36 <help><![CDATA[
0
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
37 **What it does**
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
38
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
39 This tool renames the sequence identifiers in a FASTQ/A file.
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
40
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
41 .. class:: infomark
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
42
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
43 Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc).
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
44
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
45 --------
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
46
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
47 **Example**
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
48
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
49 The following Solexa-FASTQ file::
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
50
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
51 @CSHL_4_FC042GAMMII_2_1_517_596
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
52 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
53 +CSHL_4_FC042GAMMII_2_1_517_596
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
54 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
1
defaa5ba1ee2 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
55
0
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
56 Renamed to **nucleotides sequence**::
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
57
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
58 @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
59 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
60 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
61 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
62
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
63 Renamed to **numeric counter**::
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
64
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
65 @1
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
66 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
67 +1
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
68 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
69
2
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
70 ]]></help>
2b324adf4e58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
71 <expand macro="citations" />
0
4ed1114bfe88 Uploaded
devteam
parents:
diff changeset
72 </tool>