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annotate fastx_renamer.xml @ 3:d8baeed2ce62 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
author | iuc |
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date | Wed, 22 Aug 2018 11:03:24 -0400 |
parents | 2b324adf4e58 |
children | 51b360968c30 |
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2b324adf4e58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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1 <tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy0" > |
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2 <description></description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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4 <import>macros.xml</import> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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5 </macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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6 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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7 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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8 @CATS@ fastx_renamer |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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9 -n $TYPE |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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10 -o '$output' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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11 -v |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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12 @FQQUAL@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
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13 @GZIP@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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14 ]]></command> |
0 | 15 |
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16 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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17 <expand macro="fastx_input" /> |
0 | 18 |
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19 <param name="TYPE" type="select" label="Rename sequence identifiers to"> |
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20 <option value="SEQ">Nucleotides sequence</option> |
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21 <option value="COUNT">Numeric Counter</option> |
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22 </param> |
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23 </inputs> |
0 | 24 |
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25 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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26 <data name="output" format_source="input" metadata_source="input" /> |
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27 </outputs> |
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28 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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29 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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30 <param name="input" value="fastx_renamer-in1.fastq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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31 <param name="TYPE" value="SEQ" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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32 <output name="output" file="fastx_renamer-out1.fastq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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33 </test> |
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34 </tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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35 <help><![CDATA[ |
0 | 36 **What it does** |
37 | |
38 This tool renames the sequence identifiers in a FASTQ/A file. | |
39 | |
40 .. class:: infomark | |
41 | |
42 Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc). | |
43 | |
44 -------- | |
45 | |
46 **Example** | |
47 | |
48 The following Solexa-FASTQ file:: | |
49 | |
50 @CSHL_4_FC042GAMMII_2_1_517_596 | |
51 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
52 +CSHL_4_FC042GAMMII_2_1_517_596 | |
53 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 | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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54 |
0 | 55 Renamed to **nucleotides sequence**:: |
56 | |
57 @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
58 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
59 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
60 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 | |
61 | |
62 Renamed to **numeric counter**:: | |
63 | |
64 @1 | |
65 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
66 +1 | |
67 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 | |
68 | |
69 ------ | |
70 | |
71 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
72 | |
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73 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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74 ]]></help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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75 <expand macro="citations" /> |
0 | 76 </tool> |