Mercurial > repos > devteam > fastx_renamer
comparison fastx_renamer.xml @ 1:defaa5ba1ee2 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Tue, 13 Oct 2015 12:41:46 -0400 |
parents | 4ed1114bfe88 |
children | 2b324adf4e58 |
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0:4ed1114bfe88 | 1:defaa5ba1ee2 |
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1 <tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" > | 1 <tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" > |
2 <description></description> | 2 <description></description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> |
5 </requirements> | 5 </requirements> |
6 <command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v | 6 <command> |
7 <![CDATA[ | |
8 zcat -f < '$input' | fastx_renamer -n $TYPE -o '$output' -v | |
7 #if $input.ext == "fastqsanger": | 9 #if $input.ext == "fastqsanger": |
8 -Q 33 | 10 -Q 33 |
9 #end if | 11 #end if |
10 </command> | 12 ]]> |
13 </command> | |
11 | 14 |
12 <inputs> | 15 <inputs> |
13 <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" /> | 16 <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" /> |
14 | 17 |
15 <param name="TYPE" type="select" label="Rename sequence identifiers to"> | 18 <param name="TYPE" type="select" label="Rename sequence identifiers to"> |
16 <option value="SEQ">Nucleotides sequence</option> | 19 <option value="SEQ">Nucleotides sequence</option> |
17 <option value="COUNT">Numeric Counter</option> | 20 <option value="COUNT">Numeric Counter</option> |
18 </param> | 21 </param> |
19 </inputs> | 22 </inputs> |
20 | 23 |
21 <outputs> | 24 <outputs> |
22 <data format="input" name="output" metadata_source="input" /> | 25 <data format_source="input" name="output" metadata_source="input" /> |
23 </outputs> | 26 </outputs> |
24 | 27 <tests> |
25 <help> | 28 </tests> |
26 | 29 <help> |
27 **What it does** | 30 **What it does** |
28 | 31 |
29 This tool renames the sequence identifiers in a FASTQ/A file. | 32 This tool renames the sequence identifiers in a FASTQ/A file. |
30 | 33 |
31 .. class:: infomark | 34 .. class:: infomark |
40 | 43 |
41 @CSHL_4_FC042GAMMII_2_1_517_596 | 44 @CSHL_4_FC042GAMMII_2_1_517_596 |
42 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | 45 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT |
43 +CSHL_4_FC042GAMMII_2_1_517_596 | 46 +CSHL_4_FC042GAMMII_2_1_517_596 |
44 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 | 47 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 |
45 | 48 |
46 Renamed to **nucleotides sequence**:: | 49 Renamed to **nucleotides sequence**:: |
47 | 50 |
48 @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | 51 @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT |
49 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | 52 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT |
50 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | 53 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT |
59 | 62 |
60 ------ | 63 ------ |
61 | 64 |
62 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | 65 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
63 | 66 |
64 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | 67 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
65 </help> | 68 </help> |
66 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> | 69 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |
67 </tool> | 70 </tool> |