Mercurial > repos > peterjc > seq_rename
comparison tools/seq_rename/seq_rename.xml @ 3:e1398f2ba9fe draft default tip
v0.0.8 galaxy_sequence_utils dependency etc
author | peterjc |
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date | Thu, 02 Feb 2017 11:49:03 -0500 |
parents | 7c0642fc57ad |
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2:7c0642fc57ad | 3:e1398f2ba9fe |
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1 <tool id="seq_rename" name="Rename sequences" version="0.0.4"> | 1 <tool id="seq_rename" name="Rename sequences" version="0.0.8"> |
2 <description>with ID mapping from a tabular file</description> | 2 <description>with ID mapping from a tabular file</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.62">biopython</requirement> | 4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> |
5 <requirement type="package" version="1.67">biopython</requirement> | |
5 <requirement type="python-module">Bio</requirement> | 6 <requirement type="python-module">Bio</requirement> |
6 </requirements> | 7 </requirements> |
7 <version_commmand interpreter="python">seq_rename.py --version</version_commmand> | |
8 <command interpreter="python"> | |
9 seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file | |
10 </command> | |
11 <stdio> | 8 <stdio> |
12 <!-- Anything other than zero is an error --> | 9 <!-- Anything other than zero is an error --> |
13 <exit_code range="1:" /> | 10 <exit_code range="1:" /> |
14 <exit_code range=":-1" /> | 11 <exit_code range=":-1" /> |
15 </stdio> | 12 </stdio> |
13 <version_command interpreter="python">seq_rename.py --version</version_command> | |
14 <command interpreter="python"> | |
15 seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file | |
16 </command> | |
16 <inputs> | 17 <inputs> |
17 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> | 18 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> |
18 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> | 19 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> |
19 <param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/> | 20 <param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/> |
20 <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/> | 21 <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/> |
21 </inputs> | 22 </inputs> |
22 <outputs> | 23 <outputs> |
23 <data name="output_file" format="fasta" label="Renamed ${on_string}"> | 24 <data name="output_file" format_source="input_file" metadata_source="input_file" label="Renamed ${on_string}"/> |
24 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> | |
25 <change_format> | |
26 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> | |
27 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> | |
28 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> | |
29 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | |
30 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> | |
31 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | |
32 </change_format> | |
33 </data> | |
34 </outputs> | 25 </outputs> |
35 <tests> | 26 <tests> |
36 <test> | 27 <test> |
37 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> | 28 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
38 <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> | 29 <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> |
53 | 44 |
54 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a | 45 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a |
55 new sequence file (of the same format) where the sequence identifiers have been | 46 new sequence file (of the same format) where the sequence identifiers have been |
56 renamed according to the specified columns in your tabular file. | 47 renamed according to the specified columns in your tabular file. |
57 | 48 |
49 Any original description is preserved (N/A for the SFF file format). | |
50 | |
58 WARNING: If you have any duplicates in the input sequence file, you will still | 51 WARNING: If you have any duplicates in the input sequence file, you will still |
59 have duplicate sequences in the output. | 52 have duplicate sequences in the output. |
60 | 53 |
61 WARNING: If the tabular file has more than one new name for any old ID, the | 54 WARNING: If the tabular file has more than one new name for any old ID, the |
62 last one is used. | 55 last one is used. |
56 | |
57 WARNING: The old and new names in your tabular file should not contain white space. | |
58 If they do, only the first word is used as the identifier. | |
63 | 59 |
64 **References** | 60 **References** |
65 | 61 |
66 If you use this Galaxy tool in work leading to a scientific publication please | 62 If you use this Galaxy tool in work leading to a scientific publication please |
67 cite the following papers: | 63 cite the following papers: |
79 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | 75 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
80 | 76 |
81 This tool is available to install into other Galaxy Instances via the Galaxy | 77 This tool is available to install into other Galaxy Instances via the Galaxy |
82 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename | 78 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename |
83 </help> | 79 </help> |
80 <citations> | |
81 <citation type="doi">10.7717/peerj.167</citation> | |
82 <citation type="doi">10.1093/bioinformatics/btp163</citation> | |
83 </citations> | |
84 </tool> | 84 </tool> |