| Previous changeset 12:311012138753 (2013-09-26) Next changeset 14:61cec46f6be5 (2013-11-20) |
|
Commit message:
Uploaded v0.0.4i, depend on Biopython 1.62 |
|
modified:
tools/seq_rename/repository_dependencies.xml tools/seq_rename/seq_rename.xml |
| b |
| diff -r 311012138753 -r d08767ae73ce tools/seq_rename/repository_dependencies.xml --- a/tools/seq_rename/repository_dependencies.xml Thu Sep 26 10:07:49 2013 -0400 +++ b/tools/seq_rename/repository_dependencies.xml Fri Sep 27 06:10:29 2013 -0400 |
| b |
| @@ -2,5 +2,5 @@ <repositories description="This requires Biopython as a dependency."> <!-- Leave out the tool shed and revision to get the current tool shed and latest revision at the time of upload --> -<repository changeset_revision="2f6c871cfa35" name="package_biopython_1_61" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +<repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories> |
| b |
| diff -r 311012138753 -r d08767ae73ce tools/seq_rename/seq_rename.xml --- a/tools/seq_rename/seq_rename.xml Thu Sep 26 10:07:49 2013 -0400 +++ b/tools/seq_rename/seq_rename.xml Fri Sep 27 06:10:29 2013 -0400 |
| b |
| @@ -1,62 +1,61 @@ <tool id="seq_rename" name="Rename sequences" version="0.0.4"> - <description>with ID mapping from a tabular file</description> - <requirements> - <requirement type="package" version="1.61">biopython</requirement> - <requirement type="python-module">Bio</requirement> - </requirements> - <version_commmand interpreter="python">seq_rename.py --version</version_commmand> - <command interpreter="python"> + <description>with ID mapping from a tabular file</description> + <requirements> + <requirement type="package" version="1.62">biopython</requirement> + <requirement type="python-module">Bio</requirement> + </requirements> + <version_commmand interpreter="python">seq_rename.py --version</version_commmand> + <command interpreter="python"> seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file - </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <inputs> - <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> - <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> - <param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/> - <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/> - </inputs> - <outputs> - <data name="output_file" format="fasta" label="Renamed ${on_string}"> - <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> - <change_format> - <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> - <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> - <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> - <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> - <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> - <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> - <param name="old_column" value="1" /> - <param name="new_column" value="2" /> - <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> - </test> - <test> - <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> - <param name="old_column" value="c1" /> - <param name="new_column" value="c2" /> - <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> - </test> - </tests> - <help> - + </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <inputs> + <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> + <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> + <param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/> + <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/> + </inputs> + <outputs> + <data name="output_file" format="fasta" label="Renamed ${on_string}"> + <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> + <change_format> + <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> + <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> + <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> + <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> + <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> + <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> + <param name="old_column" value="1" /> + <param name="new_column" value="2" /> + <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> + </test> + <test> + <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="input_tabular" value="four_human_proteins.rename.tabular" ftype="tabular" /> + <param name="old_column" value="c1" /> + <param name="new_column" value="c2" /> + <output name="output_file" file="four_human_proteins.rename.fasta" ftype="fasta" /> + </test> + </tests> + <help> **What it does** Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a new sequence file (of the same format) where the sequence identifiers have been -renamed according two the specified columns a the tabular file. +renamed according to the specified columns in your tabular file. -WARNING: If you have any duplicates in the intput sequence file, you will still +WARNING: If you have any duplicates in the input sequence file, you will still have duplicate sequences in the output. WARNING: If the tabular file has more than one new name for any old ID, the @@ -81,5 +80,5 @@ This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename - </help> + </help> </tool> |