Mercurial > repos > peterjc > seq_select_by_id
diff tools/seq_select_by_id/seq_select_by_id.xml @ 6:91f55ee8fea5 draft
v0.0.11; more tests and assorting minor changes
author | peterjc |
---|---|
date | Wed, 13 May 2015 10:56:29 -0400 |
parents | 6842c0c7bc70 |
children | a5602454b0ad |
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--- a/tools/seq_select_by_id/seq_select_by_id.xml Thu Nov 21 04:54:59 2013 -0500 +++ b/tools/seq_select_by_id/seq_select_by_id.xml Wed May 13 10:56:29 2015 -0400 @@ -1,35 +1,25 @@ -<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6"> +<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.11"> <description>from a tabular file</description> <requirements> <requirement type="package" version="1.62">biopython</requirement> <requirement type="python-module">Bio</requirement> </requirements> - <version_command interpreter="python">seq_select_by_id.py --version</version_command> - <command interpreter="python"> -seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file - </command> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> + <version_command interpreter="python">seq_select_by_id.py --version</version_command> + <command interpreter="python"> +seq_select_by_id.py "$input_tabular" "$column" "$input_file" "$input_file.ext" "$output_file" + </command> <inputs> <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." /> <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> </inputs> <outputs> - <data name="output_file" format="fasta" label="Selected sequences"> - <!-- 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> + <data name="output_file" format_source="input_file" metadata_source="input_file" label="Selected sequences from $input_file.name"/> </outputs> <tests> <test> @@ -37,6 +27,35 @@ <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> <param name="column" value="1" /> <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> + <assert_stdout> + <has_line line="Indexed 10 sequences" /> + <has_line line="Selected 1 sequences by ID" /> + </assert_stdout> + </test> + <!-- this version has white space in the identifier column (id and description) --> + <test> + <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> + <param name="input_tabular" value="k12_hypothetical_alt.tabular" ftype="tabular" /> + <param name="column" value="1" /> + <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> + <assert_stdout> + <has_line line="Indexed 10 sequences" /> + <has_line line="Selected 1 sequences by ID" /> + </assert_stdout> + <assert_stderr> + <has_line line="WARNING: Some of your identifiers had white space in them, using first word only. e.g.:" /> + </assert_stderr> + </test> + <test expect_failure="true" expect_exit_code="1"> + <param name="input_file" value="empty.fasta" ftype="fasta" /> + <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> + <param name="column" value="1" /> + <assert_stdout> + <has_line line="Indexed 0 sequences" /> + </assert_stdout> + <assert_stderr> + <has_line line="Identifier 'gi|16127999|ref|NP_414546.1|' not found in sequence file" /> + </assert_stderr> </test> </tests> <help> @@ -69,4 +88,8 @@ 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_select_by_id </help> + <citations> + <citation type="doi">10.7717/peerj.167</citation> + <citation type="doi">10.1093/bioinformatics/btp163</citation> + </citations> </tool>