Mercurial > repos > peterjc > seq_filter_by_id
diff tools/seq_filter_by_id/seq_filter_by_id.xml @ 10:4a7d8ad2a983 draft
Bump Biopython dependency
author | peterjc |
---|---|
date | Thu, 30 Nov 2023 09:50:34 +0000 |
parents | 141612f8c3e3 |
children | 85ef5f5a0562 |
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--- a/tools/seq_filter_by_id/seq_filter_by_id.xml Thu May 11 12:18:52 2017 -0400 +++ b/tools/seq_filter_by_id/seq_filter_by_id.xml Thu Nov 30 09:50:34 2023 +0000 @@ -1,7 +1,7 @@ -<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.7"> +<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.8"> <description>from a tabular file</description> <requirements> - <requirement type="package" version="1.67">biopython</requirement> + <requirement type="package" version="1.81">biopython</requirement> </requirements> <version_command> python $__tool_directory__/seq_filter_by_id.py --version @@ -30,20 +30,20 @@ <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." /> <conditional name="id_opts"> <param name="id_opts_selector" type="select" label="Filter using the ID list from"> - <option value="tabular" selected="True">tabular file</option> + <option value="tabular" selected="true">tabular file</option> <option value="list">provided list</option> <!-- add UNION or INTERSECTION of multiple tabular files here? --> </param> <when value="tabular"> <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> - <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" + <param name="columns" type="data_column" data_ref="input_tabular" multiple="true" numerical="false" label="Column(s) containing sequence identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> <validator type="no_options" message="Pick at least one column"/> </param> </when> <when value="list"> - <param name="id_list" type="text" size="20x80" area="True" format="tabular" + <param name="id_list" type="text" size="20x80" area="true" format="tabular" label="List of sequence identifiers (white space separated)" help="You can use both spaces and new lines to separate your identifiers."> <sanitizer> @@ -69,12 +69,12 @@ </conditional> <conditional name="adv_opts"> <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> + <option value="basic" selected="true">Hide Advanced Options</option> <option value="advanced">Show Advanced Options</option> </param> <when value="basic" /> <when value="advanced"> - <param name="strip_suffix" type="boolean" value="false" label="Remove typical pair read name suffices when matching identifiers?" help="Will remove suffices including Illumina /1 and /2, Roche 454 .f and .r, and assorted Sanger names like .p* and .q*" /> + <param name="strip_suffix" type="boolean" value="false" label="Remove typical pair read name suffixes when matching identifiers?" help="Will remove suffixes including Illumina /1 and /2, Roche 454 .f and .r, and assorted Sanger names like .p* and .q*" /> </when> </conditional> </inputs> @@ -128,7 +128,7 @@ <param name="adv_opts_selector" value="advanced" /> <param name="strip_suffix" value="true" /> <output name="output_pos" file="sanger-pairs-mixed.fastq" ftype="fastq" /> - <output name="output_neg" file="empty_file.dat" ftype="fastq" /> + <output name="output_neg" file="empty_file.dat" ftype="fastq" /> </test> <test> <param name="input_file" value="sanger-pairs-mixed.fastq" ftype="fastq" /> @@ -180,14 +180,14 @@ Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 +https://doi.org/10.7717/peerj.167 This tool uses Biopython to read and write SFF files, so you may also wish to cite the Biopython application note (and Galaxy too of course): Cock et al (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. -http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. +https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878. 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_filter_by_id