diff tools/seq_filter_by_id/seq_filter_by_id.xml @ 10:4a7d8ad2a983 draft

Bump Biopython dependency

--- 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