--- a/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml	Wed May 17 09:24:01 2017 -0400
+++ b/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml	Fri Apr 16 22:22:47 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.6">
+<tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.7">
     <description>from SAM/BAM file</description>
     <requirements>
         <requirement type="package" version="1.67">biopython</requirement>
@@ -21,7 +21,7 @@
     </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." />
-	<param name="mapping_file" type="data" format="sam,bam" multiple="true" label="SAM/BAM mapping of those sequences" help="SAM or BAM format." />
+        <param name="mapping_file" type="data" format="sam,bam" multiple="true" label="SAM/BAM mapping of those sequences" help="SAM or BAM format." />
         <conditional name="output_choice_cond">
             <param name="output_choice" type="select" label="Output mapped reads, unmapped reads, or both?">
                 <option value="both">Both mapped and unmapped reads, as two files</option>
@@ -33,12 +33,12 @@
             <when value="pos" />
             <when value="neg" />
         </conditional>
-	<param name="pair_mode" type="select" label="Paired read treatment">
+        <param name="pair_mode" type="select" label="Paired read treatment">
             <option value="lax" selected="true">Treat as a pair, allow either read to be mapped</option>
-	    <option value="strict">Treat as a pair, require both reads to be mapped</option>
-	    <!-- The following would actually be more work as have to store qname/1 and qname/2 separately for filter...
+            <option value="strict">Treat as a pair, require both reads to be mapped</option>
+            <!-- The following would actually be more work as have to store qname/1 and qname/2 separately for filter...
             <option value="solo">Treat independently (will split partners when only one maps)</option>
-	    -->
+            -->
         </param>
     </inputs>
     <outputs>
@@ -50,19 +50,19 @@
         </data>
     </outputs>
     <tests>
-	<test>
+        <test>
             <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
             <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" />
             <param name="pair_mode" value="lax" />
             <param name="output_choice" value="pos" />
             <output name="output_pos" file="SRR639755_sample_lax.fastq" ftype="fastqsanger" />
         </test>
-	<test>
+        <test>
             <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
             <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" />
             <param name="pair_mode" value="strict" />
             <param name="output_choice" value="pos" />
-            <output name="output_pos" file="SRR639755_sample_strict.fastq" ftype="fastqsanger" /> 
+            <output name="output_pos" file="SRR639755_sample_strict.fastq" ftype="fastqsanger" />
         </test>
     </tests>
     <help>
@@ -97,7 +97,7 @@
 
 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_mapping