# HG changeset patch
# User iuc
# Date 1730807513 0
# Node ID 6f66f523a9b7d31b3dbb8856fb239c7f0453b227
# Parent  03a04f48b9221e0aef3590043e7bb58ee78b928e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit 4a156b17a386e1ecf13dfb2b232a1fc7d8344adc

diff -r 03a04f48b922 -r 6f66f523a9b7 macros.xml
--- a/macros.xml	Sat Sep 28 16:34:20 2024 +0000
+++ b/macros.xml	Tue Nov 05 11:51:53 2024 +0000
@@ -2,7 +2,11 @@
 <macros>
     <token name="@TOOL_VERSION@">0.10.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">sinto</xref>
+        </xrefs>
+      </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1038/s41592-021-01282-5</citation>
diff -r 03a04f48b922 -r 6f66f523a9b7 sinto_fragments.xml
--- a/sinto_fragments.xml	Sat Sep 28 16:34:20 2024 +0000
+++ b/sinto_fragments.xml	Tue Nov 05 11:51:53 2024 +0000
@@ -3,17 +3,18 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">sinto</requirement>
     </requirements>
     <version_command>sinto --version</version_command>
     <command><![CDATA[
-    ln -s '$bam' 'input.bam' && 
+    ln -s '$bam' 'input.bam' &&
     ln -s '$bam.metadata.bam_index' 'input.bam.bai' &&
-    sinto fragments 
+    sinto fragments
     --bam 'input.bam'
-    --min_mapq $min_mapq 
-    --barcodetag '$barcodetag' 
+    --min_mapq $min_mapq
+    --barcodetag '$barcodetag'
     --barcode_regex '${ str( $barcode_regex ) }'
     --max_distance $max_distance
     --min_distance $min_distance
@@ -27,7 +28,7 @@
         <param argument="--bam" type="data" format="bam" label="Input BAM file" />
         <param argument="--min_mapq" type="integer" value="30" min="0" label="Minimum MAPQ required to retain fragment" />
         <param argument="--barcodetag" type="text" value="CB" label="Read tag storing cell barcode information" />
-        <param argument="--barcode_regex" type="text" value="[^:]*" label="Regular expression used to extract cell barcode from read name" 
+        <param argument="--barcode_regex" type="text" value="[^:]*" label="Regular expression used to extract cell barcode from read name"
             help="[^:]* matches all characters up to the first colon" >
             <sanitizer>
                 <valid initial="string.printable">
@@ -35,14 +36,14 @@
                 </valid>
             </sanitizer>
         </param>
-        <param argument="--max_distance" type="integer" value="5000" min="0" label="Maximum distance between integration sites for the fragment to be retained" 
+        <param argument="--max_distance" type="integer" value="5000" min="0" label="Maximum distance between integration sites for the fragment to be retained"
             help="Allows filtering of implausible fragments that likely result from incorrect mapping positions."/>
-        <param argument="--min_distance" type="integer" value="10" min="0" label="Minimum distance between integration sites for the fragment to be retained" 
+        <param argument="--min_distance" type="integer" value="10" min="0" label="Minimum distance between integration sites for the fragment to be retained"
             help="Allows filtering of implausible fragments that likely result from incorrect mapping positions."/>
         <param argument="--shift_plus" type="integer" value="4" label=" Number of bases to shift Tn5 insertion position by on the forward strand" />
         <param argument="--shift_minus" type="integer" value="-5" label="Number of bases to shift Tn5 insertion position by on the reverse strand" />
-        <param argument="--collapse_within" type="boolean" truevalue="--collapse_within" falsevalue="" label="Take cell barcode into account 
-            when collapsing duplicate fragments" help="Setting this flag means that fragments with the same coordinates can be identified 
+        <param argument="--collapse_within" type="boolean" truevalue="--collapse_within" falsevalue="" label="Take cell barcode into account
+            when collapsing duplicate fragments" help="Setting this flag means that fragments with the same coordinates can be identified
             provided they originate from a different cell barcode." />
     </inputs>
     <outputs>
@@ -74,14 +75,14 @@
 
 Sinto: single-cell analysis tools
 --------------------------------------------------------------------------------------------------------------
-An ATAC-seq fragment file can be created from a BAM file using the fragments command. The fragment file contains the position of each 
+An ATAC-seq fragment file can be created from a BAM file using the fragments command. The fragment file contains the position of each
 Tn5 integration site, the cell barcode associated with the fragment, and the number of times the fragment was sequenced. PCR duplicates are collapsed.
 
 **Input**
 A BAM file. Alignments in the input BAM file must contain cell barcodes either as a part of read names or in a tag (typically, in CB tag).
 
 **Output**
-The fragment file. It contains the positions of Tn5 integration sites, the cell barcode that the DNA fragment originated from, and the number of times 
+The fragment file. It contains the positions of Tn5 integration sites, the cell barcode that the DNA fragment originated from, and the number of times
 the fragment was sequenced.
 
     ]]>    </help>