# HG changeset patch
# User iuc
# Date 1681383828 0
# Node ID 3780db0073f048a395847e8d603c2b935495ce53

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f

diff -r 000000000000 -r 3780db0073f0 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Apr 13 11:03:48 2023 +0000
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">0.9.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/s41592-021-01282-5</citation>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 3780db0073f0 sinto_barcode.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sinto_barcode.xml	Thu Apr 13 11:03:48 2023 +0000
@@ -0,0 +1,77 @@
+<tool id="sinto_barcode" name="Sinto barcode" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>add cell barcodes to FASTQ read names</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">sinto</requirement>
+    </requirements>
+    <version_command>sinto --version</version_command>
+    <command><![CDATA[
+    ln -s '$barcode_fastq' barcodes.fastq.gz &&
+    ln -s '${fastq_input.read1_fastq}' read1.fastq.gz &&
+    #if str( $fastq_input.fastq_input_selector ) == "paired":
+    ln -s '${fastq_input.read2_fastq}' read2.fastq.gz &&
+    #end if
+    sinto barcode 
+    --barcode_fastq barcodes.fastq.gz 
+    --read1 read1.fastq.gz
+    #if str( $fastq_input.fastq_input_selector ) == "paired":
+    --read2 read2.fastq.gz
+    #end if
+    --bases $bases
+]]>    </command>
+    <inputs>
+        <param type="data" name="barcode_fastq" format="fastqsanger.gz" label="FASTQ file containing cell barcode sequences" />
+        <conditional name="fastq_input">
+            <param name="fastq_input_selector" type="select" label="Single or Paired-end data">
+                <option value="paired">Paired</option>
+                <option value="single">Single</option>
+            </param>
+            <when value="paired">
+                <param name="read1_fastq" type="data" format="fastqsanger.gz" label="Forward reads FASTQ file" />
+                <param name="read2_fastq" type="data" format="fastqsanger.gz" label="Reverse reads FASTQ file" />
+            </when>
+            <when value="single">
+                <param name="read1_fastq" type="data" format="fastqsanger.gz" label="Select FASTQ file" />
+            </when>
+        </conditional>
+        <param type="integer" name="bases" value="16" min="0" label="Number of bases to extract from barcode-containing FASTQ" />
+    </inputs>
+    <outputs>
+        <data name='read1_out' format='fastqsanger.gz' label="${tool.name} on ${on_string}: barcoded read 1" from_work_dir="read1.barcoded.fastq" />
+        <data name='read2_out' format='fastqsanger.gz' label="${tool.name} on ${on_string}: barcoded read 2" from_work_dir="read2.barcoded.fastq" >
+            <filter>fastq_input['fastq_input_selector'] == 'paired'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="barcode_fastq" value="barcodes.fastq.gz" />
+            <param name="fastq_input_selector" value="single"/>
+            <param name="read1_fastq" value="read1.fastq.gz" />
+            <output name="read1_out" file="read1.barcoded.fastq.gz" ftype="fastqsanger.gz"  decompress="true" />
+        </test>
+        <test expect_num_outputs="2">
+            <param name="barcode_fastq" value="barcodes.fastq.gz" />
+            <param name="fastq_input_selector" value="paired"/>
+            <param name="read1_fastq" value="read1.fastq.gz" />
+            <param name="read2_fastq" value="read2.fastq.gz" />
+            <output name="read1_out" file="read1.barcoded.fastq.gz" ftype="fastqsanger.gz"  decompress="true"/>
+            <output name="read2_out" file="read2.barcoded.fastq.gz" ftype="fastqsanger.gz"  decompress="true"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Sinto is a toolkit for processing aligned single-cell data.
+--------------------------------------------------------------------------------------------------------------
+Cell barcodes from one FASTQ file added to the read names of another, or the same, FASTQ file. This is useful when processing raw single-cell sequencing data, as the cell barcode information can easily be propagated to the aligned BAM file by encoding the cell barcode in the read name.
+
+**Inputs**
+FASTQ files containing barcodes and forward reads. An optional reverse reads FASTQ file can be provided for paired-end experiments. Note that all the FASTQs must contain the same number of reads and the reads must appear in the same order.
+
+**Outputs**
+FASTQ files with the read names modified to contain the cell barcode sequence at the beginning of the read name, separated from the original read name by a : character.
+
+    ]]>    </help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 3780db0073f0 test-data/aligned.bam
Binary file test-data/aligned.bam has changed
diff -r 000000000000 -r 3780db0073f0 test-data/barcodes.fastq.gz
Binary file test-data/barcodes.fastq.gz has changed
diff -r 000000000000 -r 3780db0073f0 test-data/read1.barcoded.fastq.gz
diff -r 000000000000 -r 3780db0073f0 test-data/read1.fastq.gz
Binary file test-data/read1.fastq.gz has changed
diff -r 000000000000 -r 3780db0073f0 test-data/read2.barcoded.fastq.gz
diff -r 000000000000 -r 3780db0073f0 test-data/read2.fastq.gz
Binary file test-data/read2.fastq.gz has changed