--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/10x_bamtofastq.xml	Tue May 10 12:02:15 2022 +0000
@@ -0,0 +1,74 @@
+<tool id="10x_bamtofastq" name="Convert a 10X BAM file to FASTQ" version="1.4.1">
+    <requirements>
+        <requirement type="package" version="1.4.1">10x_bamtofastq</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        bamtofastq --nthreads "\${GALAXY_SLOTS:-4}" --reads-per-fastq 10000000000
+        #if $convert.reads == 'subset':
+            --locus $convert.locus
+        #end if
+        $produced_from
+        $tenx_bam
+        outdir &&
+        mv outdir/*/*.fastq.gz outdir
+    ]]></command>
+    <inputs>
+        <param format="bam" name="tenx_bam" type="data" label="10X Genomics BAM file to convert to FASTQ"/>
+        <conditional name="convert">
+            <param name="reads" type="select" label="Read pairs to convert?">
+                <option value="all">Complete BAM file</option>
+                <option value="subset">Only a subset of BAM file</option>
+            </param>
+            <when value="all" />
+            <when value="subset">
+                <param name="locus" type="text" value=""
+                    label="Only include read pairs mapping to a locus."
+                    help="The format is chr:start-end, for example &quot;chr1:14300-125000&quot;.">
+                    <sanitizer>
+                        <valid initial="string.letters,string.digits">
+                            <add value=":"/>
+                            <add value="-"/>
+                         </valid>
+                    </sanitizer>
+                </param>
+            </when>
+        </conditional>
+        <param name="sort" type="boolean" label="Skip unpaired or duplicated reads instead of throwing an error?" checked="False" falsevalue="" truevalue="--relaxed"/>
+        <param name="produced_from" type="select" label="BAM file produced from">
+            <option value="">Long Ranger v2.1+ and Cell Ranger v1.2+</option>
+            <option value="--gemcode">GemCode data (Longranger 1.0 - 1.3)</option>
+            <option value="--lr20">Longranger 2.0</option>
+            <option value="--cr11">Cell Ranger 1.0-1.1</option>
+        </param>
+    </inputs>
+    <outputs>
+        <collection name="fastq_collection" type="list" label="10x FASTQs from ${on_string}">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq\.gz" directory="outdir" format="fastqsanger.gz"/>
+        </collection>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="tenx_bam" value="A10.sub.bam"/>
+            <output_collection name="fastq_collection" type="list" count="3">
+                <element name="bamtofastq_S1_L007_I1_001" file="bamtofastq_S1_L007_I1_001.fastq.gz"/>
+                <element name="bamtofastq_S1_L007_R1_001" file="bamtofastq_S1_L007_R1_001.fastq.gz"/>
+                <element name="bamtofastq_S1_L007_R2_001" file="bamtofastq_S1_L007_R2_001.fastq.gz"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+        10x Genomics BAM to FASTQ converter
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{github10xbamtofastq,
+            author = {},
+            year = {2022},
+            title = {10x bamtofastq},
+            publisher = {Github},
+            journal = {Github repository},
+            url = {https://github.com/10XGenomics/bamtofastq},
+        }</citation>
+    </citations>
+</tool>

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