diff samtools_ampliconclip.xml @ 0:a941babb9268 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_ampliconclip.xml	Mon Jun 27 20:07:59 2022 +0000
@@ -0,0 +1,83 @@
+<tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>clip primer bases from bam files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @ADDTHREADS@
+        samtools ampliconclip
+            $hard_clip_mode
+            #if $min_length:
+                --fail-len $min_length
+            #end if
+            --tolerance $tolerance
+            $strand
+            -b '${input_bed}'
+            -u 
+            $both_ends 
+            $no_excluded
+            -@ \$addthreads
+            '${input_bam}'
+            | samtools collate -@ \$addthreads -O -u -
+            | samtools fixmate -@ \$addthreads -u - - 
+            | samtools sort -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" -o '${output_bam}'
+    ]]></command>
+    <inputs>
+        <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
+        <param name="input_bam" type="data" format="bam" label="BAM file" />
+        <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" />
+        <param name="strand" argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
+        <param name="both_ends" argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
+        <param name="no_excluded" argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
+        <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" />
+        <param name="tolerance" argument="--tolerance" type="integer" value="5" min="0"  label="Tolerance" help="match region within this number of bases, default 5." />
+    
+    </inputs>
+    <outputs>
+        <data name="output_bam" format="bam" />
+    </outputs>
+    <tests>
+        <!-- 1) -->
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bam" value="eboVir3.bam" ftype="bam" />
+            <output name="output_bam" file="eboVir3.clipped.bam" ftype="bam" lines_diff="22" />
+        </test>
+        <!-- 2) testing strand -->
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bam" value="eboVir3.bam" ftype="bam" />
+            <param name="strand" value="--strand" />
+            <output name="output_bam" file="eboVir3.clipped.strand.bam" ftype="bam" lines_diff="16" />
+        </test>
+        <!-- 3) testing hard clip-->
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bam" value="eboVir3.bam" ftype="bam" />
+            <param name="hard_clip_mode" value="--hard-clip" />
+            <output name="output_bam" file="eboVir3.hardclipped.bam" ftype="bam" lines_diff="14" />
+        </test>
+        <!-- 4) testing strand and min length-->
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bam" value="eboVir3.bam" ftype="bam" />
+            <param name="min_length" value="30" />
+            <param name="strand" value="--strand" />
+            <param name="tolerance" value="6" />
+            <param name="both_ends" value="--both-ends" />
+            <param name="no_excluded" value="--no-excluded" />
+            <output name="output_bam" file="eboVir3.clipped.strand_gt30.bam" ftype="bam" lines_diff="13" />
+        </test>
+        
+    </tests>
+    <help>
+**What it does**
+ Clips read alignments where they match BED file defined regions (e.g. for amplicon sequencing).
+
+ samtools ampliconclip -b [INPUT BED] [INPUT BAM1] -o [OUTPUT]
+    </help>
+    <expand macro="citations"/>
+</tool>