Mercurial > repos > iuc > samtools_ampliconclip

changeset 5:f20b704ba069 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 2f49183ddc89c7753d447c1dc40597d4a32eadfb
author iuc
date Fri, 27 Jun 2025 10:55:12 +0000
parents f597cb9b33bf
children
files macros.xml samtools_ampliconclip.xml test-data/eboVir3.primer_counts.txt test-data/rebuild_output_bams.sh
diffstat 4 files changed, 26 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Jun 19 12:58:20 2025 +0000
+++ b/macros.xml	Fri Jun 27 10:55:12 2025 +0000
@@ -11,7 +11,7 @@
          please only bump the minor version in order to let the requirement
          version catch up eventually). To find the tools check:
         `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
-    <token name="@TOOL_VERSION@">1.21</token>
+    <token name="@TOOL_VERSION@">1.22</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.05</token>
     <token name="@FLAGS@"><![CDATA[
--- a/samtools_ampliconclip.xml	Thu Jun 19 12:58:20 2025 +0000
+++ b/samtools_ampliconclip.xml	Fri Jun 27 10:55:12 2025 +0000
@@ -19,6 +19,9 @@
             -u 
             $both_ends 
             $no_excluded
+            #if $write_primer_counts:
+                --primer-counts '${primer_counts}'
+            #end if
             -@ \$addthreads
             '${input_bam}'
             | samtools collate -@ \$addthreads -O -u -
@@ -28,40 +31,43 @@
     <inputs>
         <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
         <param name="input_bam" type="data" format="bam" label="BAM file" />
-        <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" />
+        <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchecked = default soft-clipping" />
         <param argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
         <param argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
         <param argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
         <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" />
         <param argument="--tolerance" type="integer" value="5" min="0"  label="Tolerance" help="match region within this number of bases, default 5." />
-    
+        <param name="write_primer_counts" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Write primer counts" help="If enabled, write primer counts to output file." />
     </inputs>
     <outputs>
         <data name="output_bam" format="bam" />
+        <data name="primer_counts" format="bedgraph" label="${tool.name} on ${on_string}: Primer counts">
+            <filter>write_primer_counts</filter>
+        </data>
     </outputs>
     <tests>
         <!-- 1) -->
-        <test>
+        <test expect_num_outputs="1">
             <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>
+        <test expect_num_outputs="1">
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bam" value="eboVir3.bam" ftype="bam" />
             <param name="strand" value="true" />
             <output name="output_bam" file="eboVir3.clipped.strand.bam" ftype="bam" lines_diff="16" />
         </test>
         <!-- 3) testing hard clip-->
-        <test>
+        <test expect_num_outputs="1">
             <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="true" />
             <output name="output_bam" file="eboVir3.hardclipped.bam" ftype="bam" lines_diff="14" />
         </test>
         <!-- 4) testing strand and min length-->
-        <test>
+        <test expect_num_outputs="1">
             <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" />
@@ -71,7 +77,14 @@
             <param name="no_excluded" value="true" />
             <output name="output_bam" file="eboVir3.clipped.strand_gt30.bam" ftype="bam" lines_diff="13" />
         </test>
-        
+        <!-- 5) testing write_primer_counts -->
+        <test expect_num_outputs="2">
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bam" value="eboVir3.bam" ftype="bam" />
+            <param name="write_primer_counts" value="true" />
+            <output name="output_bam" file="eboVir3.clipped.bam" ftype="bam" lines_diff="22" />
+            <output name="primer_counts" file="eboVir3.primer_counts.txt" ftype="bedgraph" />
+        </test>
     </tests>
     <help>
 **What it does**
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/eboVir3.primer_counts.txt	Fri Jun 27 10:55:12 2025 +0000
@@ -0,0 +1,4 @@
+#CHR	LEFT	RIGHT	NAME	SCORE	STRAND	NUM_CLIPPED
+eboVir3	500	1500	1	0	.	115
+eboVir3	1500	2000	2	0	.	20
+eboVir3	1500	3000	3	0	.	119
--- a/test-data/rebuild_output_bams.sh	Thu Jun 19 12:58:20 2025 +0000
+++ b/test-data/rebuild_output_bams.sh	Fri Jun 27 10:55:12 2025 +0000
@@ -1,4 +1,4 @@
-samtools ampliconclip -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.clipped.bam
+samtools ampliconclip -b eboVir3.1.bed --primer-counts eboVir3.primer_counts.txt eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.clipped.bam
 samtools ampliconclip --strand -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.clipped.strand.bam
 samtools ampliconclip --hard-clip -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.hardclipped.bam
 samtools ampliconclip --both-ends --no-excluded --strand --fail-len 30 -b eboVir3.1.bed eboVir3.bam | samtools collate -@ 0 -O -u - | samtools fixmate -@ 0 -u - - | samtools sort -o eboVir3.clipped.strand_gt30.bam