Mercurial > repos > devteam > samtools_stats

diff samtools_stats.xml @ 13:c03b52838177 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_stats commit 26763d398d563ccafd2d66ab325f50f5708b5ebc
author iuc
date Fri, 06 Mar 2026 10:39:57 +0000
parents 8fecc86e574a
children
line wrap: on
line diff
--- a/samtools_stats.xml	Sun Sep 08 03:23:56 2024 +0000
+++ b/samtools_stats.xml	Fri Mar 06 10:39:57 2026 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_stats" name="Samtools stats" version="2.0.5" profile="@PROFILE@">
+<tool id="samtools_stats" name="Samtools stats" version="2.0.9" profile="@PROFILE@">
     <description>generate statistics for BAM dataset</description>
     <macros>
         <import>macros.xml</import>
@@ -169,16 +169,16 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="test.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->
         <test expect_num_outputs="1">
             <param name="input" value="2_equal_cigar_full_seq.sam" ftype="sam" />
             <conditional name="addref_cond">
-                <param name="addref_select" value="history" />
-                <param name="ref" value="test.fa" ftype="fasta" />
+                <param name="addref_select" value="cached" />
+                <param name="ref" value="test" />
             </conditional>
-            <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
         <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);-->
@@ -191,7 +191,7 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="test.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
         <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); -->
@@ -207,7 +207,7 @@
                 <param name="select_region" value="tab"/>
                 <param name="targetregions" value="11.stats.targets" ftype="tabular" />
             </conditional>
-            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); -->
 
@@ -222,7 +222,7 @@
                 <param name="regions_repeat_1|region" value="ref1:30-46"/>
                 <param name="regions_repeat_2|region" value="ref1:39-56"/>
             </conditional>
-            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix);
 -->
@@ -236,7 +236,7 @@
                 <param name="targetregions" value="11.stats.targets" ftype="tabular" />
             </conditional>
             <param name="cov_threshold" value="4" />
-            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);-->
         <test expect_num_outputs="1">
@@ -251,7 +251,7 @@
                 <param name="regions_repeat_2|region" value="ref1:39-56"/>
             </conditional>
             <param name="cov_threshold" value="4" />
-            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->
         <test expect_num_outputs="1">
@@ -263,7 +263,7 @@
                 <param name="select_region" value="tab"/>
                 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
             </conditional>
-            <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/12.3reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
         <test expect_num_outputs="1">
@@ -275,8 +275,8 @@
                 <param name="select_region" value="tab"/>
                 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
             </conditional>
-            <param name="remove_overlaps" value="-p"/>
-            <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
+            <param name="remove_overlaps" value="true"/>
+            <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
         <test expect_num_outputs="1">
@@ -288,7 +288,7 @@
                 <param name="select_region" value="tab"/>
                 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
             </conditional>
-            <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/12.2reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
         <test expect_num_outputs="1">
@@ -300,8 +300,8 @@
                 <param name="select_region" value="tab"/>
                 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
             </conditional>
-            <param name="remove_overlaps" value="-p"/>
-            <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
+            <param name="remove_overlaps" value="true"/>
+            <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
         <test expect_num_outputs="1">
@@ -310,7 +310,7 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />
+            <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="8" />
         </test>
         <test expect_num_outputs="1">
             <param name="input" value="samtools_stats_input.bam" ftype="bam" />
@@ -325,7 +325,7 @@
             <output_collection name="output_collection" type="list">
                 <element name="ACGT content per cycle" ftype="tabular" file="samtools_stats_out1__gcc.tab"/>
                 <element name="Mismatches per cycle and quality" ftype="tabular" file="samtools_stats_out1__mpc.tab" />
-                <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" />
+                <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" lines_diff="2" />
             </output_collection>
         </test>
         <!-- test filtering by read group -->