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changeset 14:1ed8ed887035 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 2f49183ddc89c7753d447c1dc40597d4a32eadfb
author iuc
date Fri, 27 Jun 2025 10:56:32 +0000
parents e221fe58c2f5
children
files macros.xml samtools_stats.xml
diffstat 2 files changed, 15 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Jun 19 13:01:32 2025 +0000
+++ b/macros.xml	Fri Jun 27 10:56:32 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_stats.xml	Thu Jun 19 13:01:32 2025 +0000
+++ b/samtools_stats.xml	Fri Jun 27 10:56:32 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_stats" name="Samtools stats" version="2.0.6" profile="@PROFILE@">
+<tool id="samtools_stats" name="Samtools stats" version="2.0.7" profile="@PROFILE@">
     <description>generate statistics for BAM dataset</description>
     <macros>
         <import>macros.xml</import>
@@ -169,7 +169,7 @@
                 <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 $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->
         <test expect_num_outputs="1">
@@ -178,7 +178,7 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="test.fa" ftype="fasta" />
             </conditional>
-            <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$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=>$efix);-->
         <test expect_num_outputs="1">
@@ -276,7 +276,7 @@
                 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
             </conditional>
             <param name="remove_overlaps" value="true"/>
-            <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($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=>$efix);-->
         <test expect_num_outputs="1">
@@ -301,7 +301,7 @@
                 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
             </conditional>
             <param name="remove_overlaps" value="true"/>
-            <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
+            <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="8" />
         </test>
         <!-- test_cmd($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 -->