| Previous changeset 13:e221fe58c2f5 (2025-06-19) Next changeset 15:57934e90e27c (2025-11-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 2f49183ddc89c7753d447c1dc40597d4a32eadfb |
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modified:
macros.xml samtools_stats.xml |
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| diff -r e221fe58c2f5 -r 1ed8ed887035 macros.xml --- a/macros.xml Thu Jun 19 13:01:32 2025 +0000 +++ b/macros.xml Fri Jun 27 10:56:32 2025 +0000 |
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| @@ -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[ |
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| diff -r e221fe58c2f5 -r 1ed8ed887035 samtools_stats.xml --- a/samtools_stats.xml Thu Jun 19 13:01:32 2025 +0000 +++ b/samtools_stats.xml Fri Jun 27 10:56:32 2025 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="samtools_stats" name="Samtools stats" version="2.0.6" profile="@PROFILE@">\n+<tool id="samtools_stats" name="Samtools stats" version="2.0.7" profile="@PROFILE@">\n <description>generate statistics for BAM dataset</description>\n <macros>\n <import>macros.xml</import>\n@@ -169,7 +169,7 @@\n <param name="addref_select" value="history" />\n <param name="ref" value="test.fa" ftype="fasta" />\n </conditional>\n- <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="8" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/1.stats.expected\',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->\n <test expect_num_outputs="1">\n@@ -178,7 +178,7 @@\n <param name="addref_select" value="history" />\n <param name="ref" value="test.fa" ftype="fasta" />\n </conditional>\n- <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="8" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/2.stats.expected\',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->\n <!-- test_cmd($opts,out=>\'stat/3.stats.expected\',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);-->\n@@ -191,7 +191,7 @@\n <param name="addref_select" value="history" />\n <param name="ref" value="test.fa" ftype="fasta" />\n </conditional>\n- <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="8" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/6.stats.expected\',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->\n <!-- test_cmd($opts,out=>\'stat/7.stats.expected\',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); -->\n@@ -207,7 +207,7 @@\n <param name="select_region" value="tab"/>\n <param name="targetregions" value="11.stats.targets" ftype="tabular" />\n </conditional>\n- <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="8" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/11.stats.expected\',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); -->\n \n@@ -222,7 +222,7 @@\n <param name="regions_repeat_1|region" value="ref1:30-46"/>\n <param name="regions_repeat_2|region" value="ref1:39-56"/>\n </conditional>\n- <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="8" />\n </test>\n <!-- test_cmd($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);\n -->\n@@ -236,7 +236,7 @@\n <param name="targetregions" value="11.stats.targets" ftype="tabular" />\n </conditional>\n <param name="cov_threshold" value="4" />\n- <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="11.stats.g4'..b'md=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->\n <test expect_num_outputs="1">\n@@ -263,7 +263,7 @@\n <param name="select_region" value="tab"/>\n <param name="targetregions" value="12_3reads.bed" ftype="tabular" />\n </conditional>\n- <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="8" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.3reads.overlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->\n <test expect_num_outputs="1">\n@@ -276,7 +276,7 @@\n <param name="targetregions" value="12_3reads.bed" ftype="tabular" />\n </conditional>\n <param name="remove_overlaps" value="true"/>\n- <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="8" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.3reads.nooverlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->\n <test expect_num_outputs="1">\n@@ -288,7 +288,7 @@\n <param name="select_region" value="tab"/>\n <param name="targetregions" value="12_2reads.bed" ftype="tabular" />\n </conditional>\n- <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="8" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.2reads.overlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->\n <test expect_num_outputs="1">\n@@ -301,7 +301,7 @@\n <param name="targetregions" value="12_2reads.bed" ftype="tabular" />\n </conditional>\n <param name="remove_overlaps" value="true"/>\n- <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="8" />\n </test>\n <!-- test_cmd($opts,out=>\'stat/12.2reads.nooverlap.expected\',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->\n <test expect_num_outputs="1">\n@@ -310,7 +310,7 @@\n <param name="addref_select" value="history" />\n <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />\n </conditional>\n- <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />\n+ <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="8" />\n </test>\n <test expect_num_outputs="1">\n <param name="input" value="samtools_stats_input.bam" ftype="bam" />\n@@ -325,7 +325,7 @@\n <output_collection name="output_collection" type="list">\n <element name="ACGT content per cycle" ftype="tabular" file="samtools_stats_out1__gcc.tab"/>\n <element name="Mismatches per cycle and quality" ftype="tabular" file="samtools_stats_out1__mpc.tab" />\n- <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" />\n+ <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" lines_diff="2" />\n </output_collection>\n </test>\n <!-- test filtering by read group -->\n' |