| Previous changeset 0:046cbf29795a (2018-09-28) Next changeset 2:a312a0fdaf31 (2021-04-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27" |
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modified:
samtools_markdup.xml |
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added:
test-data/stats.txt |
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| diff -r 046cbf29795a -r 83b8e36e9cbe samtools_markdup.xml --- a/samtools_markdup.xml Fri Sep 28 04:29:07 2018 -0400 +++ b/samtools_markdup.xml Fri Sep 06 06:35:26 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@"> +<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy2"> <description>marks duplicate alignments</description> <macros> <import>macros.xml</import> @@ -11,7 +11,7 @@ ## coordinate sort input #if not $bamfile.is_of_type('bam'): samtools sort - -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp + -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" -O sam -o coordsort.sam '$bamfile' && @@ -30,51 +30,66 @@ $supp coordsort.sam '$output' +#if $stats + 2> '$stats_output' +#end if ]]></command> <inputs> <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Alignment" /> <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" /> <param name="maxlen" type="integer" optional="true" argument="-l" min="0" label="Expected maximum read length of INT bases. (default 300)"/> - <param name="stats" type="boolean" argument="-s" truevalue="-s" falsevalue="" label="Print basic statistics" /> - <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" /> + <param name="stats" type="boolean" argument="-s" truevalue="-s" falsevalue="" label="Print basic statistics" /> + <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" /> </inputs> <outputs> - <!-- output bam, if input was name sorted then restore this sorting order --> - <data name="output" format="bam"/> + <!-- output bam, if input was name sorted then restore this sorting order --> + <data name="output" format="bam"/> + <data name="stats_output" format="txt"> + <filter>stats</filter> + </data> </outputs> <tests> <!-- tests and data extracted from - https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2616 + https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2616 TODO the 1st 4 tests are negative, I do not know how to test for the error code --> <!-- test_cmd($opts, out=>'markdup/1_name_sort.expected.sam', err=>'1_name_sort.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/1_name_sort.sam -", expect_fail=>1); test_cmd($opts, out=>'markdup/2_bad_order.expected.sam', err=>'2_bad_order.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/2_bad_order.sam -", expect_fail=>1); test_cmd($opts, out=>'markdup/3_missing_mc.expected.sam', err=>'3_missing_mc.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/3_missing_mc.sam -", expect_fail=>1); test_cmd($opts, out=>'markdup/4_missing_ms.expected.sam', err=>'4_missing_ms.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/4_missing_ms.sam -", expect_fail=>1);--> - <test> + <!-- test_cmd($opts, out=>'markdup/5_markdup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/5_markdup.sam -");--> + <test expect_num_outputs="1"> <param name="bamfile" value="5_markdup.sam" /> <output name="output" file="5_markdup.expected.bam" /> </test> - <!-- test_cmd($opts, out=>'markdup/5_markdup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/5_markdup.sam -");--> - <test> + <!-- test_cmd($opts, out=>'markdup/6_remove_dups.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam -r $$opts{path}/markdup/6_remove_dups.sam -");--> + <test expect_num_outputs="1"> <param name="bamfile" value="6_remove_dups.sam" /> <param name="remove" value="-r" /> <output name="output" file="6_remove_dups.expected.bam" /> </test> - <!-- test_cmd($opts, out=>'markdup/6_remove_dups.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam -r $$opts{path}/markdup/6_remove_dups.sam -");--> - <test> + <!-- test_cmd($opts, out=>'markdup/7_mark_supp_dup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -S -O sam $$opts{path}/markdup/7_mark_supp_dup.sam -");--> + <test expect_num_outputs="1"> <param name="bamfile" value="7_mark_supp_dup.bam" /> <param name="supp" value="-S" /> <output name="output" file="7_mark_supp_dup.expected.bam" /> </test> - <!-- - test_cmd($opts, out=>'markdup/7_mark_supp_dup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -S -O sam $$opts{path}/markdup/7_mark_supp_dup.sam -");--> + <!-- test stats output --> + <test expect_num_outputs="2"> + <param name="bamfile" value="5_markdup.sam" /> + <param name="stats" value="-s" /> + <output name="output" file="5_markdup.expected.bam" /> + <output name="stats_output" file="stats.txt" /> + </test> </tests> <help> Mark duplicate alignments from a coordinate sorted file that has been run through fixmate with the -m option. This program relies on the MC and ms tags that fixmate provides. Note: The Galaxy tool sorts the data automatically if the input is SAM or query name sorted. The output is BAM (which is query name sorted again if the input is). - </help> + +The optional basic statistics output of samtools markdup can be visualized with MultiQC. + + </help> <expand macro="citations"/> </tool> |
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| diff -r 046cbf29795a -r 83b8e36e9cbe test-data/stats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats.txt Fri Sep 06 06:35:26 2019 -0400 |
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| @@ -0,0 +1,5 @@ +READ 16 WRITTEN 16 +EXCLUDED 3 EXAMINED 13 +PAIRED 10 SINGLE 3 +DULPICATE PAIR 4 DUPLICATE SINGLE 2 +DUPLICATE TOTAL 6 |