Mercurial > repos > iuc > samtools_fixmate
diff samtools_fixmate.xml @ 1:595ae1ba934a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:13:23 +0000 |
| parents | bc0cc7bfbfe9 |
| children | 41e36c99a008 |
line wrap: on
line diff
--- a/samtools_fixmate.xml Fri Sep 28 04:28:45 2018 -0400 +++ b/samtools_fixmate.xml Tue Sep 28 16:13:23 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@"> +<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>fill mate coordinates, ISIZE and mate related flags</description> <macros> <import>macros.xml</import> @@ -8,11 +8,11 @@ <expand macro="version_command"/> <command><![CDATA[ @ADDTHREADS@ - ## name sort input + ## name sort input #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'): samtools sort - -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp - -n + -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" + -n -O BAM -o namesorted.bam '$bamfile' && @@ -38,44 +38,44 @@ <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." /> </inputs> <outputs> - <!--<data name="output" format="sam" />--> - <data name="output" format="qname_sorted.bam"/> + <!--<data name="output" format="sam" />--> + <data name="output" format="qname_sorted.bam"/> </outputs> <tests> -<!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493--> -<!-- test_cmd($opts,out=>'fixmate/1_coord_sort.sam.expected', err=>'fixmate/1_coord_sort.sam.expected.err', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/1_coord_sort.sam -", expect_fail=>1);--> -<test> - <param name="bamfile" value="2_isize_overflow.sam" /> - <output name="output" file="2_isize_overflow.bam.expected" /> -</test> -<!-- test_cmd($opts,out=>'fixmate/2_isize_overflow.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/2_isize_overflow.sam -");--> -<test> - <param name="bamfile" value="3_reverse_read_pp_lt.sam" /> - <output name="output" file="3_reverse_read_pp_lt.bam.expected" /> -</test> -<!-- test_cmd($opts,out=>'fixmate/3_reverse_read_pp_lt.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/3_reverse_read_pp_lt.sam -");--> -<test> - <param name="bamfile" value="4_reverse_read_pp_equal.sam" /> - <output name="output" file="4_reverse_read_pp_equal.bam.expected" /> -</test> -<!-- test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");--> -<test> - <param name="bamfile" value="5_ct.sam" /> - <param name="tempcigar" value="-c" /> - <output name="output" file="5_ct.bam.expected" /> -</test> -<!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");--> -<test> - <param name="bamfile" value="6_ct_replace.sam" /> - <param name="tempcigar" value="-c" /> - <output name="output" file="6_ct_replace.bam.expected" /> -</test> -<!-- test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");--> -<test> - <param name="bamfile" value="7_two_read_mapped.sam" /> - <output name="output" file="7_two_read_mapped.bam.expected" /> -</test> -<!--test_cmd($opts,out=>'fixmate/7_two_read_mapped.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/7_two_read_mapped.sam -");--> + <!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493--> + <!-- test_cmd($opts,out=>'fixmate/1_coord_sort.sam.expected', err=>'fixmate/1_coord_sort.sam.expected.err', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/1_coord_sort.sam -", expect_fail=>1);--> + <test> + <param name="bamfile" value="2_isize_overflow.sam" ftype="sam" /> + <output name="output" file="2_isize_overflow.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!-- test_cmd($opts,out=>'fixmate/2_isize_overflow.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/2_isize_overflow.sam -");--> + <test> + <param name="bamfile" value="3_reverse_read_pp_lt.sam" ftype="sam" /> + <output name="output" file="3_reverse_read_pp_lt.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!-- test_cmd($opts,out=>'fixmate/3_reverse_read_pp_lt.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/3_reverse_read_pp_lt.sam -");--> + <test> + <param name="bamfile" value="4_reverse_read_pp_equal.sam" ftype="sam" /> + <output name="output" file="4_reverse_read_pp_equal.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!-- test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");--> + <test> + <param name="bamfile" value="5_ct.sam" ftype="sam" /> + <param name="tempcigar" value="-c" /> + <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");--> + <test> + <param name="bamfile" value="6_ct_replace.sam" ftype="sam" /> + <param name="tempcigar" value="-c" /> + <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!-- test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");--> + <test> + <param name="bamfile" value="7_two_read_mapped.sam" ftype="sam" /> + <output name="output" file="7_two_read_mapped.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> + </test> + <!--test_cmd($opts,out=>'fixmate/7_two_read_mapped.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/7_two_read_mapped.sam -");--> </tests> <help> **What it does**