Mercurial > repos > iuc > samtools_fixmate
comparison 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 |
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| 0:bc0cc7bfbfe9 | 1:595ae1ba934a |
|---|---|
| 1 <tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@"> | 1 <tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@" profile="@PROFILE@"> |
| 2 <description>fill mate coordinates, ISIZE and mate related flags</description> | 2 <description>fill mate coordinates, ISIZE and mate related flags</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
| 8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 @ADDTHREADS@ | 10 @ADDTHREADS@ |
| 11 ## name sort input | 11 ## name sort input |
| 12 #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'): | 12 #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'): |
| 13 samtools sort | 13 samtools sort |
| 14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp | 14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" |
| 15 -n | 15 -n |
| 16 -O BAM | 16 -O BAM |
| 17 -o namesorted.bam | 17 -o namesorted.bam |
| 18 '$bamfile' && | 18 '$bamfile' && |
| 19 #else: | 19 #else: |
| 20 ln -s '$bamfile' namesorted.bam && | 20 ln -s '$bamfile' namesorted.bam && |
| 36 <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" /> | 36 <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" /> |
| 37 <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" /> | 37 <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" /> |
| 38 <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." /> | 38 <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." /> |
| 39 </inputs> | 39 </inputs> |
| 40 <outputs> | 40 <outputs> |
| 41 <!--<data name="output" format="sam" />--> | 41 <!--<data name="output" format="sam" />--> |
| 42 <data name="output" format="qname_sorted.bam"/> | 42 <data name="output" format="qname_sorted.bam"/> |
| 43 </outputs> | 43 </outputs> |
| 44 <tests> | 44 <tests> |
| 45 <!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493--> | 45 <!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493--> |
| 46 <!-- test_cmd($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);--> | 46 <!-- 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);--> |
| 47 <test> | 47 <test> |
| 48 <param name="bamfile" value="2_isize_overflow.sam" /> | 48 <param name="bamfile" value="2_isize_overflow.sam" ftype="sam" /> |
| 49 <output name="output" file="2_isize_overflow.bam.expected" /> | 49 <output name="output" file="2_isize_overflow.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> |
| 50 </test> | 50 </test> |
| 51 <!-- 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 -");--> | 51 <!-- 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 -");--> |
| 52 <test> | 52 <test> |
| 53 <param name="bamfile" value="3_reverse_read_pp_lt.sam" /> | 53 <param name="bamfile" value="3_reverse_read_pp_lt.sam" ftype="sam" /> |
| 54 <output name="output" file="3_reverse_read_pp_lt.bam.expected" /> | 54 <output name="output" file="3_reverse_read_pp_lt.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> |
| 55 </test> | 55 </test> |
| 56 <!-- 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 -");--> | 56 <!-- 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 -");--> |
| 57 <test> | 57 <test> |
| 58 <param name="bamfile" value="4_reverse_read_pp_equal.sam" /> | 58 <param name="bamfile" value="4_reverse_read_pp_equal.sam" ftype="sam" /> |
| 59 <output name="output" file="4_reverse_read_pp_equal.bam.expected" /> | 59 <output name="output" file="4_reverse_read_pp_equal.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> |
| 60 </test> | 60 </test> |
| 61 <!-- 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 -");--> | 61 <!-- 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 -");--> |
| 62 <test> | 62 <test> |
| 63 <param name="bamfile" value="5_ct.sam" /> | 63 <param name="bamfile" value="5_ct.sam" ftype="sam" /> |
| 64 <param name="tempcigar" value="-c" /> | 64 <param name="tempcigar" value="-c" /> |
| 65 <output name="output" file="5_ct.bam.expected" /> | 65 <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> |
| 66 </test> | 66 </test> |
| 67 <!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");--> | 67 <!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");--> |
| 68 <test> | 68 <test> |
| 69 <param name="bamfile" value="6_ct_replace.sam" /> | 69 <param name="bamfile" value="6_ct_replace.sam" ftype="sam" /> |
| 70 <param name="tempcigar" value="-c" /> | 70 <param name="tempcigar" value="-c" /> |
| 71 <output name="output" file="6_ct_replace.bam.expected" /> | 71 <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> |
| 72 </test> | 72 </test> |
| 73 <!-- 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 -");--> | 73 <!-- 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 -");--> |
| 74 <test> | 74 <test> |
| 75 <param name="bamfile" value="7_two_read_mapped.sam" /> | 75 <param name="bamfile" value="7_two_read_mapped.sam" ftype="sam" /> |
| 76 <output name="output" file="7_two_read_mapped.bam.expected" /> | 76 <output name="output" file="7_two_read_mapped.bam.expected" ftype="qname_sorted.bam" lines_diff="4" /> |
| 77 </test> | 77 </test> |
| 78 <!--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 -");--> | 78 <!--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 -");--> |
| 79 </tests> | 79 </tests> |
| 80 <help> | 80 <help> |
| 81 **What it does** | 81 **What it does** |
| 82 | 82 |
| 83 Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment. | 83 Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment. |