Mercurial > repos > iuc > samtools_merge

annotate samtools_merge.xml @ 5:84f122ab14d6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:23:00 +0000
parents 95fd8bf80632
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
84f122ab14d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
1 <tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
2 <description>merge multiple sorted alignment files</description>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
3 <macros>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
4 <import>macros.xml</import>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
5 </macros>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
7 <expand macro="stdio"/>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
8 <expand macro="version_command"/>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
9 <command><![CDATA[
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
10 @ADDTHREADS@
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
11 ## prepare input (sort sam, link other), determine input ordering
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
12 ## and check for consistent input ordering
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
13 #set sortby=''
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
14 #for $i, $bam in enumerate( $bamfiles ):
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
15 #if $bam.is_of_type('sam', 'cram', ):
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
16 samtools sort
1
a27cd1e0d9a5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
iuc
parents: 0
diff changeset
17 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
18 -O sam
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
19 -o ${i}.sam
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
20 '$bam' &&
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
21 #else:
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
22 ln -s '$bam' ${i}.sam &&
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
23 #end if
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
24 #if ($sortby=='coord' or $sortby=='') and $bam.is_of_type('sam','bam','cram'):
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
25 #set sortby='coord'
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
26 #else if ($sortby=='name' or $sortby=='') and $bam.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
27 #set $sortby='name'
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
28 #else:
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
29 >&2 echo "inconsistently sorted input" &&
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
30 exit 1 &&
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
31 #end if
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
32 #end for
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
33 #if $bed_file
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
34 #for $i, $bam in enumerate( $bamfiles ):
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
35 samtools index ${i}.sam &&
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
36 #end for
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
37 #end if
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
38 samtools merge
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
39 -@ \$addthreads
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
40 -s $seed
5
84f122ab14d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
41 ## force overwrite seems necessay (but I do not understand why ...)
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
42 -f
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
43 ## Galaxy provides only default compression
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
44 ## #if $compression == 'levelone'
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
45 ## -1
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
46 ## #else if $compression == 'uncompressed'
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
47 ## -u
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
48 ## #end if
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
49 #if str($headerbam) != 'None'
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
50 -h '$headerbam'
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
51 #end if
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
52 #if $sortby=='name'
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
53 -n
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
54 #end if
5
84f122ab14d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
55 ## since galaxy can't represent this as data type at the moment this option is unsupported
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
56 ## -t TAG The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given).
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
57 #if str($region) != ''
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
58 -R '$region'
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
59 #end if
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
60 ## Attach an RG tag to each alignment. The tag value is inferred from file names.
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
61 ## -r
5
84f122ab14d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
62 ## -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used?
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
63 #if $bed_file:
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
64 -L '$bed_file'
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
65 #end if
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
66 $idrg
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
67 $idpg
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
68 $output
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
69 #for $i, $bam in enumerate( $bamfiles ):
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
70 ${i}.sam
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
71 #end for
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
72 ]]></command>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
73 <inputs>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
74 <param name="bamfiles" type="data" format="sam,bam,cram" multiple="true" optional="false" label="Alignments in BAM format" help="Sets of aligned reads." />
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
75 <param name="bed_file" type="data" optional="true" format="bed" label="Merge only reads overlapping the specified regions in the BED file" />
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
76 <param name="region" type="text" optional="true" argument="-n" label="Merge files in a region" help="Merge files in the specified region indicated by a string" />
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
77 <param name="headerbam" type="data" format="sam,bam" argument="-h" multiple="false" optional="true" label="File to take @headers from" help="Use the lines of FILE as `@' headers to be copied to out.bam, replacing any header lines that would otherwise be copied from in1.bam. (FILE is actually in SAM format, though any alignment records it may contain are ignored.)" />
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
78 <param name="idrg" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Make @RG headers unique" help="When several input files contain @RG headers with the same ID, emit only one of them (namely, the header line from the first file we find that ID in) to the merged output file. Combining these similar headers is usually the right thing to do when the files being merged originated from the same file. Without -c, all @RG headers appear in the output file, with random suffices added to their IDs where necessary to differentiate them." />
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
79 <param name="idpg" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Make @PG headers unique" help="Similarly, for each @PG ID in the set of files to merge, use the @PG line of the first file we find that ID in rather than adding a suffix to differentiate similar IDs." />
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
80 <param name="seed" type="integer" argument="-s" value="1" label="random seed" />
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
81 <!-- compression options are not accessible in galaxy
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
82 <param name="compression" type="select" label="Advanced compression options" help="Select advanced compression options">
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
83 <option value="default" selected="true">default</option>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
84 <option value="levelone">Use zlib compression level 1</option>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
85 <option value="uncompressed">Uncompressed output</option>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
86 </param>-->
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
87 </inputs>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
88 <outputs>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
89 <data name="output" format="bam" />
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
90 </outputs>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
91 <tests>
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
92 <!--tests and data extracted from
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
93 https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
94 https://github.com/samtools/samtools/tree/develop/test/merge -->
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
95 <!-- Merge 1 - Standard 3 file SAM merge all presented on the command line (only checks for similar size, because generated header info differs) -->
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
96 <test>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
97 <param name="bamfiles" value="test_input_1_a.sam,test_input_1_b.sam,test_input_1_c.sam" />
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
98 <output name="output" file="1.merge.expected.bam" ftype="bam" lines_diff="16" />
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
99 </test>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
100 <!-- Merge 2 - Standard 3 file BAM merge all files presented on the command line -->
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
101 <test>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
102 <param name="bamfiles" value="test_input_1_a.bam,test_input_1_b.bam,test_input_1_c.bam" />
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
103 <output name="output" file="2.merge.expected.bam" ftype="bam" lines_diff="16" />
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
104 </test>
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
105 <!-- Merge 3 - 1 file BAM merge with file presented on the command line -->
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
106 <test>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
107 <param name="bamfiles" value="test_input_1_b.bam" />
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
108 <output name="output" file="3.merge.expected.bam" ftype="bam" lines_diff="16" />
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
109 </test>
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
110 <!--Merge 4 - merge all presented on the command line, combine PG and RG rather than dedup -->
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
111 <test>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
112 <param name="bamfiles" value="test_input_1_a.bam,test_input_1_b.bam" />
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
113 <param name="idrg" value="-c" />
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
114 <param name="idpg" value="-p" />
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
115 <output name="output" file="4.merge.expected.bam" ftype="bam" lines_diff="16" />
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
116 </test>
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
117 <!-- Merge 5 - ID and SN with regex in them (probably not necessary for the galaxy tool because just different input) -->
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
118 <test>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
119 <param name="bamfiles" value="test_input_1_a_regex.sam,test_input_1_b_regex.sam" />
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
120 <output name="output" file="5.merge.expected.bam" ftype="bam" lines_diff="16" />
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
121 </test>
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
122 <!-- Merge 6 - Merging with bedfile -->
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
123 <test>
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
124 <param name="bamfiles" value="test_input_1_a.bam,test_input_1_b.bam,test_input_1_c.bam" />
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
125 <param name="bed_file" value="test_input_1_a.bed" />
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
126 <output name="output" file="6.merge.expected.bam" ftype="bam" lines_diff="16" />
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
127 </test>
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
128 <!--Merge - 3 file SAM merge all presented on the command line override IDs to file names (not implemented in tool) -->
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
129 <!-- Sort inputs by PG, then merge (not implemented, since -t not supported in the tool) -->
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
130 <!-- Sort inputs by PG, then merge (name sorted) (not implemented, since -t not supported in the tool) -->
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
131 </tests>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
132 <help>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
133 **What it does**
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
134 Merge multiple sorted alignment files, producing a single sorted output file that contains all the input records and maintains the existing sort order.
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
135
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
136 If a file to take @headers from is specified the @SQ headers of input files will be merged into the specified header, otherwise they will be merged into a composite header created from the input headers. If in the process of merging @SQ lines for coordinate sorted input files, a conflict arises as to the order (for example input1.bam has @SQ for a,b,c and input2.bam has b,a,c) then the resulting output file will need to be re-sorted back into coordinate order.
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
137
2
09015d802fdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 1
diff changeset
138 Unless the @PG/@RG headers are made unique when merging @RG and @PG records into the output header then any IDs found to be duplicates of existing IDs in the output header will have a suffix appended to them to differentiate them from similar header records from other files and the read records will be updated to reflect this.
0
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
139 </help>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
140 <expand macro="citations"/>
ce3f4ecc9258 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit 322cbb9a3bb01f858068bda319e72b0a3ff4251b
iuc
parents:
diff changeset
141 </tool>