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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
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4:95fd8bf80632 5:84f122ab14d6
1 <tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>merge multiple sorted alignment files</description> 2 <description>merge multiple sorted alignment files</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"/>
36 #end for 36 #end for
37 #end if 37 #end if
38 samtools merge 38 samtools merge
39 -@ \$addthreads 39 -@ \$addthreads
40 -s $seed 40 -s $seed
41 ## TODO force overwrite seems necessay (but I do not understand why ...) 41 ## force overwrite seems necessay (but I do not understand why ...)
42 -f 42 -f
43 ## Galaxy provides only default compression 43 ## Galaxy provides only default compression
44 ## #if $compression == 'levelone' 44 ## #if $compression == 'levelone'
45 ## -1 45 ## -1
46 ## #else if $compression == 'uncompressed' 46 ## #else if $compression == 'uncompressed'
50 -h '$headerbam' 50 -h '$headerbam'
51 #end if 51 #end if
52 #if $sortby=='name' 52 #if $sortby=='name'
53 -n 53 -n
54 #end if 54 #end if
55 ## TODO since galaxy can't represent this as data type at the moment this option is unsupported 55 ## since galaxy can't represent this as data type at the moment this option is unsupported
56 ## -t TAG The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given). 56 ## -t TAG The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given).
57 #if str($region) != '' 57 #if str($region) != ''
58 -R '$region' 58 -R '$region'
59 #end if 59 #end if
60 ## Attach an RG tag to each alignment. The tag value is inferred from file names. 60 ## Attach an RG tag to each alignment. The tag value is inferred from file names.
61 ## -r 61 ## -r
62 ## TODO -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used? 62 ## -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used?
63 #if $bed_file: 63 #if $bed_file:
64 -L '$bed_file' 64 -L '$bed_file'
65 #end if 65 #end if
66 $idrg 66 $idrg
67 $idpg 67 $idpg