comparison samtools_merge.xml @ 4:65a38e8c8e2a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit cd62639660bef041ba14ecff337fb98e84e75d8a

3:36677f429310

<tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>merge multiple sorted alignment files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    #end for
#end if
samtools merge
-@ \$addthreads
-s $seed
## TODO force overwrite seems necessay (but I do not understand why ...)
-f
## Galaxy provides only default compression
## #if $compression == 'levelone'
##     -1
## #else if $compression == 'uncompressed'

    -h '$headerbam'
#end if
#if $sortby=='name'
    -n
#end if
## TODO since galaxy can't represent this as data type at the moment this option is unsupported
## -t TAG    The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given).
#if str($region) != ''
    -R '$region'
#end if
## Attach an RG tag to each alignment. The tag value is inferred from file names.
## -r
## TODO -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used?
#if $bed_file:
    -L '$bed_file'
#end if
$idrg
$idpg

4:65a38e8c8e2a

<tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>merge multiple sorted alignment files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    #end for
#end if
samtools merge
-@ \$addthreads
-s $seed
## force overwrite seems necessay (but I do not understand why ...)
-f
## Galaxy provides only default compression
## #if $compression == 'levelone'
##     -1
## #else if $compression == 'uncompressed'

    -h '$headerbam'
#end if
#if $sortby=='name'
    -n
#end if
## since galaxy can't represent this as data type at the moment this option is unsupported
## -t TAG    The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given).
#if str($region) != ''
    -R '$region'
#end if
## Attach an RG tag to each alignment. The tag value is inferred from file names.
## -r
## -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used?
#if $bed_file:
    -L '$bed_file'
#end if
$idrg
$idpg