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comparison samtools_sort_transcriptome/samtools_sort.xml @ 5:21eceda8a1ae draft default tip

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author jackcurragh
date Tue, 07 Jun 2022 12:32:37 +0000
parents 9445a308fb7e
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4:9445a308fb7e 5:21eceda8a1ae
1 <tool id="samtools_transcriptome_sort" name="Samtools sort" version="2.0.5" profile="@PROFILE@"> 1 <tool id="samtools_transcriptome_sort" name="Samtools sort" version="2.0.6" profile="@PROFILE@">
2 <description>Sort Alignment Files (SAM/BAM)</description> 2 <description>Sort Alignment Files (SAM/BAM)</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"/>
20 -O bam 20 -O bam
21 -T "\${TMPDIR:-.}" 21 -T "\${TMPDIR:-.}"
22 '${input1}' 22 '${input1}'
23 > '${output1}' 23 > '${output1}'
24 ]]> 24 ]]>
25 <!-- <![CDATA[ 25 </command>
26 @ADDTHREADS@
27 @ADDMEMORY@
28 samtools sort
29 -@ \$addthreads
30 -m \$addmemory"M"
31 ###if str(compression):
32 ## -l '$compression'
33 ###end if
34 $prim_key_cond.prim_key_select
35 #if $prim_key_cond.prim_key_select == '-t':
36 $prim_key_cond.tag
37 $prim_key_cond.sec_key_select
38 #end if
39 $minhash
40 -O bam
41 -T "\${TMPDIR:-.}"
42 '${input1}'
43 > '${output1}'
44 ]]>--></command>
45 <inputs> 26 <inputs>
46 <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" /> 27 <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" />
47 <conditional name="prim_key_cond"> 28 <conditional name="prim_key_cond">
48 <param name="prim_key_select" type="select" label="Primary sort key"> 29 <param name="prim_key_select" type="select" label="Primary sort key">
49 <option value="">coordinate</option> 30 <option value="">coordinate</option>