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comparison samtools_sort_transcriptome/samtools_sort.xml @ 4:9445a308fb7e draft

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author jackcurragh
date Tue, 07 Jun 2022 11:33:01 +0000
parents 0421e96d203a
children 21eceda8a1ae
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3:0421e96d203a 4:9445a308fb7e
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 samtools sort
11 ###if str(compression):
12 ## -l '$compression'
13 ###end if
14 $prim_key_cond.prim_key_select
15 #if $prim_key_cond.prim_key_select == '-t':
16 $prim_key_cond.tag
17 $prim_key_cond.sec_key_select
18 #end if
19 $minhash
20 -O bam
21 -T "\${TMPDIR:-.}"
22 '${input1}'
23 > '${output1}'
24 ]]>
25 <!-- <![CDATA[
10 @ADDTHREADS@ 26 @ADDTHREADS@
11 @ADDMEMORY@ 27 @ADDMEMORY@
12 samtools sort 28 samtools sort
13 -@ \$addthreads 29 -@ \$addthreads
14 -m \$addmemory"M" 30 -m \$addmemory"M"
23 $minhash 39 $minhash
24 -O bam 40 -O bam
25 -T "\${TMPDIR:-.}" 41 -T "\${TMPDIR:-.}"
26 '${input1}' 42 '${input1}'
27 > '${output1}' 43 > '${output1}'
28 ]]></command> 44 ]]>--></command>
29 <inputs> 45 <inputs>
30 <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" /> 46 <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" />
31 <conditional name="prim_key_cond"> 47 <conditional name="prim_key_cond">
32 <param name="prim_key_select" type="select" label="Primary sort key"> 48 <param name="prim_key_select" type="select" label="Primary sort key">
33 <option value="">coordinate</option> 49 <option value="">coordinate</option>