Mercurial > repos > iuc > stacks2_tsv2bam

comparison stacks_tsv2bam.xml @ 1:8c2617661c49 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 14:20:19 -0400
parents 1b270fc77c81
children bf0e43ab0416
comparison
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0:1b270fc77c81 1:8c2617661c49
7 <expand macro="version_cmd"/> 7 <expand macro="version_cmd"/>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 @FASTQ_INPUT_FUNCTIONS@ 9 @FASTQ_INPUT_FUNCTIONS@
10 10
11 mkdir stacks_inputs stacks_outputs && 11 mkdir stacks_inputs stacks_outputs &&
12
13 #if $output_log
14 ln -s '$output_log' stacks_inputs/tsv2bam.log &&
15 #end if
12 16
13 @LINK_STACKS_INPUT@ 17 @LINK_STACKS_INPUT@
14 @LINK_CAT_INPUT@ 18 @LINK_CAT_INPUT@
15 @LINK_MATCHES_INPUT@ 19 @LINK_MATCHES_INPUT@
16 20
41 ## tsv2bam writes to stdout and creates a log file 45 ## tsv2bam writes to stdout and creates a log file
42 ## - make stdout stderr 46 ## - make stdout stderr
43 ## - move the additional log file 47 ## - move the additional log file
44 2>&1 48 2>&1
45 49
46 #if $output_log
47 && mv stacks_inputs/tsv2bam.log $output_log
48 #end if
49 && mv stacks_inputs/*matches.bam stacks_outputs 50 && mv stacks_inputs/*matches.bam stacks_outputs
50 ]]></command> 51 ]]></command>
51 52
52 <inputs> 53 <inputs>
53 <expand macro="input_stacks_macro"/> 54 <expand macro="input_stacks_macro"/>