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comparison samtools_plugin.xml @ 27:7591bce96601 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
author iuc
date Tue, 18 Feb 2025 23:18:25 +0000
parents a7e081ceb76a
children
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26:d2aaac19f42f 27:7591bce96601
4 @CREATE_REPEAT_DIR_2@ 4 @CREATE_REPEAT_DIR_2@
5 #if str($repeat2.type.type) == "stats" 5 #if str($repeat2.type.type) == "stats"
6 #set $pattern = "This file was produced by samtools stats" 6 #set $pattern = "This file was produced by samtools stats"
7 @LN_3_FILES@ 7 @LN_3_FILES@
8 #elif str($repeat2.type.type) == "flagstat" 8 #elif str($repeat2.type.type) == "flagstat"
9 #set $pattern = "in total (QC-passed reads + QC-failed reads)" 9 #set $pattern = "in total \(QC-passed reads \+ QC-failed reads\)"
10 @LN_3_FILES@ 10 @LN_3_FILES@
11 #elif str($repeat2.type.type) == "idxstats" 11 #elif str($repeat2.type.type) == "idxstats"
12 #for $file in $repeat2.type.input 12 #for $file in $repeat2.type.input
13 @ESCAPE_IDENTIFIER@ 13 @ESCAPE_IDENTIFIER@
14 #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat') 14 #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat')
15 ln -s '$file' '$file_path' && 15 ln -s '$file' '$file_path' &&
16 #end for 16 #end for
17 #elif str($repeat2.type.type) == "rmdup" 17 #elif str($repeat2.type.type) == "rmdup"
18 #set $pattern = "[bam_rmdup" 18 #set $pattern = "\[bam_rmdup"
19 @LN_3_FILES@ 19 @LN_3_FILES@
20 #end if 20 #end if
21 #end for 21 #end for
22 ]]></token> 22 ]]></token>
23 <xml name="samtools_form"> 23 <xml name="samtools_form">