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comparison picard_FastqToSam.xml @ 12:05087b27692a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:50 -0500
parents 5eaa8a968300
children 7e6fd3d0f16e
comparison
equal deleted inserted replaced
11:efc56ee1ade4 12:05087b27692a
2 <description>convert Fastq data into unaligned BAM</description> 2 <description>convert Fastq data into unaligned BAM</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <stdio> 7 <command detect_errors="exit_code"><![CDATA[
8 <exit_code range="1:" level="fatal"/>
9 </stdio>
10 <command>
11 @java_options@ 8 @java_options@
12 9
13 java -jar \$JAVA_JAR_PATH/picard.jar 10 picard
14 FastqToSam 11 FastqToSam
15 12
16 #if str( $input_type.input_type_selector ) == "se": 13 #if str( $input_type.input_type_selector ) == "se":
17 FASTQ="${input_type.fastq}" 14 FASTQ="${input_type.fastq}"
18 #elif str( $input_type.input_type_selector ) == "pe": 15 #elif str( $input_type.input_type_selector ) == "pe":
68 SORT_ORDER=coordinate 65 SORT_ORDER=coordinate
69 VALIDATION_STRINGENCY="${validation_stringency}" 66 VALIDATION_STRINGENCY="${validation_stringency}"
70 QUIET=true 67 QUIET=true
71 VERBOSITY=ERROR 68 VERBOSITY=ERROR
72 69
73 </command> 70 ]]></command>
74 <inputs> 71 <inputs>
75 <conditional name="input_type"> 72 <conditional name="input_type">
76 <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types"> 73 <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
77 <option value="se">Single end (single dataset)</option> 74 <option value="se">Single end (single dataset)</option>
78 <option value="pe">Paired end (two datasets)</option> 75 <option value="pe">Paired end (two datasets)</option>