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comparison je-demultiplex-illu.xml @ 5:69c77f9fc064 draft

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planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
author gbcs-embl-heidelberg
date Wed, 02 Aug 2017 10:59:09 -0400
parents 01fdc6d10660
children 370d9764f670
comparison
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4:7895e352c09b 5:69c77f9fc064
1 <tool id="je_demultiplex_illu" name="Je-Demultiplex-Illu" version="@VERSION_STRING@"> 1 <tool id="je_demultiplex_illu" name="Je-Demultiplex-Illu" version="@VERSION_STRING@">
2 <description>demultiplexes fastq files using Illumina Index file</description> 2 <description>demultiplexes fastq files using Illumina Index file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" />
6 <stdio> 7 <stdio>
7 <exit_code range="1:" level="fatal" description="Tool exception" /> 8 <exit_code range="1:" level="fatal" description="Tool exception" />
8 </stdio> 9 </stdio>
9 <version_command>echo '1.0'</version_command> 10 <expand macro="version_command" />
10 <command interpreter="bash"> 11 <command>
11 <![CDATA[ 12 <![CDATA[
12 je demultiplex-illu 13 je demultiplex-illu
13 14
14 ## Fastq inputs 15 ## Fastq inputs
15 @single_or_paired_illu_cmd@ 16 @single_or_paired_illu_cmd@
91 <param name="BM" value="BOTH"/> 92 <param name="BM" value="BOTH"/>
92 <param name="BRED" value="false"/> 93 <param name="BRED" value="false"/>
93 <param name="MM" value="3"/> 94 <param name="MM" value="3"/>
94 <param name="MMD" value="2"/> 95 <param name="MMD" value="2"/>
95 <param name="Q" value="20"/> 96 <param name="Q" value="20"/>
96 <param name="DIAG" value="false"/> 97 <param name="DIAG" value="false"/>
97 <output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4"> 98 <output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4">
98 <discovered_dataset designation="unassigned_1" file="illu_unassigned_1_PE.txt" /> 99 <discovered_dataset designation="unassigned_1" file="illu_unassigned_1_PE.txt" />
99 <discovered_dataset designation="unassigned_2" file="illu_unassigned_2_PE.txt" /> 100 <discovered_dataset designation="unassigned_2" file="illu_unassigned_2_PE.txt" />
100 <discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_2" file="emb681m5_GGACTCCTCTCTCTAT_2.txt"/> 101 <discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_2" file="emb681m5_GGACTCCTCTCTCTAT_2.txt"/>
101 <discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_1" file="emb681m5_GGACTCCTCTCTCTAT_1.txt"/> 102 <discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_1" file="emb681m5_GGACTCCTCTCTCTAT_1.txt"/>
109 <discovered_dataset designation="emb6801m1_CGTACTAGTAGATCGC_1" file="emb6801m1_CGTACTAGTAGATCGC_1.txt"/> 110 <discovered_dataset designation="emb6801m1_CGTACTAGTAGATCGC_1" file="emb6801m1_CGTACTAGTAGATCGC_1.txt"/>
110 </output> 111 </output>
111 </test> 112 </test>
112 </tests> 113 </tests>
113 114
114 115 <help>
115 <help>
116 <![CDATA[ 116 <![CDATA[
117 **What it does** 117 **What it does**
118 118
119 Je demultiplex-illu: demultiplex fastq files using Illumina Index files, 119 Je demultiplex-illu: demultiplex fastq files using Illumina Index files,
120 with optional handling of Unique Molecular Identifiers for further use in 'markdupes' module 120 with optional handling of Unique Molecular Identifiers for further use in 'markdupes' module
421 barcoded. 421 barcoded.
422 N.B: this file will have a size of about one of the fastq input files. 422 N.B: this file will have a size of about one of the fastq input files.
423 423
424 Default value: null. 424 Default value: null.
425 ]]> 425 ]]>
426 </help> 426 </help>
427 427 <expand macro="citations"/>
428 </tool> 428 </tool>