Mercurial > repos > gbcs-embl-heidelberg > je_clip

comparison je-clip.xml @ 5:8b4ccdf5f7dd 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 10:58:49 -0400
parents 2cfed59e4d27
children
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4:9d85f5915da9 5:8b4ccdf5f7dd
1 <tool id="je_clip" name="Je-Clip" version="@VERSION_STRING@"> 1 <tool id="je_clip" name="Je-Clip" version="@VERSION_STRING@">
2 <description>clips Unique Molecular Identifiers (UMIs) from fastq files</description> 2 <description>clips Unique Molecular Identifiers (UMIs) from fastq files</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 clip 13 je clip
13 14
14 ## Fastq inputs 15 ## Fastq inputs
15 @single_or_paired_cmd@ 16 @single_or_paired_cmd@
83 <output name="OF1" file="clip_dataset1_PE.fastq"/> 84 <output name="OF1" file="clip_dataset1_PE.fastq"/>
84 <output name="OF2" file="clip_dataset2_PE.fastq"/> 85 <output name="OF2" file="clip_dataset2_PE.fastq"/>
85 </test> 86 </test>
86 </tests> 87 </tests>
87 88
88 89 <help>
89 <help>
90 <![CDATA[ 90 <![CDATA[
91 **What it does** 91 **What it does**
92 92
93 Je clip: Clips barcodes or Unique Molecular Identifiers (UMIs) from the input fastq files 93 Je clip: Clips barcodes or Unique Molecular Identifiers (UMIs) from the input fastq files
94 Input files are fastq files, and can be in gzip compressed format. 94 Input files are fastq files, and can be in gzip compressed format.
240 + barcode + quality from read_2 (col 4 and 5 respectively) when relevant. 240 + barcode + quality from read_2 (col 4 and 5 respectively) when relevant.
241 Can either be a name (in which case the file will be created in the output dir) or a full path. 241 Can either be a name (in which case the file will be created in the output dir) or a full path.
242 Default value: null. 242 Default value: null.
243 243
244 ]]> 244 ]]>
245 </help> 245 </help>
246 246 <expand macro="citations"/>
247 </tool> 247 </tool>