Commit 726a49b2 authored by Jelle Scholtalbers's avatar Jelle Scholtalbers

updated for toolshed suite using auto_tool_repositories

parent 58a5df4f
categories:
- Fastq Manipulation
- SAM
description: The Je tool suite
name: je
owner: gbcs-embl-heidelberg
homepage_url: http://gbcs.embl.de/Je
remote_repository_url: https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy
auto_tool_repositories:
name_template: "{{ tool_id }}"
description_template: "Wrapper for Je tool: {{ tool_name }}"
suite:
name: "suite_je"
description: "Je is a suite to handle barcoded fastq files with (or without) Unique Molecule Identifiers (UMIs) and filter read duplicates using these UMIs"
long_description: |
If you have barcodes and/or UMIs in your fastq files, you'll most likely enjoy Je. Je currently offers 4 tools:
demultiplex to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not)
demultiplex-illu to demultiplex fastq files according to associated index files (contain the sample encoding barcodes). Reads can additionally contain UMIs (inline)
clip to remove UMIs contained in reads of fastq files that do not need sample demultiplexing
markdupes to filter BAM files for read duplicates taking UMIs into account
<tool id="je-clip" name="Je-Clip" version="1.0">
<tool id="je_clip" name="Je-Clip" version="1.0">
<description>clips Unique Molecular Identifiers (UMIs) from fastq files</description>
<macros>
<import>macros.xml</import>
......
<tool id="je-demultiplex-illu" name="Je-Demultiplex-Illu" version="1.0">
<tool id="je_demultiplex_illu" name="Je-Demultiplex-Illu" version="1.0">
<description>demultiplexes fastq files using Illumina Index file</description>
<macros>
<import>macros.xml</import>
......
<tool id="je-demultiplex" name="Je-Demultiplex" version="1.0">
<tool id="je_demultiplex" name="Je-Demultiplex" version="1.0">
<description>demultiplexes fastq files</description>
<macros>
<import>macros.xml</import>
......
<tool id="je-markdupes" name="Je-MarkDuplicates" version="1.0">
<tool id="je_markdupes" name="Je-MarkDuplicates" version="1.0">
<description>to filter BAM files for read duplicates taking UMIs into account</description>
<macros>
<import>macros.xml</import>
......@@ -7,7 +7,6 @@
<exit_code range="1:" level="fatal" description="Tool exception" />
</stdio>
<version_command>echo '1.0'</version_command>
<command interpreter="bash">
<![CDATA[
je markdupes
......@@ -63,7 +62,7 @@
</configfiles>
<inputs>
<param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset"
<param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset"
help="If empty, upload or import a SAM/BAM dataset"/>
<param name="remove_duplicates" type="boolean" label="If true do not write duplicates to the output file
instead of writing them with appropriate flags set" help="REMOVE_DUPLICATES; default=False"/>
......
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