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comparison flaimapper.xml @ 39:62d46dd9ac42 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit beb30713f9b8510c22f46d94cb58c92cf26c799c
author erasmus-medical-center
date Fri, 28 Apr 2017 07:05:35 -0400
parents ee6d8c07205b
children af0ee8dc5471
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38:ee6d8c07205b 39:62d46dd9ac42
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="flaimapper" name="FlaiMapper" version="2.3.4-0"> 2 <tool id="flaimapper" name="FlaiMapper" version="2.4.0-0">
3 <description>detects small ncRNA derived fragments in small RNA-Seq data</description> 3 <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.3.4">flaimapper</requirement> 5 <requirement type="package" version="2.4.0">flaimapper</requirement>
6 </requirements> 6 </requirements>
7 7
8 <version_command>flaimapper --version 2&gt;&amp;1 | head -n 1</version_command> 8 <version_command>flaimapper --version 2&gt;&amp;1 | head -n 1</version_command>
9 9
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
40 <option value="2">GTF</option> 40 <option value="2">GTF</option>
41 </param> 41 </param>
42 42
43 <when value="1"> 43 <when value="1">
44 <param name="fasta" type="data" format="fasta" optional="true" 44 <param name="fasta" type="data" format="fasta" optional="true"
45 label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database" help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" /> 45 label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database"
46 help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
46 </when> 47 </when>
47 48
48 <when value="2"> 49 <when value="2">
49 <param name="offset5p" type="integer" value="4" 50 <param name="offset5p" type="integer" value="4"
50 label="5' offset added to the exon-type GTF entry" 51 label="Add 5'-offset to exon-type entry in GTF output file"
51 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to use an offset." argument="--offset5p" /> 52 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset5p" />
52 <param name="offset3p" type="integer" value="4" 53 <param name="offset3p" type="integer" value="4"
53 label="3' offset added to the exon-type GTF entry" 54 label="Add 3'-offset to exon-type entry in GTF output file"
54 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to use an offset." argument="--offset3p" /> 55 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset3p" />
55 </when> 56 </when>
56 </conditional> 57 </conditional>
57 58
58 <param name="parameters" type="data" format="txt,tabular" optional="true" 59 <param name="parameters" type="data" format="txt,tabular" optional="true"
59 label="(Optional) Custom parameters file" help="" argument="-p" /> 60 label="(Optional) Custom parameters file" help="" argument="-p" />