Mercurial > repos > iuc > seq2hla

comparison seq2hla.xml @ 1:1db16e5fde32 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit c6f68e0efd9aa7e566289650ad126e0c7d192a8b"
author iuc
date Wed, 07 Apr 2021 12:37:16 +0000
parents 00b89af60f18
children 62423040f17e
comparison
equal deleted inserted replaced
0:00b89af60f18 1:1db16e5fde32
1 <tool id="seq2hla" name="seq2HLA" version="2.2.0"> 1 <tool id="seq2hla" name="seq2HLA" version="2.2.0+galaxy1">
2 <description>HLA genotype and expression from RNA-seq</description> 2 <description>HLA genotype and expression from RNA-seq</description>
3 <requirements> 3 <requirements>
4 <!-- needed because of some non POSIX compliant wc usage --> 4 <!-- needed because of some non POSIX compliant wc usage -->
5 <requirement type="package" version="8.31">coreutils</requirement> 5 <requirement type="package" version="8.31">coreutils</requirement>
6 <requirement type="package" version="2.2">seq2hla</requirement> 6 <requirement type="package" version="2.2">seq2hla</requirement>
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis"> 22 <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis">
23 <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator> 23 <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator>
24 </param> 24 </param>
25 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/> 25 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
26 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> 26 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
27 <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime" 27 <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime"
28 help="trim this many bases from the low-quality end of each read" /> 28 help="trim this many bases from the low-quality end of each read" />
29 </inputs> 29 </inputs>
30 <outputs> 30 <outputs>
31 <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/> 31 <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/>
38 <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/> 38 <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/>
39 </outputs> 39 </outputs>
40 <tests> 40 <tests>
41 <test> 41 <test>
42 <param name="run_name" value="test"/> 42 <param name="run_name" value="test"/>
43 <param name="fastq_input1" ftype="fastqsanger" value="reads1.fastq"/> 43 <param name="fastq_input1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
44 <param name="fastq_input2" ftype="fastqsanger" value="reads2.fastq"/> 44 <param name="fastq_input2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
45 <output name="c1_genotype4digits"> 45 <output name="c1_genotype4digits">
46 <assert_contents> 46 <assert_contents>
47 <has_text text="A*24:02" /> 47 <has_text text="A*24:02" />
48 </assert_contents> 48 </assert_contents>
49 </output> 49 </output>