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comparison optitype.xml @ 2:bf36e0afdfb4 draft default tip

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/optitype commit 703114ab7ad18b1b0e824b103f1df213448c6e97-dirty"
author jjohnson
date Tue, 09 Feb 2021 15:41:49 +0000
parents 54c9c71dabe8
children
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1:54c9c71dabe8 2:bf36e0afdfb4
1 <tool id="optitype" name="OptiType" version="1.3.2"> 1 <tool id="optitype" name="OptiType" version="1.3.5">
2 <description>HLA genotyping predictions from NGS data</description> 2 <description>HLA genotyping predictions from NGS data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.2">optitype</requirement> 4 <requirement type="package" version="1.3.5">optitype</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"> 6 <command detect_errors="aggressive">
7 <![CDATA[ 7 <![CDATA[
8 #set $fastqs = [] 8 #set $fastqs = []
9 #if str( $fastq_input.fastq_input_selector ) == "paired": 9 #if str( $fastq_input.fastq_input_selector ) == "paired":
10 ln -s "${fastq_input.fastq_input1}" reads_1.fastq 10 ln -s '${fastq_input.fastq_input1}' reads_1.fastq
11 && ln -s "${fastq_input.fastq_input2}" reads_2.fastq 11 && ln -s '${fastq_input.fastq_input2}' reads_2.fastq
12 #set $fastqs = ['reads_1.fastq','reads_2.fastq'] 12 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
13 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection": 13 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
14 ln -s "${fastq_input.fastq_input1.forward}" reads_1.fastq 14 ln -s '${fastq_input.fastq_input1.forward}' reads_1.fastq
15 && ln -s "${fastq_input.fastq_input1.reverse}" reads_2.fastq 15 && ln -s '${fastq_input.fastq_input1.reverse}' reads_2.fastq
16 #set $fastqs = ['reads_1.fastq','reads_2.fastq'] 16 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
17 #elif str( $fastq_input.fastq_input_selector ) == "single": 17 #elif str( $fastq_input.fastq_input_selector ) == "single":
18 ln -s "${fastq_input.fastq_input1}" reads.fastq 18 ln -s '${fastq_input.fastq_input1}' reads.fastq
19 #set $fastqs = ['reads.fastq'] 19 #set $fastqs = ['reads.fastq']
20 #end if 20 #end if
21 && RAZERS3=`which razers3` 21 && RAZERS3=`which razers3`
22 && sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\$GALAXY_SLOTS/" > config.ini 22 && sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\${GALAXY_SLOTS}/" > config.ini
23 #set $input_fq = ' '.join($fastqs) 23 #set $input_fq = ' '.join($fastqs)
24 && OptiTypePipeline.py 24 && OptiTypePipeline.py
25 $read_type --input ${' '.join($fastqs)} 25 $read_type --input ${' '.join($fastqs)}
26 #if str($beta) != '': 26 #if str($beta) != '':
27 --beta $beta 27 --beta $beta
28 #end if 28 #end if
29 #if str($enumerations) != '': 29 #if str($enumerations) != '':
30 --enumerate $enumerations 30 --enumerate $enumerations
144 <conditional name="fastq_input"> 144 <conditional name="fastq_input">
145 <param name="fastq_input_selector" value="paired"/> 145 <param name="fastq_input_selector" value="paired"/>
146 <param name="fastq_input1" ftype="fastqsanger" value="rna/CRC_81_N_1_fished.fastq"/> 146 <param name="fastq_input1" ftype="fastqsanger" value="rna/CRC_81_N_1_fished.fastq"/>
147 <param name="fastq_input2" ftype="fastqsanger" value="rna/CRC_81_N_2_fished.fastq"/> 147 <param name="fastq_input2" ftype="fastqsanger" value="rna/CRC_81_N_2_fished.fastq"/>
148 </conditional> 148 </conditional>
149 <param name="read_type" value="--rna"/>
149 <output name="result"> 150 <output name="result">
150 <assert_contents> 151 <assert_contents>
151 <has_text text="A*31:01" /> 152 <has_text text="A*31:01" />
153 </assert_contents>
154 </output>
155 </test>
156 <test>
157 <conditional name="fastq_input">
158 <param name="fastq_input_selector" value="paired"/>
159 <param name="fastq_input1" ftype="fastqsanger" value="exome/NA11995_SRR766010_1_fished.fastq"/>
160 <param name="fastq_input2" ftype="fastqsanger" value="exome/NA11995_SRR766010_2_fished.fastq"/>
161 </conditional>
162 <param name="read_type" value="--dna"/>
163 <param name="unpaired_weight" value="0.2"/>
164 <output name="result">
165 <assert_contents>
166 <has_text text="A*01:01" />
152 </assert_contents> 167 </assert_contents>
153 </output> 168 </output>
154 </test> 169 </test>
155 </tests> 170 </tests>
156 <help> 171 <help>