Mercurial > repos > jjohnson > optitype
diff optitype.xml @ 2:bf36e0afdfb4 draft default tip
"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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--- a/optitype.xml Thu Mar 12 12:38:06 2020 -0400 +++ b/optitype.xml Tue Feb 09 15:41:49 2021 +0000 @@ -1,28 +1,28 @@ -<tool id="optitype" name="OptiType" version="1.3.2"> +<tool id="optitype" name="OptiType" version="1.3.5"> <description>HLA genotyping predictions from NGS data</description> <requirements> - <requirement type="package" version="1.3.2">optitype</requirement> + <requirement type="package" version="1.3.5">optitype</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ #set $fastqs = [] #if str( $fastq_input.fastq_input_selector ) == "paired": - ln -s "${fastq_input.fastq_input1}" reads_1.fastq - && ln -s "${fastq_input.fastq_input2}" reads_2.fastq + ln -s '${fastq_input.fastq_input1}' reads_1.fastq + && ln -s '${fastq_input.fastq_input2}' reads_2.fastq #set $fastqs = ['reads_1.fastq','reads_2.fastq'] #elif str( $fastq_input.fastq_input_selector ) == "paired_collection": - ln -s "${fastq_input.fastq_input1.forward}" reads_1.fastq - && ln -s "${fastq_input.fastq_input1.reverse}" reads_2.fastq + ln -s '${fastq_input.fastq_input1.forward}' reads_1.fastq + && ln -s '${fastq_input.fastq_input1.reverse}' reads_2.fastq #set $fastqs = ['reads_1.fastq','reads_2.fastq'] #elif str( $fastq_input.fastq_input_selector ) == "single": - ln -s "${fastq_input.fastq_input1}" reads.fastq + ln -s '${fastq_input.fastq_input1}' reads.fastq #set $fastqs = ['reads.fastq'] #end if && RAZERS3=`which razers3` -&& sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\$GALAXY_SLOTS/" > config.ini +&& sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\${GALAXY_SLOTS}/" > config.ini #set $input_fq = ' '.join($fastqs) && OptiTypePipeline.py -$read_type --input ${' '.join($fastqs)} +$read_type --input ${' '.join($fastqs)} #if str($beta) != '': --beta $beta #end if @@ -146,12 +146,27 @@ <param name="fastq_input1" ftype="fastqsanger" value="rna/CRC_81_N_1_fished.fastq"/> <param name="fastq_input2" ftype="fastqsanger" value="rna/CRC_81_N_2_fished.fastq"/> </conditional> + <param name="read_type" value="--rna"/> <output name="result"> <assert_contents> <has_text text="A*31:01" /> </assert_contents> </output> </test> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="exome/NA11995_SRR766010_1_fished.fastq"/> + <param name="fastq_input2" ftype="fastqsanger" value="exome/NA11995_SRR766010_2_fished.fastq"/> + </conditional> + <param name="read_type" value="--dna"/> + <param name="unpaired_weight" value="0.2"/> + <output name="result"> + <assert_contents> + <has_text text="A*01:01" /> + </assert_contents> + </output> + </test> </tests> <help> <![CDATA[