Mercurial > repos > iuc > vapor
changeset 3:f11d2dd29b2b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
| author | iuc |
|---|---|
| date | Mon, 17 Oct 2022 07:28:50 +0000 |
| parents | b1ca81ce88f9 |
| children | 244812f5bd1f |
| files | vapor.xml |
| diffstat | 1 files changed, 67 insertions(+), 37 deletions(-) [+] |
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--- a/vapor.xml Tue Oct 04 21:13:05 2022 +0000 +++ b/vapor.xml Mon Oct 17 07:28:50 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy1" profile="21.05"> +<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy2" profile="21.05"> <description> Classify Influenza samples from raw short read sequence data </description> @@ -12,18 +12,20 @@ <requirement type="package" version="@TOOL_VERSION@">vapor</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - #set $fastq_files = [] - mkdir fastq_files && - #for $i, $fastq in enumerate($fastq_file) - #if $fastq.ext.endswith(".gz") - #set $ext='.fastq.gz' - #else - #set $ext='.fastq' - #end if - #set $out = './fastq_files/input_%s%s' % ($i, $ext) - ln -s '${fastq}' $out && - $fastq_files.append($out) - #end for + #if str($fastq_input.fastq_input_selector) == "paired" + #set r1_ext = $fastq_input.fastq1.extension + #set r2_ext = $fastq_input.fastq2.extension + ln -s '$fastq_input.fastq1' fastq1.$r1_ext && + ln -s '$fastq_input.fastq2' fastq2.$r2_ext && + #elif str($fastq_input.fastq_input_selector) == "paired_collection" + #set r1_ext = $fastq_input.fastq_pairs.forward.extension + #set r2_ext = $fastq_input.fastq_pairs.reverse.extension + ln -s '$fastq_input.fastq_pairs.forward' fastq1.$r1_ext && + ln -s '$fastq_input.fastq_pairs.reverse' fastq2.$r2_ext && + #else + #set r1_ext = $fastq_input.fastq_single.extension + ln -s '$fastq_input.fastq_single' fastq1.$r1_ext && + #end if vapor.py --return_best_n $opt.return_best_n #if $output_type == "fasta" @@ -35,16 +37,33 @@ -m '$opt.min_kmer_prop' -fa '$fasta_file' -fq - #for $fq in $fastq_files - '${fq}' - #end for + fastq1.$r1_ext + #if str($fastq_input.fastq_input_selector) in ["paired", "paired_collection"] + fastq2.$r2_ext + #end if -f '$opt.top_seed_frac' -q > out_file ]]> </command> <inputs> <param name="fasta_file" format="fasta" type="data" label="FASTA file" help="Raw short read sequences (full length reference segment sequences)" /> - <param name="fastq_file" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" multiple="true" label="FASTQ file(s)" help="WGS reads" /> + <conditional name="fastq_input"> + <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> + <option value="single">Single</option> + <option value="paired">Paired</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="single"> + <param name="fastq_single" format="fastqsanger,fastqsanger.gz" type="data" label="FASTQ file" help="Raw short read sequences (full length reference segment sequences)" /> + </when> + <when value="paired"> + <param name="fastq1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify reads dataset with forward reads"/> + <param name="fastq2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify reads dataset with reverse reads"/> + </when> + <when value="paired_collection"> + <param name="fastq_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="Dataset collection with forward and reverse reads"/> + </when> + </conditional> <param name="output_type" type="select" label="Output type"> <option value="scores" selected="true">Return scores only</option> <option value="fasta">Return FASTA only</option> @@ -70,29 +89,37 @@ </data> </outputs> <tests> - <test expect_num_outputs="1"><!-- Test 1: fastq --> - <param name="fasta_file" value="HA_sample.fa" /> - <param name="fastq_file" ftype="fastq" value="test_reads.fq" /> - <output name="output_scores" file="output1.tab" /> - </test> - <test expect_num_outputs="1"><!-- Test 2: multiple fastq --> + <test expect_num_outputs="1"> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="single" /> + <param name="fastq_single" ftype="fastq" value="test_reads.fq" /> + </conditional> <param name="fasta_file" value="HA_sample.fa" /> - <param name="fastq_file" ftype="fastq" value="test_reads.fq,test_reads2.fq" /> - <output name="output_scores" file="output2.tab" /> - </test> - <test expect_num_outputs="1"><!-- Test 3: fastqsanger.gz --> - <param name="fasta_file" value="HA_sample.fa" /> - <param name="fastq_file" ftype="fastqsanger.gz" value="test_reads.fastqsanger.gz" /> - <output name="output_scores" file="output1.tab" /> - </test> - <test expect_num_outputs="1"><!-- Test 4: opt --> - <param name="fasta_file" value="HA_sample.fa" /> - <param name="fastq_file" value="test_reads.fastqsanger.gz" /> <output name="output_scores" file="output1.tab" /> </test> <test expect_num_outputs="1"> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired" /> + <param name="fastq1" ftype="fastq" value="test_reads.fq" /> + <param name="fastq2" ftype="fastq" value="test_reads2.fq" /> + </conditional> <param name="fasta_file" value="HA_sample.fa" /> - <param name="fastq_file" value="test_reads.fq" /> + <output name="output_scores" file="output2.tab" /> + </test> + <test expect_num_outputs="1"> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="single" /> + <param name="fastq_single" ftype="fastqsanger.gz" value="test_reads.fastqsanger.gz" /> + </conditional> + <param name="fasta_file" value="HA_sample.fa" /> + <output name="output_scores" file="output1.tab" /> + </test> + <test expect_num_outputs="1"> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="single" /> + <param name="fastq_single" value="test_reads.fq" /> + </conditional> + <param name="fasta_file" value="HA_sample.fa" /> <section name="opt"> <param name="kmer_length" value="29" /> <param name="score_threshold" value="0.5" /> @@ -102,9 +129,12 @@ </section> <output name="output_scores" file="output4.tab" /> </test> - <test expect_num_outputs="1"><!-- Test 5: fasta output--> + <test expect_num_outputs="1"> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="single" /> + <param name="fastq_single" value="test_reads.fq" /> + </conditional> <param name="fasta_file" value="HA_sample.fa" /> - <param name="fastq_file" value="test_reads.fq" /> <param name="output_type" value="fasta" /> <section name="opt"> <param name="return_best_n" value="3" />