| Previous changeset 1:57bf9a0d49a5 (2019-01-20) Next changeset 3:24657d5edede (2019-01-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3 |
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modified:
slamdunk.xml |
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| diff -r 57bf9a0d49a5 -r fae4a5ec0653 slamdunk.xml --- a/slamdunk.xml Sun Jan 20 06:51:15 2019 -0500 +++ b/slamdunk.xml Mon Jan 21 07:34:47 2019 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy1"> +<tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy2"> <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description> <macros> <import>macros.xml</import> @@ -6,33 +6,42 @@ <expand macro="requirements" /> <version_command>slamdunk --version</version_command> <command detect_errors="exit_code"><![CDATA[ - #if $reference_source.reference_source_selector == 'history': - ln -f -s '$reference_source.ref_file' reference.fa && - #else: - ln -f -s '$reference_source.ref_file.fields.path' reference.fa && - #end if - slamdunk all -r reference.fa -b '$Reference' -o ./out - -n $multimapper.multimappers - $multimapper.multimap - #if $multimapper.filterbed.bedtofilter: - -fb $multimapper.filterbed.bedtofilter - #end if - -5 $quantseq.trim5 - -a $quantseq.maxpolyA - $advanced.endtoend - -mq $advanced.minMQ - -mi $advanced.minID - -nm=$advanced.maxNM - -mc $advanced.minCov - -mv $advanced.minVar - -mbq $advanced.minBaseQual - -rl $readLength - -c $covThresh - '$Reads' +#import re + +#if $reference_source.reference_source_selector == 'history': + ln -f -s '$reference_source.ref_file' reference.fa && +#else: + ln -f -s '$reference_source.ref_file.fields.path' reference.fa && +#end if + +mkdir ./fastq && +#for $fastq in $reads: + #set $fastq_name = re.sub('[^\w\-\.]', '_', str($fastq.element_identifier)) + ln -s '$fastq' './fastq/${fastq_name}' && +#end for + + slamdunk all -r reference.fa -b '$Reference' -o ./out + -n $multimapper.multimappers + $multimapper.multimap + #if $multimapper.filterbed.bedtofilter: + -fb $multimapper.filterbed.bedtofilter + #end if + -5 $quantseq.trim5 + -a $quantseq.maxpolyA + $advanced.endtoend + -mq $advanced.minMQ + -mi $advanced.minID + -nm=$advanced.maxNM + -mc $advanced.minCov + -mv $advanced.minVar + -mbq $advanced.minBaseQual + -rl $readLength + -c $covThresh + ./fastq/* ]]></command> <inputs> <expand macro="reference_files" /> - <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ files"/> + <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="True" label="FASTQ files"/> <section name="multimapper" title="Multimapper recovery" expanded="false"> <section name="filterbed" @@ -86,9 +95,15 @@ help="Maximum read length (before trimming)." /> </inputs> <outputs> - <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" label="${tool.name} on ${on_string}: BAM"/> - <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" label="${tool.name} on ${on_string}: Count TSV"/> - <data name="outputVcf" format="vcf" from_work_dir="./out/snp/*vcf" label="${tool.name} on ${on_string}: VCF"/> + <collection name="outputBam" type="list" label="${tool.name} on ${on_string}: BAM"> + <discover_datasets pattern="(?P<name>.+)\.bam$" format="bam" directory="./out/filter" visible="false" /> + </collection> + <collection name="outputTsv" type="list" label="${tool.name} on ${on_string}: Count TSV"> + <discover_datasets pattern="(?P<name>.+)_tcount.tsv$" format="tabular" directory="./out/count" visible="false" /> + </collection> + <collection name="outputVcf" type="list" label="${tool.name} on ${on_string}: VCF"> + <discover_datasets pattern="(?P<name>.+)_snp.vcf$" format="vcf" directory="./out/snp" visible="false" /> + </collection> </outputs> <tests> <test> @@ -96,7 +111,7 @@ <param name="reference_source_selector" value="history" /> <param name="ref_file" value="ref.fa" /> <param name="Reference" value="actb.bed" /> - <param name="Reads" value="reads.fq" /> + <param name="reads" value="reads.fq" /> <param name="readLength" value="100" /> <section name="quantseq"> <param name="trim5" value="0" /> @@ -104,16 +119,22 @@ <section name="advanced"> <param name="minBaseQual" value="27" /> </section> - <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/> - <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" - lines_diff="2" /> - <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/> + <output_collection name="outputBam"> + <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" /> + </output_collection> + <output_collection name="outputTsv"> + <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" + lines_diff="2" /> + </output_collection> + <output_collection name="outputVcf"> + <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" /> + </output_collection> </test> <test> <!--Ensure built-in fasta works --> <param name="reference_source_selector" value="cached" /> <param name="Reference" value="actb.bed" /> - <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" /> + <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" /> <param name="readLength" value="100" /> <section name="quantseq"> <param name="trim5" value="0" /> @@ -121,10 +142,16 @@ <section name="advanced"> <param name="minBaseQual" value="27" /> </section> - <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/> - <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" - lines_diff="2" /> - <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/> + <output_collection name="outputBam"> + <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" /> + </output_collection> + <output_collection name="outputTsv"> + <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" + lines_diff="2" /> + </output_collection> + <output_collection name="outputVcf"> + <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" /> + </output_collection> </test> </tests> <help><![CDATA[ |