| Previous changeset 0:93704f98f56e (2016-09-06) Next changeset 2:04b73d626680 (2018-09-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2 |
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modified:
star_fusion.xml |
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added:
test-data/test1.fastqsanger.gz |
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| diff -r 93704f98f56e -r 0b44456754e2 star_fusion.xml --- a/star_fusion.xml Tue Sep 06 04:55:21 2016 -0400 +++ b/star_fusion.xml Thu Apr 20 08:12:14 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-2" profile="16.07"> +<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3" profile="17.01"> <description>detect fusion genes in RNA-Seq data</description> <requirements> <!-- Bio-conda --> @@ -46,15 +46,34 @@ --CPU \${GALAXY_SLOTS:-1} --output_dir "\$(pwd)/tmp_star_fusion_genome_dir" && + + ## Link in fastq files so they have appropriate extensions + #if str($input_params.input_source) != "use_chimeric": + #if $input_params.left_fq.is_of_type("fastq.gz"): + #set read1 = 'input_1.fastq.gz' + #else: + #set read1 = 'input_1.fastq' + #end if + ln -f -s '${input_params.left_fq}' ${read1} && + + #if $input_params.right_fq: + #if $input_params.right_fq.is_of_type("fastq.gz"): + #set read2 = 'input_2.fastq.gz' + #else: + #set read2 = 'input_2.fastq' + #end if + ln -f -s '${input_params.right_fq}' ${read2} && + #end if + #end if ## 3. Run STAR-Fusion STAR-Fusion #if str($input_params.input_source) == "use_chimeric": --chimeric_junction '${input_params.chimeric_junction}' #else: - --left_fq '${input_params.left_fq}' + --left_fq ${read1} #if $input_params.right_fq: - --right_fq '${input_params.right_fq}' + --right_fq ${read2} #end if #end if @@ -89,12 +108,12 @@ <when value="use_fastq"> <param name="left_fq" type="data" - format="fastqsanger" + format="fastqsanger,fastqsanger.gz" argument="--left_fq" label="left.fq file"/> <param name="right_fq" type="data" - format="fastqsanger" + format="fastqsanger,fastqsanger.gz" optional="true" argument="--right_fq" label="right.fq file (actually optional, but highly recommended)"/> @@ -121,7 +140,6 @@ <param name="ownFile" type="data" format="fasta" - metadata_name="dbkey" label="Select the reference genome (FASTA file)"/> </when> </conditional> @@ -220,6 +238,23 @@ </assert_contents> </output> </test> + <test> + <param name="input_source" value="use_fastq" /> + <param name="left_fq" ftype="fastqsanger.gz" value="test1.fastqsanger.gz"/> + <param name="fasta_type_selector" value="history" /> + <param name="ownFile" ftype="fasta" value="test1.fa" /> + <param name="geneModel" ftype="gtf" value="test1.gtf" /> + <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" /> + <param name="settingsType" value="default" /> + + <!-- Last column of the results contains data in a random order so exact matching is not feasible --> + <output name="output_final"> + <assert_contents> + <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	JunctionReads	SpanningFrags" /> + <has_text text="GENE1--GENE2	24	0	INCL_NON_REF_SPLICE	GENE1^GENE1	chr1:240:+	GENE2^GENE2	chr2:241:+" /> + </assert_contents> + </output> + </test> </tests> <help> **What it does** |
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| diff -r 93704f98f56e -r 0b44456754e2 test-data/test1.fastqsanger.gz |
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| Binary file test-data/test1.fastqsanger.gz has changed |