| Previous 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 7e10d9499da95a5011936d0650810687a66574dd" |
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modified:
star_fusion.xml |
| b |
| diff -r 04b73d626680 -r 137942fac417 star_fusion.xml --- a/star_fusion.xml Fri Sep 07 11:30:25 2018 -0400 +++ b/star_fusion.xml Mon Jan 06 11:08:46 2020 -0500 |
| [ |
| @@ -1,7 +1,6 @@ -<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3" profile="17.01"> +<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3+galaxy1" profile="17.01"> <description>detect fusion genes in RNA-Seq data</description> <requirements> - <!-- Bio-conda --> <requirement type="package" version="0.5.4">star-fusion</requirement> </requirements> @@ -26,68 +25,60 @@ <version_command>STAR-Fusion --version 2>&1 | grep version | grep -o -E "software version.*?"</version_command> <command><![CDATA[ - ## 1. ensure the blastn file is provided as *.gz - if file --mime-type '${blast_pairs}' | grep -q /gzip\$; then - gzip_suffix='' ; - else - ## Older versions of gzip do not support the -k option to keep - ## the original file - this should be an universion solution - - gzip -1 -c -- '${blast_pairs}' > '${blast_pairs}.gz' && - gzip_suffix='.gz' ; - fi && - - ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory - ## - @todo once write a decent STAR and STAR Fusion data manager - prep_genome_lib.pl - --genome_fa '${fasta_type.ownFile}' - --gtf '${geneModel}' - --blast_pairs "${blast_pairs}\$gzip_suffix" - --CPU \${GALAXY_SLOTS:-1} - --output_dir "\$(pwd)/tmp_star_fusion_genome_dir" - && +## 1. ensure the blastn file is provided as *.gz +gzip -1 -c -- '${blast_pairs}' > blast_pairs.gz && - ## Link in fastq files so they have appropriate extensions - #if str($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}' ${read1} && +## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory +## - @todo once write a decent STAR and STAR Fusion data manager +prep_genome_lib.pl + --genome_fa '${fasta_type.ownFile}' + --gtf '${geneModel}' + --blast_pairs blast_pairs.gz + --CPU \${GALAXY_SLOTS:-1} + --output_dir "\$(pwd)/tmp_star_fusion_genome_dir" +&& + +## Link in fastq files so they have appropriate extensions +#if str($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 + #if $input_params.right_fq: + #if $input_params.right_fq.is_of_type("fastq.gz"): + #set read2 = 'input_2.fastq.gz' + #else: + #set read2 = 'input_2.fastq' #end if - - ## 3. Run STAR-Fusion - STAR-Fusion - #if str($input_params.input_source) == "use_chimeric": - --chimeric_junction '${input_params.chimeric_junction}' - #else: - --left_fq ${read1} - #if $input_params.right_fq: - --right_fq ${read2} - #end if - #end if + ln -f -s '${input_params.right_fq}' ${read2} && + #end if +#end if - --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir" +## 3. Run STAR-Fusion +STAR-Fusion + #if str($input_params.input_source) == "use_chimeric": + --chimeric_junction '${input_params.chimeric_junction}' + #else: + --left_fq ${read1} + #if $input_params.right_fq: + --right_fq ${read2} + #end if + #end if - #if str($params.settingsType) == "full": - --min_junction_reads $params.min_junction_reads - --min_sum_frags $params.min_sum_frags - --max_promiscuity $params.max_promiscuity - --min_novel_junction_support $params.min_novel_junction_support - --min_alt_pct_junction $params.min_alt_pct_junction - --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist - --E $params.E - #end if + --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir" + +#if str($params.settingsType) == "full": + --min_junction_reads $params.min_junction_reads + --min_sum_frags $params.min_sum_frags + --max_promiscuity $params.max_promiscuity + --min_novel_junction_support $params.min_novel_junction_support + --min_alt_pct_junction $params.min_alt_pct_junction + --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist + --E $params.E +#end if ]]></command> <inputs> |