Mercurial > repos > yboursin > rsem_eba
changeset 1:73a9e9df80da draft
Uploaded
| author | yboursin |
|---|---|
| date | Wed, 25 May 2016 10:08:02 -0400 |
| parents | 7146e81bc886 |
| children | 67c078448bea |
| files | rsem_calculate_expression.xml rsem_prepare_reference.xml |
| diffstat | 2 files changed, 43 insertions(+), 24 deletions(-) [+] |
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--- a/rsem_calculate_expression.xml Wed May 25 08:35:34 2016 -0400 +++ b/rsem_calculate_expression.xml Wed May 25 10:08:02 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="rsem_calculate_expression" name="RSEM calculate expression" version="1.1.17"> +<tool id="rsem_calculate_expression" name="RSEM calculate expression" version="EBA2016-v1"> <description>RNA-Seq by Expectation-Maximization</description> <requirements> <requirement type="package" version="1.2.28">rsem</requirement> @@ -34,26 +34,32 @@ #end if #end if ## Calculate 95% credibility intervals and posterior mean estimates. - #if $rsem_options.useci.ci == 'yes': + #if $rsem_options.ci == 'yes': --calc-ci - #if $rsem_options.useci.cimem: - --ci-memory $rsem_options.useci.cimem - #end if + --ci-memory 2048 #end if #end if - ## --num-threads $GALAXY_SLOTS - #if $input.format != 'bam' and $input.bowtie_options.fullparams == 'fullset': + ## Calculate PME + $rsem_options.pme + --num-threads \${GALAXY_SLOTS:-4} + #if str($input.usebowtie.bowtie) == "one": + #if $input.format != 'bam' and $input.usebowtie.bowtie_options.fullparams == 'fullset': ## Bowtie params - #if $bowtie_options.bowtie_e: - --bowtie-e $bowtie_options.bowtie_e + #if $input.usebowtie.bowtie_options.bowtie_e: + --bowtie-e $input.usebowtie.bowtie_options.bowtie_e #end if - #if $bowtie_options.bowtie_m: - --bowtie-m $bowtie_options.bowtie_m + #if $input.usebowtie.bowtie_options.bowtie_m: + --bowtie-m $input.usebowtie.bowtie_options.bowtie_m + #end if + #if $input.usebowtie.bowtie_options.bowtie_n: + --bowtie-n $input.usebowtie.bowtie_options.bowtie_n #end if - #if $bowtie_options.bowtie_n: - --bowtie-n $bowtie_options.bowtie_n - #end if + #end if + + #elif str($input.usebowtie.bowtie) == "two": + --bowtie2 #end if + ## Outputs #if $rsem_outputs.result_bams == 'none': --no-bam-output @@ -143,21 +149,23 @@ </param> </when> </conditional> - <conditional name="useci"> <param name="ci" type="select" label="Calculate 95% Credibility Intervals"> <option value="no" selected="true">no</option> <option value="yes">yes</option> </param> - <when value="no"/> - <when value="yes"> - <param name="cimem" size="4" type="text" value="1024" label="Amount of memory in (MB) for computing CI" /> - </when> - </conditional> + + <param name="pme" type="boolean" truevalue="--calc-pme" falsevalue="" label="Calculate posterior mean estimates ? (collapsed Gibbs sampler)" /> </when> </conditional> </macro> <macro name="bowtie_options"> - <conditional name="bowtie_options"> + <conditional name="usebowtie"> + <param name="bowtie" type="select" label="Use bowtie 1 or 2 ?"> + <option value="one" selected="true">Bowtie 1</option> + <option value="two">Bowtie 2</option> + </param> + <when value="one"> + <conditional name="bowtie_options"> <param name="fullparams" type="select" label="bowtie settings"> <option value="default">use bowtie defaults</option> <option value="fullset">set bowtie options</option> @@ -173,6 +181,9 @@ </param> </when> </conditional> + </when> + <when value="two" /> + </conditional> </macro> <macro name="sampling_for_bam"> <param name="sampling_for_bam" type="boolean" truevalue="--sampling-for-bam" falsevalue="" checked="false" label="Use sampling for BAM">
--- a/rsem_prepare_reference.xml Wed May 25 08:35:34 2016 -0400 +++ b/rsem_prepare_reference.xml Wed May 25 10:08:02 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="rsem_prepare_reference" name="RSEM prepare reference" version="1.1.17"> +<tool id="rsem_prepare_reference" name="RSEM prepare reference" version="EBA2016-v1"> <description></description> <requirements> <requirement type="package" version="1.2.28">rsem</requirement> @@ -23,13 +23,19 @@ --no-polyA #end if $ntog + $bowtie + $bowtietwo #if $transcript_to_gene_map: --transcript-to-gene-map $transcript_to_gene_map #end if #if $reference.ref_type == 'transcripts': $reference.reference_fasta_file #else: + #if $reference.gtf.extension == 'gtf': --gtf $reference.gtf + #elif $reference.gtf.extension == 'gff3': + --gff3 $reference.gtf + #end if $reference.reference_fasta_file #end if $reference_name @@ -48,8 +54,8 @@ <when value="genomic"> <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" help="The file should contain the sequence of an entire genome."/> - <param name="gtf" type="data" format="gtf" label="gtf" - help="extract transcript reference sequences using the gene annotations specified in this GTF" /> + <param name="gtf" type="data" format="gtf,gff3" label="gtf or gff3 file" + help="extract transcript reference sequences using the gene annotations specified in this GTF or GFF3 file" /> </when> </conditional> <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" > @@ -86,6 +92,8 @@ </when> <when value="none"/> </conditional> + <param name="bowtie" type="boolean" truevalue="--bowtie" falsevalue="" checked="false" label="Use bowtie" /> + <param name="bowtietwo" type="boolean" truevalue="--bowtie2" falsevalue="" checked="false" label="Use bowtie2" /> <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowite uses the automatic N to G conversion to to align against all positions in the reference."/> </inputs> <stdio>