Mercurial > repos > artbio > rsem
changeset 10:6aba6cca3fab draft
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 36c2780df597aa4b14ae9c620457f7460166aaa5
| author | artbio |
|---|---|
| date | Tue, 03 Apr 2018 18:27:15 -0400 |
| parents | cf60c3338279 |
| children | c86ed39b72eb |
| files | macros.xml rsem-bwt2.xml rsem.xml |
| diffstat | 3 files changed, 6 insertions(+), 44 deletions(-) [+] |
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--- a/macros.xml Sun Apr 01 18:10:44 2018 -0400 +++ b/macros.xml Tue Apr 03 18:27:15 2018 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">0.5.1</token> + <token name="@WRAPPER_VERSION@">0.5.4</token> <xml name="rsem_options"> <param name="seedlength" type="integer" value="25" optional="true" label="Seed length used by the read aligner" help="Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads. RSEM uses this value for Bowtie's seed length parameter. The minimum value is 25. (Default:25)"> </param>
--- a/rsem-bwt2.xml Sun Apr 01 18:10:44 2018 -0400 +++ b/rsem-bwt2.xml Tue Apr 03 18:27:15 2018 -0400 @@ -46,15 +46,15 @@ && #end if - #if $run_rsem.select == "Yes": + #if $run_rsem.select == "Yes" and $run_rsem.input.format == 'fastq': ## uncompress fastq.gz or fastqsanger.gz if needed - #if $run_rsem.input.fastq.matepair=="single": + #if $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="single": #if $run_rsem.input.fastq.singlefastq.is_of_type('fastq.gz') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger.gz'): gunzip < '$run_rsem.input.fastq.singlefastq' > uncomp_single.fastq && #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'): ln -f -s '$run_rsem.input.fastq.singlefastq' 'uncomp_single.fastq' && #end if - #elif $run_rsem.input.fastq.matepair=="paired": + #elif $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="paired": #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'): gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq && gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq && @@ -141,16 +141,6 @@ $run_rsem.input.fasta.fasta1 $run_rsem.input.fasta.fasta2 #end if - #elif $run_rsem.input.format=="sam" - #if $run_rsem.input.matepair=="paired": - --paired-end - #end if - #if $run_rsem.input.rsem_sam._extension == 'sam': - --sam - #elif $run_rsem.input.rsem_sam._extension == 'bam': - --bam - #end if - $run_rsem.input.rsem_sam #end if ## RSEM reference #if $run_rsem.reference.refSrc == 'history': @@ -250,7 +240,6 @@ <param name="format" type="select" label="RSEM Input file type"> <option value="fastq">FASTQ</option> <option value="fasta">FASTA</option> - <option value="sam">SAM/BAM</option> </param> <when value="fastq"> <param name="fastq_select" size="15" type="select" label="FASTQ type" > @@ -289,14 +278,6 @@ </conditional> <expand macro="bowtie2_options"/> </when> - <when value="sam"> - <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam --> - <param name="matepair" type="select" label="Library Type"> - <option value="single">Single End Reads</option> - <option value="paired">Paired End Reads</option> - </param> - <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" /> - </when> </conditional> <expand macro="rsem_options"/> <conditional name="rsem_outputs">
--- a/rsem.xml Sun Apr 01 18:10:44 2018 -0400 +++ b/rsem.xml Tue Apr 03 18:27:15 2018 -0400 @@ -48,13 +48,13 @@ #if $run_rsem.select == "Yes": ## uncompress fastq.gz or fastqsanger.gz if needed - #if $run_rsem.input.fastq.matepair=="single": + #if $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="single": #if $run_rsem.input.fastq.singlefastq.is_of_type('fastq.gz') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger.gz'): gunzip < '$run_rsem.input.fastq.singlefastq' > uncomp_single.fastq && #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'): ln -f -s '$run_rsem.input.fastq.singlefastq' 'uncomp_single.fastq' && #end if - #elif $run_rsem.input.fastq.matepair=="paired": + #elif $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="paired": #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'): gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq && gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq && @@ -148,16 +148,6 @@ $run_rsem.input.fasta.fasta1 $run_rsem.input.fasta.fasta2 #end if - #elif $run_rsem.input.format=="sam" - #if $run_rsem.input.matepair=="paired": - --paired-end - #end if - #if $run_rsem.input.rsem_sam._extension == 'sam': - --sam - #elif $run_rsem.input.rsem_sam._extension == 'bam': - --bam - #end if - $run_rsem.input.rsem_sam #end if ## RSEM reference #if $run_rsem.reference.refSrc == 'history': @@ -257,7 +247,6 @@ <param name="format" type="select" label="RSEM Input file type"> <option value="fastq">FASTQ</option> <option value="fasta">FASTA</option> - <option value="sam">SAM/BAM</option> </param> <when value="fastq"> <param name="fastq_select" size="15" type="select" label="FASTQ type" > @@ -296,14 +285,6 @@ </conditional> <expand macro="bowtie_options"/> </when> - <when value="sam"> - <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam --> - <param name="matepair" type="select" label="Library Type"> - <option value="single">Single End Reads</option> - <option value="paired">Paired End Reads</option> - </param> - <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" /> - </when> </conditional> <expand macro="rsem_options"/> <conditional name="rsem_outputs">