Mercurial > repos > artbio > rsem
changeset 3:26ead8419b63 draft
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 36c2780df597aa4b14ae9c620457f7460166aaa5
| author | artbio |
|---|---|
| date | Tue, 03 Apr 2018 18:25:39 -0400 |
| parents | 9fa602bc29ec |
| children | 1823c8e07d96 |
| files | macros.xml rsem-bwt2.xml rsem.xml |
| diffstat | 3 files changed, 1 insertions(+), 39 deletions(-) [+] |
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--- a/macros.xml Mon Apr 02 13:23:17 2018 -0400 +++ b/macros.xml Tue Apr 03 18:25:39 2018 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">0.5.3</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 Mon Apr 02 13:23:17 2018 -0400 +++ b/rsem-bwt2.xml Tue Apr 03 18:25:39 2018 -0400 @@ -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.is_of_type('sam'): - --sam - #elif $run_rsem.input.rsem_sam.is_of_type('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="sam,bam" label="RSEM formatted SAM file" /> - </when> </conditional> <expand macro="rsem_options"/> <conditional name="rsem_outputs">
--- a/rsem.xml Mon Apr 02 13:23:17 2018 -0400 +++ b/rsem.xml Tue Apr 03 18:25:39 2018 -0400 @@ -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.is_of_type('sam'): - --sam - #elif $run_rsem.input.rsem_sam.is_of_type('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="sam,bam" label="RSEM formatted SAM file" /> - </when> </conditional> <expand macro="rsem_options"/> <conditional name="rsem_outputs">