Mercurial > repos > rnateam > segemehl
changeset 9:90b8941e5115 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 5d14c257183ec8dd0236bbbf63db4a890b9e954a
author | bgruening |
---|---|
date | Mon, 04 Sep 2017 10:12:30 -0400 |
parents | 338ecc1500e4 |
children | ee6a5ec6963c |
files | segemehl.tar.gz segemehl.xml |
diffstat | 2 files changed, 32 insertions(+), 19 deletions(-) [+] |
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--- a/segemehl.xml Wed Jul 26 15:30:57 2017 -0400 +++ b/segemehl.xml Mon Sep 04 10:12:30 2017 -0400 @@ -10,7 +10,31 @@ description="Execution halted." /> </stdio> <command> - <![CDATA[ + <!-- + ## check for single/pair-end + #if str( $library.type ) == "single": + #set $query_list = list() + ## prepare inputs + #for $fastq in $library.input_query: + $query_list.append('%s' % $fastq ) + #end for + -q "#echo ' '.join( $query_list )#" + #else + ## prepare inputs + #set $mate1 = list() + #set $mate2 = list() + #for $mate_pair in $library.mate_list: + $mate1.append( str($mate_pair.first_strand_query) ) + $mate2.append( str($mate_pair.second_strand_query) ) + #end for + + -q #echo ','.join($mate1) + -p #echo ','.join($mate2) + + -I $library.maxinsertsize + #end if + --> + <![CDATA[ ## prepare segemehl index if no reference genome is supplied #if $refGenomeSource.genomeSource == "history": mkdir ./temp_index/ && @@ -36,25 +60,13 @@ ## check for single/pair-end #if str( $library.type ) == "single": - #set $query_list = list() ## prepare inputs - #for $fastq in $library.input_query: - $query_list.append('%s' % $fastq ) - #end for - -q "#echo ' '.join( $query_list )#" - #else - ## prepare inputs - #set $mate1 = list() - #set $mate2 = list() - #for $mate_pair in $library.mate_list: - $mate1.append( str($mate_pair.first_strand_query) ) - $mate2.append( str($mate_pair.second_strand_query) ) - #end for + -q ${library.input_query} + #else + -q ${mate_pair.first_strand_query} + -p ${mate_pair.second_strand_query} - -q #echo ','.join($mate1) - -p #echo ','.join($mate2) - - -I $library.maxinsertsize + -I ${library.maxinsertsize} #end if -m $minsize -A $accuracy @@ -116,7 +128,8 @@ <option value="paired">Paired-end</option> </param> <when value="single"> - <param name="input_query" type="data" multiple="True" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" /> + <!-- <param name="input_query" type="data" multiple="True" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" /> --> + <param name="input_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" /> </when> <when value="paired"> <!-- ToDo paired coolections -->