diff fastq_dump_pe.xml @ 13:66bc1016ec2a draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty

--- a/fastq_dump_pe.xml	Wed Sep 27 16:49:22 2017 -0400
+++ b/fastq_dump_pe.xml	Wed Sep 27 16:54:07 2017 -0400
@@ -8,7 +8,7 @@
         <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
     </requirements>
     <description>
-        Download and extract single end reads in fastq or fasta format from NCBI SRA. The output is a list of datasets
+        Download and extract paired end reads in fastq or fasta format from NCBI SRA. The output is a list of paired datasets
         collection.
     </description>
     <stdio>
@@ -27,7 +27,6 @@
                 -p $split_files
 
                 -r $report
-                -d $report.files_path
                 -s $sink_message
 
                 -t '${__tool_directory__}/fastq_dump_pe.Rmd'
@@ -38,9 +37,6 @@
                help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
         <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="false"
                label="output files in fastq (true) or fasta (false)?"/>
-        <param type="boolean" name="split_files" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Split files"
-               help="Dump each read into separate file. Files will receive suffix corresponding to read number"/>
-
         <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
                label="Display analysis code in report?"/>
     </inputs>