diff fastq_dump_se.xml @ 21:3c859d094074 draft default tip

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/aurora-tools/rmarkdown_fastq_dump commit ffa886b188215708786e3c49877fc08fea60659e

--- a/fastq_dump_se.xml	Wed Sep 27 21:38:54 2017 -0400
+++ b/fastq_dump_se.xml	Wed Apr 04 10:10:26 2018 -0400
@@ -1,8 +1,8 @@
-<tool id="rmarkdown_fastqc_dump_se" name="fastqc-dump-se" version="1.0.0">
+<tool id="rmarkdown_fastq_dump_se" name="fastq-dump-se" version="1.0.2">
     <requirements>
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="1.2">r-rmarkdown</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
         <requirement type="package" version="0.3.5">r-htmltools</requirement>
         <requirement type="package" version="0.5.0">r-dplyr</requirement>
         <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
@@ -16,13 +16,12 @@
         <regex match="XXX"
                source="stderr"
                level="warning"
-               description="Check the warnings_and_errors.txt file for more details." />
+               description="Check the warnings_and_errors.txt file for more details."/>
     </stdio>
     <command>
         <![CDATA[
             Rscript '${__tool_directory__}/fastq_dump_se_render.R'
                 -i '$sra_accession'
-                -e $echo
                 -f $format
 
                 -r $report
@@ -35,14 +34,16 @@
     <inputs>
         <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions"
                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="true" label="output files in fastq (Yes) or fasta (No)?"/>
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+        <param type="select" name="format" label="Output format">
+            <option value="fastq" selected="true">fastq</option>
+            <option value="fasta">fasta</option>
+        </param>
     </inputs>
     <outputs>
-        <data format="html" name="report" label="Fastq-dump report" />
+        <data format="html" name="report" label="Fastq-dump report"/>
         <collection type="list" name="list_collection" label="Fastq-dump (single end reads)">
-            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory" />
+            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory"/>
         </collection>
-        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" />
+        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
     </outputs>
 </tool>
\ No newline at end of file