diff bdss_client_sra_se.xml @ 3:c707a4178832 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty

--- a/bdss_client_sra_se.xml	Tue Oct 10 20:22:55 2017 -0400
+++ b/bdss_client_sra_se.xml	Wed Oct 11 11:23:04 2017 -0400
@@ -6,6 +6,7 @@
         <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>
+        <requirement type="package" version="1.95_4.8">r-rcurl</requirement>
     </requirements>
     <description>
         Download and extract single end reads in fastq or fasta format from NCBI SRA. The output is a list of datasets
@@ -16,7 +17,7 @@
         <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[
@@ -24,6 +25,7 @@
                 -i '$sra_accession'
                 -e $echo
                 -f $format
+                -S $sra
 
                 -r $report
                 -d $report.files_path
@@ -35,14 +37,18 @@
     <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="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true"
+               label="output files in fastq (Yes) or fasta (No)?"/>
+        <param type="boolean" name="sra" truevalue="TRUE" falsevalue="FALSE" checked="false"
+               label="Download SRA or Fastq"/>
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
+               label="Display analysis code in report?"/>
     </inputs>
     <outputs>
-        <data format="html" name="report" label="BDSS report" />
+        <data format="html" name="report" label="BDSS report"/>
         <collection type="list" name="list_collection" label="BDSS fastq/fasta (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>
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