diff fastq_dump.xml @ 15:f5ea3ce9b9b0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"

--- a/fastq_dump.xml	Tue Dec 04 15:00:55 2018 -0500
+++ b/fastq_dump.xml	Tue Sep 10 11:35:35 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@.3">
+<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@.4">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -70,6 +70,12 @@
     #elif str( $outputformat ) == "fastqsanger.bz2":   
         --bzip2
     #end if
+
+    #if str($adv.table) != "":
+        --table $adv.table
+    #end if
+
+
     #if $input.input_select=="file":
         --stdout
         "$input.file" > "$output_file"
@@ -80,6 +86,7 @@
     #end if
 
     #if $input.input_select=="file_list":
+        "\$acc"
         ) ; done
 
         ;
@@ -126,6 +133,7 @@
             <param name="spotgroups" type="text" label="Filter by spot-groups" optional="true" argument="--spot-groups"/>
             <param name="clip" type="boolean" truevalue="--clip" falsevalue="" argument="--clip" label="Apply left and right clips" />
             <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads" argument="--skip-technical"/>
+            <param name="table" label="Table name within cSRA object" type="text" value="" optional="true" help="For SRA of noisy long-reads put SEQUENCE" argument="--table"/>
         </section>
     </inputs>
     <outputs>
@@ -226,7 +234,15 @@
             <output_collection name="output_collection" type="list">
                 <element name="SRR1993644" file="SRR1993644.fastqsanger"/>
             </output_collection>
-        </test>            
+        </test>
+        <test>
+            <param name="input_select" value="accession_number"/>
+            <param name="outputformat" value="fastqsanger.gz"/>
+            <param name="accession" value="SRR6982805"/>
+            <param name="maxID" value="2"/>
+            <param name="table" value="SEQUENCE"/>
+            <output name="output_accession" file="SRR6982805.fastqsanger.gz" ftype="fastqsanger.gz" decompress="True"/>
+        </test>  
     </tests>
     <help><![CDATA[
 **What it does?**