diff fastq_dump.xml @ 15:54366e4d692a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"

--- a/fastq_dump.xml	Tue Dec 04 15:00:32 2018 -0500
+++ b/fastq_dump.xml	Fri Mar 20 16:36:52 2020 +0000
@@ -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@+galaxy1" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -6,14 +6,12 @@
     <expand macro="requirements"/>
     <version_command>fastq-dump --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-
     @SET_ACCESSIONS@
 
     ## Need to set the home directory to the current working directory,
     ## else the tool tries to write to home/.ncbi and fails when used
     ## with a cluster manager.
-    export HOME=\$PWD &&
-    vdb-config --restore-defaults &&
+    @CONFIGURE_TIMEOUT@
     #if $input.input_select == "file":
         fastq-dump --log-level fatal --accession '${input.file.name}'
     #else:
@@ -21,9 +19,7 @@
         ## Do not use prefetch if region is specified, to avoid downloading
         ## the complete sra file.
         #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
-            ASCP_PATH=`command -v ascp` &&
-            ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
-            prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
+            prefetch -X 200000000 "\$acc" &&
             ## Duplicate vdb-config, in case settings changed between prefetch and
             ## dump command.
             vdb-config -s "/repository/user/main/public/root=\$PWD" &&
@@ -70,6 +66,12 @@
     #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 +82,7 @@
     #end if
 
     #if $input.input_select=="file_list":
+        "\$acc"
         ) ; done
 
         ;
@@ -126,6 +129,7 @@
             <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 +230,15 @@
             <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?**