# HG changeset patch
# User iuc
# Date 1474061043 14400
# Node ID f256cb3982620a11e17573f95e5d3d95c9691c01
# Parent  462ee06c9358a7135d49872844acff869445f8d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026

diff -r 462ee06c9358 -r f256cb398262 fastq_dump.xml
--- a/fastq_dump.xml	Tue May 17 14:14:50 2016 -0400
+++ b/fastq_dump.xml	Fri Sep 16 17:24:03 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Extract reads" version="1.3.0">
+<tool id="fastq_dump" name="Extract reads" version="2.6.2">
     <description>in FASTQ/A format from NCBI SRA.</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -21,10 +21,10 @@
     #if $input.input_select=="file_list" or $input.input_select=="accession_number":
           [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
     #end if
-    
+
     ## 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. 
+    ## else the tool tries to write to home/.ncbi and fails when used
+    ## with a cluster manager.
     export HOME=\$PWD &&
     vdb-config --restore-defaults &&
     #if $input.input_select == "file":
@@ -76,7 +76,7 @@
     #end if
     $adv.clip
     $adv.skip_technical
-    
+
     #if str( $outputformat ) == "fasta":
         --fasta
     #end if
@@ -97,15 +97,15 @@
 
 
     #if str( $outputformat ) == "fasta":
-    
+
         for f in *_2.fasta ; do   mv "\$f" "`basename \$f _2.fasta`_reverse.fasta" ;  mv "`basename \$f _2.fasta`_1.fasta" "`basename \$f _2.fasta`_forward.fasta"  ; done &&
         for f in *_1.fasta; do mv "\$f" "`basename \$f _1.fasta`__single.fasta"; done
-        
+
     #else:
 
         for f in *_2.fastq ; do   mv "\$f" "`basename \$f _2.fastq`_reverse.fastq" ;  mv "`basename \$f _2.fastq`_1.fastq" "`basename \$f _2.fastq`_forward.fastq"  ; done &&
         for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`__single.fastq"; done
-        
+
     #end if
 
 
@@ -114,7 +114,7 @@
 
     #end if
 
-    
+
     ]]>
     </command>
     <inputs>
@@ -202,7 +202,7 @@
         This tool extracts reads from SRA archives using fastq-dump.
         The fastq-dump program is developed at NCBI, and is available at
         http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-        
+
         NB: Single-end or pair-end collections may be empty if given SRRs LibraryLayout contains only either SINGLE or PAIRED respectively
         @SRATOOLS_ATTRRIBUTION@
     </help>
diff -r 462ee06c9358 -r f256cb398262 sam_dump.xml
--- a/sam_dump.xml	Tue May 17 14:14:50 2016 -0400
+++ b/sam_dump.xml	Fri Sep 16 17:24:03 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Extract reads" version="1.3.0">
+<tool id="sam_dump" name="Extract reads" version="2.6.2">
     <description>in SAM or BAM format from NCBI SRA.</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -21,8 +21,8 @@
 
 
         ## 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. 
+        ## else the tool tries to write to home/.ncbi and fails when used
+        ## with a cluster manager.
         export HOME=\$PWD &&
         vdb-config --restore-defaults &&
         vdb-config -s "/repository/user/main/public/root=\$PWD" &&
@@ -67,7 +67,7 @@
         #elif $input.input_select=="file_list":
             "\$acc"
         #end if
-        
+
         #if str( $outputformat ) == "bam":
             | samtools view -Sb - 2> /dev/null
         #end if
@@ -117,7 +117,7 @@
           <filter>input['input_select'] == "file_list"</filter>
           <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
           <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
-        </collection>      
+        </collection>
         <data name="output_accession" format="bam" label="${input.accession}.${outputformat}">
             <filter>input['input_select'] == "accession_number"</filter>
             <change_format>
diff -r 462ee06c9358 -r f256cb398262 sra_macros.xml
--- a/sra_macros.xml	Tue May 17 14:14:50 2016 -0400
+++ b/sra_macros.xml	Fri Sep 16 17:24:03 2016 -0400
@@ -1,11 +1,7 @@
 <macros>
     <macro name="requirements">
         <requirements>
-            <requirement type="package" version="1.2.3">ngs_sdk</requirement>
-            <requirement type="package" version="2.6.2">ncbi_vdb</requirement>
-            <requirement type="package" version="2.6.2">sra_toolkit</requirement>
             <requirement type="package" version="2.6.2">sra-tools</requirement>
-            <requirement type="package" version="5.18.1">perl</requirement>
         </requirements>
     </macro>
     <macro name="input_conditional">
@@ -23,7 +19,7 @@
             </when>
             <when value="file_list">
                 <param format="txt" name="file_list" type="data" label="sra accession list"/>
-            </when>            
+            </when>
         </conditional>
     </macro>
     <macro name="alignments">
@@ -52,14 +48,14 @@
     </macro>
     <token name="@SRATOOLS_ATTRRIBUTION@">
         Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
-        
+
         Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
 
-        Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ). 
-        
+        Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
+
         Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
-        
+
         For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.
-        
+
     </token>
 </macros>
diff -r 462ee06c9358 -r f256cb398262 sra_pileup.xml
--- a/sra_pileup.xml	Tue May 17 14:14:50 2016 -0400
+++ b/sra_pileup.xml	Fri Sep 16 17:24:03 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="sra_pileup" name="Generate pileup format" version="1.2.5">
+<tool id="sra_pileup" name="Generate pileup format" version="2.6.2">
     <description>from NCBI sra.</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -8,8 +8,8 @@
     <command>
         <![CDATA[
         ## 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. 
+        ## else the tool tries to write to home/.ncbi and fails when used
+        ## with a cluster manager.
         export HOME=\$PWD &&
         vdb-config --restore-defaults &&
         vdb-config -s "/repository/user/main/public/root=\$PWD" &&
diff -r 462ee06c9358 -r f256cb398262 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue May 17 14:14:50 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="ncbi_vdb" version="2.6.2">
-        <repository changeset_revision="be38d36c735d" name="package_ncbi_vdb_2_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="ngs_sdk" version="1.2.3">
-        <repository changeset_revision="3da0f4d34e92" name="package_ngs_sdk_1_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="sra_toolkit" version="2.6.2">
-        <repository changeset_revision="98414d1f9480" name="package_sra_toolkit_2_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>