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changeset 3:4732693f4661 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd
author iuc
date Tue, 18 Oct 2016 14:54:40 -0400
parents f256cb398262
children 62e4d56ebb6f
files fastq_dump.xml sam_dump.xml sra_macros.xml sra_pileup.xml
diffstat 4 files changed, 8 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_dump.xml	Fri Sep 16 17:24:03 2016 -0400
+++ b/fastq_dump.xml	Tue Oct 18 14:54:40 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Extract reads" version="2.6.2">
+<tool id="fastq_dump" name="Extract reads" version="@VERSION@">
     <description>in FASTQ/A format from NCBI SRA.</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -36,7 +36,7 @@
         #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 --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
+            prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
             ## Duplicate vdb-config, in case settings changed between prefetch and
             ## dump command.
             vdb-config -s "/repository/user/main/public/root=\$PWD" &&
--- a/sam_dump.xml	Fri Sep 16 17:24:03 2016 -0400
+++ b/sam_dump.xml	Tue Oct 18 14:54:40 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Extract reads" version="2.6.2">
+<tool id="sam_dump" name="Extract reads" version="@VERSION@">
     <description>in SAM or BAM format from NCBI SRA.</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -31,7 +31,7 @@
         #if ( str( $adv.region ) == "" ):
             ASCP_PATH=`command -v ascp` &&
             ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
-            prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
+            prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
             ## Duplicate vdb-config, in case settings changed between prefetch and
             ## dump command.
             vdb-config -s "/repository/user/main/public/root=\$PWD" &&
--- a/sra_macros.xml	Fri Sep 16 17:24:03 2016 -0400
+++ b/sra_macros.xml	Tue Oct 18 14:54:40 2016 -0400
@@ -1,7 +1,8 @@
 <macros>
+    <token name="@VERSION@">2.7.0</token>
     <macro name="requirements">
         <requirements>
-            <requirement type="package" version="2.6.2">sra-tools</requirement>
+            <requirement type="package" version="2.7.0">sra-tools</requirement>
         </requirements>
     </macro>
     <macro name="input_conditional">
--- a/sra_pileup.xml	Fri Sep 16 17:24:03 2016 -0400
+++ b/sra_pileup.xml	Tue Oct 18 14:54:40 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="sra_pileup" name="Generate pileup format" version="2.6.2">
+<tool id="sra_pileup" name="Generate pileup format" version="@VERSION@">
     <description>from NCBI sra.</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -16,7 +16,7 @@
         #if ( str( $adv.region ) == "" ):
             ASCP_PATH=`command -v ascp` &&
             ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
-            prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" &&
+            prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" &&
             ## Duplicate vdb-config, in case settings changed between prefetch and
             ## sra-pileup command.
             vdb-config -s "/repository/user/main/public/root=\$PWD" &&