Previous changeset 2:f256cb398262 (2016-09-16) Next changeset 4:62e4d56ebb6f (2016-10-21) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd |
modified:
fastq_dump.xml sam_dump.xml sra_macros.xml sra_pileup.xml |
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diff -r f256cb398262 -r 4732693f4661 fastq_dump.xml --- a/fastq_dump.xml Fri Sep 16 17:24:03 2016 -0400 +++ b/fastq_dump.xml Tue Oct 18 14:54:40 2016 -0400 |
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@@ -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" && |
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diff -r f256cb398262 -r 4732693f4661 sam_dump.xml --- a/sam_dump.xml Fri Sep 16 17:24:03 2016 -0400 +++ b/sam_dump.xml Tue Oct 18 14:54:40 2016 -0400 |
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@@ -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" && |
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diff -r f256cb398262 -r 4732693f4661 sra_macros.xml --- a/sra_macros.xml Fri Sep 16 17:24:03 2016 -0400 +++ b/sra_macros.xml Tue Oct 18 14:54:40 2016 -0400 |
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@@ -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"> |
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diff -r f256cb398262 -r 4732693f4661 sra_pileup.xml --- a/sra_pileup.xml Fri Sep 16 17:24:03 2016 -0400 +++ b/sra_pileup.xml Tue Oct 18 14:54:40 2016 -0400 |
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@@ -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" && |