Mercurial > repos > iuc > sra_tools
changeset 2:f256cb398262 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
| author | iuc |
|---|---|
| date | Fri, 16 Sep 2016 17:24:03 -0400 |
| parents | 462ee06c9358 |
| children | 4732693f4661 |
| files | fastq_dump.xml sam_dump.xml sra_macros.xml sra_pileup.xml tool_dependencies.xml |
| diffstat | 5 files changed, 24 insertions(+), 43 deletions(-) [+] |
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--- 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>
--- 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( $outputformat ) == "bam": | samtools view -Sb - 2> /dev/null #end if @@ -117,7 +117,7 @@ <filter>input['input_select'] == "file_list"</filter> <discover_datasets pattern="(?P<designation>.+)\.bam" directory="." ext='bam'/> <discover_datasets pattern="(?P<designation>.+)\.sam" directory="." ext='sam'/> - </collection> + </collection> <data name="output_accession" format="bam" label="${input.accession}.${outputformat}"> <filter>input['input_select'] == "accession_number"</filter> <change_format>
--- 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>
--- 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" &&
--- 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>