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view sam_dump.xml @ 6:30775c836c77 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ee50324111351323cc294e051a6fab1733a89ec1
author | iuc |
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date | Wed, 22 Mar 2017 05:23:31 -0400 |
parents | 62e4d56ebb6f |
children | c7620aa7e1f0 |
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<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> </macros> <expand macro="requirements"/> <version_command>sam-dump --version</version_command> <command detect_errors="exit_code"> <![CDATA[ #if $input.input_select=="file_list": for acc in `cat $input.file_list` ; do #elif $input.input_select=="accession_number": acc="$input.accession" && #end if #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. export HOME=\$PWD && vdb-config --restore-defaults && vdb-config -s "/repository/user/main/public/root=\$PWD" && ## Do not use prefetch if region is specified, to avoid downloading ## the complete sra file. #if ( str( $adv.region ) == "" ): 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" && ## Duplicate vdb-config, in case settings changed between prefetch and ## dump command. vdb-config -s "/repository/user/main/public/root=\$PWD" && #end if sam-dump --log-level fatal --disable-multithreading #if str( $adv.region ) != "": --aligned-region "$adv.region" #end if #if str( $adv.matepairDist ) != "": --matepair-distance "$adv.matepairDist" #end if #if str( $adv.minMapq ) != "": --min-mapq "$adv.minMapq" #end if #if str( $adv.header ) == "yes": --header #else: --no-header #end if #if str( $adv.alignments ) == "both": --unaligned #end if #if str( $adv.alignments ) == "unaligned": --unaligned-spots-only #end if #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ): --primary #end if #if $input.input_select == "file": "$input.file" #elif $input.input_select == "accession_number": "\$acc" #elif $input.input_select=="file_list": "\$acc" #end if #if str( $outputformat ) == "bam": | samtools view -Sb - 2> /dev/null #end if #if $input.input_select == "file": > "$output_file" #elif $input.input_select == "accession_number": > "$output_accession" ) #end if #if $input.input_select=="file_list": #if str( $outputformat ) == "bam": > "\$acc.bam" #elif str( $outputformat ) == "sam": > "\$acc.sam" #end if ) ; done #end if ]]> </command> <inputs> <expand macro="input_conditional"/> <param name="outputformat" type="select" label="select output format"> <option value="bam">bam</option> <option value="sam">sam</option> </param> <section name="adv" title="Advanced Options" expanded="False"> <param name="header" type="select" value="yes"> <label>output header</label> <option value="yes">Yes</option> <option value="no">No</option> </param> <expand macro="alignments"/> <expand macro="region"/> <expand macro="matepairDist"/> <param name="primary" type="select" value="no"> <label>only primary aligments</label> <option value="no">No</option> <option value="yes">Yes</option> </param> <expand macro="minMapq"></expand> </section> </inputs> <outputs> <collection name="output_collection" type='list'> <filter>input['input_select'] == "file_list"</filter> <discover_datasets pattern="(?P<designation>.+)\.bam" directory="." ext='bam'/> <discover_datasets pattern="(?P<designation>.+)\.sam" directory="." ext='sam'/> </collection> <data name="output_accession" format="bam" label="${input.accession}.${outputformat}"> <filter>input['input_select'] == "accession_number"</filter> <change_format> <when input="outputformat" value="sam" format="sam"/> </change_format> </data> <data name="output_file" format="bam" label="${input.file.name}.${outputformat}"> <filter>input['input_select'] == "file"</filter> <change_format> <when input="outputformat" value="sam" format="sam"/> </change_format> </data> </outputs> <tests> <test> <param name="input_select" value="accession_number"/> <param name="accession" value="SRR925743"/> <param name="outputformat" value="sam"/> <param name="region" value="17:41243452-41277500"/> <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/> </test> </tests> <help> This tool extracts reads from sra archives using sam-dump. The sam-dump program is developed at NCBI, and is available at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. @SRATOOLS_ATTRRIBUTION@ </help> <expand macro="citation"/> </tool>