Mercurial > repos > iuc > sra_tools
diff sam_dump.xml @ 0:b723c120161a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
author | iuc |
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date | Sun, 06 Dec 2015 09:04:37 -0500 |
parents | |
children | 462ee06c9358 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_dump.xml Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,118 @@ +<tool id="sam_dump" name="Extract reads" version="1.2.5"> + <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> + <![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. + 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( $adv.region ) == "" ): + ASCP_PATH=`command -v ascp` && + ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && + prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" && + ## 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 $input.input_select == "accession_number": + "$input.accession" + #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 + ]]> + </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> + <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>