Mercurial > repos > iuc > sra_tools
view sra_pileup.xml @ 4:62e4d56ebb6f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4091428e9e28ca06263bc00cdf938d20f620aa4d
author | iuc |
---|---|
date | Fri, 21 Oct 2016 04:32:19 -0400 |
parents | 4732693f4661 |
children | c7620aa7e1f0 |
line wrap: on
line source
<tool id="sra_pileup" name="Generate pileup format" version="@VERSION@"> <description>from NCBI sra.</description> <macros> <import>sra_macros.xml</import> </macros> <expand macro="requirements"/> <version_command>sra-pileup --version</version_command> <command detect_errors="exit_code"> <![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" && #if ( str( $adv.region ) == "" ): ASCP_PATH=`command -v ascp` && ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" && ## Duplicate vdb-config, in case settings changed between prefetch and ## sra-pileup command. vdb-config -s "/repository/user/main/public/root=\$PWD" && #end if sra-pileup --log-level fatal #if str( $adv.region ) != "": --aligned-region "$adv.region" #end if #if str( $adv.minMapq ) != "": --minmapq "$adv.minMapq" #end if #if $input.input_select == "file": "$input.file" > "$output_file" #elif $input.input_select == "accession_number": "$input.accession" > "$output_accession" #elif $input.input_select == "text": `cat "$input.text"` > "$output_text" #end if ]]> </command> <inputs> <conditional name="input"> <param name="input_select" type="select" label="select input type"> <option value="accession_number">SRR accession</option> <option value="file">SRA archive in current history</option> <option value="text">text file containing SRR accession</option> </param> <when value="file"> <param format="sra" name="file" type="data" label="sra archive"/> </when> <when value="accession_number"> <param format="text" name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743"/> </when> <when value="text"> <param format="txt" name="text" type="data" label="text file"/> </when> </conditional> <section name="adv" title="Advanced Options" expanded="False"> <expand macro="region"/> <expand macro="minMapq"/> </section> </inputs> <outputs> <data format="pileup" name="output_accession" label="${input.accession}.pileup"> <filter>input['input_select'] == "accession_number"</filter> </data> <data format="pileup" name="output_file" label="${input.file.name}.pileup"> <filter>input['input_select'] == "file"</filter> </data> <data format="pileup" name="output_text" label="${input.text.name}.pileup"> <filter>input['input_select'] == "text"</filter> </data> </outputs> <tests> <test> <param name="input_select" value="accession_number"/> <param name="accession" value="SRR925743"/> <param name="region" value="17:41243452-41277500"/> <output name="output_accession" file="sra_pileup_result.pileup" compare="contains" ftype="pileup"/> </test> </tests> <help> This tool produces pileup format from sra archives using sra-pileup. The sra-pileup 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>