Mercurial > repos > iuc > sra_tools
view sra_macros.xml @ 20:964579f93c54 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ec1cc6c0c290e9931780ea128bb48caac37977db"
author | iuc |
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date | Wed, 01 Jul 2020 17:48:02 -0400 |
parents | 248f85ff0733 |
children | 494b2ec08162 |
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<macros> <token name="@VERSION@">2.10.7</token> <token name="@ACCESSIONS_FROM_FILE@"> grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$' </token> <token name="@COMPRESS@"><![CDATA[pigz -cqp \${GALAXY_SLOTS:-1}]]></token> <token name="@CONFIGURE_RETRY@"><![CDATA[ export SRA_PREFETCH_RETRIES=3 && export SRA_PREFETCH_ATTEMPT=1 && ]]></token> <token name="@COPY_CONFIGFILE@"><![CDATA[ mkdir -p ~/.ncbi && cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg && vdb-config -s "/repository/user/main/public/root=\$PWD" && vdb-config -s "/repository/user/ad/public/root=\$PWD" && vdb-config -s "/repository/user/default-path=\$PWD" && vdb-config -s "/repository/user/main/public/root=\$PWD" && vdb-config -s /http/timeout/read=10000 && ]]></token> <token name="@SET_ACCESSIONS@"><![CDATA[ #if $input.input_select=="file_list": #if $input.file_list.is_of_type('sra_manifest.tabular'): #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1 cut -f $column '$input.file_list'| tail -n +2 > "manifest" && #else ln -s '$input.file_list' manifest && #end if for acc in `@ACCESSIONS_FROM_FILE@ manifest` ; do ( #elif $input.input_select=="accession_number": acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( #end if ]]></token> <macro name="requirements"> <requirements> <requirement type="package" version="@VERSION@">sra-tools</requirement> <requirement type="package" version="2.3.4">pigz</requirement> <yield/> </requirements> </macro> <macro name="configfile_hack"> <configfiles> <configfile name="user_settings_mkfg"><![CDATA[ /LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec" /config/default = "false" /libs/temp_cache = "." /tools/prefetch/download_to_cache = "false" ]]></configfile> </configfiles> </macro> <macro name="sanitize_query"> <sanitizer> <valid initial="string.printable"> <remove value=" "/> <remove value="'" /> </valid> <mapping initial="none"> <add source=" " target=""/> <add source="'" target="'"'"'" /> </mapping> </sanitizer> </macro> <macro name="input_conditional"> <conditional name="input"> <param name="input_select" type="select" label="select input type"> <option value="accession_number">SRR accession</option> <option value="file_list">List of SRA accession, one per line</option> <option value="file">SRA archive in current history</option> </param> <when value="accession_number"> <param name="accession" type="text" label="Accession" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809"> <expand macro="sanitize_query" /> <validator type="empty_field" message="An accession is required"/> </param> </when> <when value="file"> <param format="sra" name="file" type="data" label="sra archive"/> </when> <when value="file_list"> <param format="txt" name="file_list" type="data" label="sra accession list"/> </when> </conditional> </macro> <macro name="alignments"> <param name="alignments" type="select" value="both" label="Output aligned or unaligned reads" help="Output reads according to their alignment status." argument="--aligned and --unaligned"> <option value="both">both</option> <option value="aligned">aligned only</option> <option value="unaligned">unaligned only</option> </param> </macro> <macro name="minMapq"> <param name="minMapq" type="integer" min="0" max="42" label="Minimum mapping quality" optional="true" help="Minimum mapping quality an alignment has to have, to be dumped." argument="--min-mapq"/> </macro> <macro name="region"> <param format="text" name="region" type="text" label="aligned region" optional="true" help="Filter by position on genome. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)." argument="--aligned-region"/> </macro> <macro name="matepairDist"> <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true" help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference" argument="--matepair-distance"/> </macro> <macro name="citation"> <citations> <citation type="doi">10.1093/nar/gkq1019</citation> </citations> </macro> <token name="@ACCESSION_LIST_HOWTO@"> ----- **How to generate accession lists** 1. Go to **SRA Run Selector** by clicking this link_ 2. Find the study you are interested in by typing a search term within the **Search** box. This can be a word (e.g., *mitochondria*) or an accession you have gotten from a paper (e.g., *SRR1582967*). 3. Once you click on the study of interest you will see the number of datasets in this study within the **Related SRA data** box 4. Click on the Runs number 5. On the page that would open you will see **Accession List** button 6. Clicking of this button will produce a file that you will need to upload into Galaxy and use as the input to this tool. </token> <token name="@SRATOOLS_ATTRRIBUTION@"> Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com). 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>