Mercurial > repos > iuc > sra_tools
view sra_macros.xml @ 5:26b7446bb17e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cb834fdb9ac48d8a5af99621be1e27f3119c5414
author | iuc |
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date | Wed, 07 Dec 2016 09:10:29 -0500 |
parents | 62e4d56ebb6f |
children | c7620aa7e1f0 |
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<macros> <token name="@VERSION@">2.8.0</token> <macro name="requirements"> <requirements> <requirement type="package" version="2.8.0">sra-tools</requirement> </requirements> </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">SRA archive in current history</option> <option value="file_list">List of SRA accession, one per line</option> </param> <when value="accession_number"> <param name="accession" type="text" label="SRR accession" help="Must start with SRR,DRR or ERR, e.g. SRR925743 , ERR343809"/> </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>aligned or unaligned reads</label> <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"/> </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)."/> </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"/> </macro> <macro name="citation"> <citations> <citation type="doi">10.1093/nar/gkq1019</citation> </citations> </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 ). 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>