Mercurial > repos > iuc > sra_tools
view sra_macros.xml @ 10:8c00bc7fd8de draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 48c9d7f30655d48c9b46b9ca7a17c454eb54694d
author | iuc |
---|---|
date | Fri, 17 Nov 2017 13:22:37 -0500 |
parents | c7620aa7e1f0 |
children | 5e6237d58b0c |
line wrap: on
line source
<macros> <token name="@VERSION@">2.8.1</token> <macro name="requirements"> <requirements> <requirement type="package" version="2.8.1">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_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"> <sanitizer> <valid initial="string.printable"> <remove value=" "/> </valid> <mapping initial="none"> <add source=" " target=""/> </mapping> </sanitizer> </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>