Mercurial > repos > iuc > sra_tools
annotate sra_macros.xml @ 7:c7620aa7e1f0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
author | iuc |
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date | Wed, 10 May 2017 10:45:41 -0400 |
parents | 26b7446bb17e |
children | 5e6237d58b0c |
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b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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1 <macros> |
7
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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2 <token name="@VERSION@">2.8.1</token> |
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b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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3 <macro name="requirements"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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4 <requirements> |
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c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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5 <requirement type="package" version="2.8.1">sra-tools</requirement> |
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b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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6 </requirements> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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7 </macro> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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8 <macro name="input_conditional"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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9 <conditional name="input"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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10 <param name="input_select" type="select" label="select input type"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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11 <option value="accession_number">SRR accession</option> |
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c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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12 <option value="file_list">List of SRA accession, one per line</option> |
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b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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13 <option value="file">SRA archive in current history</option> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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14 </param> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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15 <when value="accession_number"> |
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c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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16 <param name="accession" type="text" label="Accession" help="Must start with SRR,DRR or ERR, e.g. SRR925743 ,ERR343809"> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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17 <sanitizer> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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18 <valid initial="string.printable"> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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19 <remove value=" "/> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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20 </valid> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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21 <mapping initial="none"> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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22 <add source=" " target=""/> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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23 </mapping> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents:
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24 </sanitizer> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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25 </param> |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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26 </when> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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27 <when value="file"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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28 <param format="sra" name="file" type="data" label="sra archive"/> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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29 </when> |
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462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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30 <when value="file_list"> |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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31 <param format="txt" name="file_list" type="data" label="sra accession list"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
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32 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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33 </conditional> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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34 </macro> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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35 <macro name="alignments"> |
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c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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36 <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"> |
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b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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37 <option value="both">both</option> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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38 <option value="aligned">aligned only</option> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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39 <option value="unaligned">unaligned only</option> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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40 </param> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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41 </macro> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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42 <macro name="minMapq"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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43 <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"/> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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44 </macro> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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45 <macro name="region"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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46 <param format="text" name="region" type="text" label="aligned region" optional="true" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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47 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"/> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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48 </macro> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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49 <macro name="matepairDist"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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50 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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51 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"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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52 </macro> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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53 <macro name="citation"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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54 <citations> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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55 <citation type="doi">10.1093/nar/gkq1019</citation> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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56 </citations> |
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57 </macro> |
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58 <token name="@ACCESSION_LIST_HOWTO@"> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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59 ----- |
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60 |
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61 **How to generate accession lists** |
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62 |
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63 1. Go to **SRA Run Selector** by clicking this link_ |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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64 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*). |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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65 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 |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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66 4. Click on the Runs number |
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67 5. On the page that would open you will see **Accession List** button |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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68 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. |
c7620aa7e1f0
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69 </token> |
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70 |
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71 <token name="@SRATOOLS_ATTRRIBUTION@"> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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72 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com). |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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73 Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ). |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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74 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com). |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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75 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc. |
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76 </token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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77 </macros> |