Mercurial > repos > iuc > sra_tools

annotate sra_macros.xml @ 16:aad3885b3216 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
author iuc
date Fri, 20 Mar 2020 12:47:18 -0400
parents f5ea3ce9b9b0
children c441583adae5
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1 <macros>
16
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2 <token name="@VERSION@">2.10.4</token>
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3 <token name="@ACCESSIONS_FROM_FILE@">
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4 grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
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5 </token>
16
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6 <token name="@CONFIGURE_TIMEOUT@"><![CDATA[
aad3885b3216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
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7 vdb-config --restore-defaults && vdb-config -s /http/timeout/read=10000 || true &&
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8 ]]></token>
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9 <token name="@SET_ACCESSIONS@"><![CDATA[
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10 #if $input.input_select=="file_list":
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11 for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
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12 do (
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13 #elif $input.input_select=="accession_number":
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14 acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
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15 #end if
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16 ]]></token>
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17
0
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18 <macro name="requirements">
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19 <requirements>
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20 <requirement type="package" version="2.10.3">sra-tools</requirement>
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21 <yield/>
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22 </requirements>
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23 </macro>
13
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24 <macro name="sanitize_query">
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25 <sanitizer>
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26 <valid initial="string.printable">
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27 <remove value=" "/>
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28 <remove value="&apos;" />
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29 </valid>
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30 <mapping initial="none">
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31 <add source=" " target=""/>
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32 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
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33 </mapping>
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34 </sanitizer>
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35 </macro>
0
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36 <macro name="input_conditional">
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37 <conditional name="input">
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38 <param name="input_select" type="select" label="select input type">
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39 <option value="accession_number">SRR accession</option>
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40 <option value="file_list">List of SRA accession, one per line</option>
0
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41 <option value="file">SRA archive in current history</option>
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42 </param>
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43 <when value="accession_number">
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44 <param name="accession" type="text" label="Accession" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809">
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45 <expand macro="sanitize_query" />
11
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46 <validator type="empty_field" message="An accession is required"/>
7
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47 </param>
0
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48 </when>
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49 <when value="file">
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50 <param format="sra" name="file" type="data" label="sra archive"/>
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51 </when>
1
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52 <when value="file_list">
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53 <param format="txt" name="file_list" type="data" label="sra accession list"/>
2
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54 </when>
0
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55 </conditional>
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56 </macro>
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57 <macro name="alignments">
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58 <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">
0
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59 <option value="both">both</option>
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60 <option value="aligned">aligned only</option>
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61 <option value="unaligned">unaligned only</option>
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62 </param>
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63 </macro>
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64 <macro name="minMapq">
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65 <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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66 </macro>
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67 <macro name="region">
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68 <param format="text" name="region" type="text" label="aligned region" optional="true"
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69 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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70 </macro>
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71 <macro name="matepairDist">
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72 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
7
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73 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"/>
0
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74 </macro>
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75 <macro name="citation">
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76 <citations>
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77 <citation type="doi">10.1093/nar/gkq1019</citation>
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78 </citations>
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79 </macro>
7
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80 <token name="@ACCESSION_LIST_HOWTO@">
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81 -----
2
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82
7
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83 **How to generate accession lists**
1
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84
7
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85 1. Go to **SRA Run Selector** by clicking this link_
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86 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*).
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87 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
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88 4. Click on the Runs number
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89 5. On the page that would open you will see **Accession List** button
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90 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.
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91 </token>
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92
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93 <token name="@SRATOOLS_ATTRRIBUTION@">
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94 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
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95 Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
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96 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
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97 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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98 </token>
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99 </macros>