Mercurial > repos > iuc > sra_tools

annotate sra_macros.xml @ 18:c8d04fc889f2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
author iuc
date Mon, 06 Jul 2020 22:18:55 +0000
parents 37f09413ddbf
children adc510b2288d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
1 <macros>
17
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2 <token name="@VERSION@">2.10.7</token>
13
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3 <token name="@ACCESSIONS_FROM_FILE@">
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
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4 grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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parents: 12
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5 </token>
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
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6 <token name="@COMPRESS@"><![CDATA[pigz -cqp \${GALAXY_SLOTS:-1}]]></token>
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
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7 <token name="@CONFIGURE_RETRY@"><![CDATA[
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
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8 export SRA_PREFETCH_RETRIES=3 &&
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
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9 export SRA_PREFETCH_ATTEMPT=1 &&
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
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10 ]]></token>
17
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
iuc
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11 <token name="@COPY_CONFIGFILE@"><![CDATA[
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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12 mkdir -p ~/.ncbi &&
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
iuc
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13 cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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14 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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15 vdb-config -s "/repository/user/ad/public/root=\$PWD" &&
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
iuc
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16 vdb-config -s "/repository/user/default-path=\$PWD" &&
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
iuc
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17 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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18 vdb-config -s /http/timeout/read=10000 &&
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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19 ]]></token>
13
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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20 <token name="@SET_ACCESSIONS@"><![CDATA[
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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21 #if $input.input_select=="file_list":
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22 #if $input.file_list.is_of_type('sra_manifest.tabular'):
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
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23 #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
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24 cut -f $column '$input.file_list'| tail -n +2 > "manifest" &&
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
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25 #else
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
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26 ln -s '$input.file_list' manifest &&
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
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27 #end if
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
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28 for acc in `@ACCESSIONS_FROM_FILE@ manifest` ;
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29 do (
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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30 #elif $input.input_select=="accession_number":
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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31 acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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32 #end if
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33 ]]></token>
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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34
0
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iuc
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35 <macro name="requirements">
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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36 <requirements>
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37 <requirement type="package" version="@VERSION@">sra-tools</requirement>
16
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38 <requirement type="package" version="2.3.4">pigz</requirement>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
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39 <yield/>
0
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40 </requirements>
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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41 </macro>
17
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42 <macro name="configfile_hack">
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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43 <configfiles>
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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44 <configfile name="user_settings_mkfg"><![CDATA[
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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45 /LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec"
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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46 /config/default = "false"
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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47 /libs/temp_cache = "."
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48 /tools/prefetch/download_to_cache = "false"
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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49 ]]></configfile>
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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50 </configfiles>
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
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51 </macro>
13
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52 <macro name="sanitize_query">
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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53 <sanitizer>
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54 <valid initial="string.printable">
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55 <remove value=" "/>
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56 <remove value="&apos;" />
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57 </valid>
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58 <mapping initial="none">
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59 <add source=" " target=""/>
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60 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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61 </mapping>
74dd3d0a33d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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62 </sanitizer>
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63 </macro>
0
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64 <macro name="input_conditional">
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65 <conditional name="input">
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66 <param name="input_select" type="select" label="select input type">
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67 <option value="accession_number">SRR accession</option>
7
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68 <option value="file_list">List of SRA accession, one per line</option>
0
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69 <option value="file">SRA archive in current history</option>
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70 </param>
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71 <when value="accession_number">
11
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72 <param name="accession" type="text" label="Accession" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809">
13
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73 <expand macro="sanitize_query" />
11
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74 <validator type="empty_field" message="An accession is required"/>
7
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75 </param>
0
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76 </when>
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77 <when value="file">
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78 <param format="sra" name="file" type="data" label="sra archive"/>
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79 </when>
1
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80 <when value="file_list">
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81 <param format="txt" name="file_list" type="data" label="sra accession list"/>
2
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82 </when>
0
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83 </conditional>
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84 </macro>
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85 <macro name="alignments">
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86 <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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87 <option value="both">both</option>
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88 <option value="aligned">aligned only</option>
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89 <option value="unaligned">unaligned only</option>
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90 </param>
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91 </macro>
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92 <macro name="minMapq">
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93 <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"/>
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94 </macro>
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95 <macro name="region">
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96 <param format="text" name="region" type="text" label="aligned region" optional="true"
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97 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"/>
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98 </macro>
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99 <macro name="matepairDist">
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100 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
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101 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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102 </macro>
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103 <macro name="citation">
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104 <citations>
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105 <citation type="doi">10.1093/nar/gkq1019</citation>
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106 </citations>
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107 </macro>
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108 <token name="@ACCESSION_LIST_HOWTO@">
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109 -----
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110
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111 **How to generate accession lists**
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112
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113 1. Go to **SRA Run Selector** by clicking this link_
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114 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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115 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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116 4. Click on the Runs number
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117 5. On the page that would open you will see **Accession List** button
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118 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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119 </token>
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120
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121 <token name="@SRATOOLS_ATTRRIBUTION@">
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122 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
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123 Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
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124 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
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125 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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126 </token>
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127 </macros>