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comparison sra_macros.xml @ 1:462ee06c9358 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
author iuc
date Tue, 17 May 2016 14:14:50 -0400
parents b723c120161a
children f256cb398262
comparison
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0:b723c120161a 1:462ee06c9358
1 <macros> 1 <macros>
2 <macro name="requirements"> 2 <macro name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.3">ngs_sdk</requirement> 4 <requirement type="package" version="1.2.3">ngs_sdk</requirement>
5 <requirement type="package" version="2.5.2">ncbi_vdb</requirement> 5 <requirement type="package" version="2.6.2">ncbi_vdb</requirement>
6 <requirement type="package" version="2.5.2">sra_toolkit</requirement> 6 <requirement type="package" version="2.6.2">sra_toolkit</requirement>
7 <requirement type="package" version="2.6.2">sra-tools</requirement>
7 <requirement type="package" version="5.18.1">perl</requirement> 8 <requirement type="package" version="5.18.1">perl</requirement>
8 </requirements> 9 </requirements>
9 </macro> 10 </macro>
10 <macro name="input_conditional"> 11 <macro name="input_conditional">
11 <conditional name="input"> 12 <conditional name="input">
12 <param name="input_select" type="select" label="select input type"> 13 <param name="input_select" type="select" label="select input type">
13 <option value="accession_number">SRR accession</option> 14 <option value="accession_number">SRR accession</option>
14 <option value="file">SRA archive in current history</option> 15 <option value="file">SRA archive in current history</option>
16 <option value="file_list">List of SRA accession, one per line</option>
15 </param> 17 </param>
16 <when value="accession_number"> 18 <when value="accession_number">
17 <param name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743"/> 19 <param name="accession" type="text" label="SRR accession" help="Must start with SRR,DRR or ERR, e.g. SRR925743 , ERR343809"/>
18 </when> 20 </when>
19 <when value="file"> 21 <when value="file">
20 <param format="sra" name="file" type="data" label="sra archive"/> 22 <param format="sra" name="file" type="data" label="sra archive"/>
21 </when> 23 </when>
24 <when value="file_list">
25 <param format="txt" name="file_list" type="data" label="sra accession list"/>
26 </when>
22 </conditional> 27 </conditional>
23 </macro> 28 </macro>
24 <macro name="alignments"> 29 <macro name="alignments">
25 <param name="alignments" type="select" value="both"> 30 <param name="alignments" type="select" value="both">
26 <label>aligned or unaligned reads</label> 31 <label>aligned or unaligned reads</label>
43 <macro name="citation"> 48 <macro name="citation">
44 <citations> 49 <citations>
45 <citation type="doi">10.1093/nar/gkq1019</citation> 50 <citation type="doi">10.1093/nar/gkq1019</citation>
46 </citations> 51 </citations>
47 </macro> 52 </macro>
48 <token name="@SRATOOLS_ATTRRIBUTION@">Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 53 <token name="@SRATOOLS_ATTRRIBUTION@">
54 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
55
49 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com). 56 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
57
58 Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
59
50 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com). 60 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
51 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.</token> 61
62 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.
63
64 </token>
52 </macros> 65 </macros>