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comparison sra_macros.xml @ 13:c38286ea7047 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
author iuc
date Wed, 17 Oct 2018 11:44:12 -0400
parents 5534eb46de20
children 1790dcf3c32d
comparison
equal deleted inserted replaced
12:5534eb46de20 13:c38286ea7047
1 <macros> 1 <macros>
2 <token name="@VERSION@">2.9.1</token> 2 <token name="@VERSION@">2.9.1</token>
3 <token name="@ACCESSIONS_FROM_FILE@">
4 grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
5 </token>
6 <token name="@SET_ACCESSIONS@"><![CDATA[
7 #if $input.input_select=="file_list":
8 for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
9 do (
10 #elif $input.input_select=="accession_number":
11 acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
12 #end if
13 ]]></token>
14
3 <macro name="requirements"> 15 <macro name="requirements">
4 <requirements> 16 <requirements>
5 <requirement type="package" version="2.9.1">sra-tools</requirement> 17 <requirement type="package" version="2.9.1">sra-tools</requirement>
6 </requirements> 18 </requirements>
19 </macro>
20 <macro name="sanitize_query">
21 <sanitizer>
22 <valid initial="string.printable">
23 <remove value=" "/>
24 <remove value="&apos;" />
25 </valid>
26 <mapping initial="none">
27 <add source=" " target=""/>
28 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
29 </mapping>
30 </sanitizer>
7 </macro> 31 </macro>
8 <macro name="input_conditional"> 32 <macro name="input_conditional">
9 <conditional name="input"> 33 <conditional name="input">
10 <param name="input_select" type="select" label="select input type"> 34 <param name="input_select" type="select" label="select input type">
11 <option value="accession_number">SRR accession</option> 35 <option value="accession_number">SRR accession</option>
12 <option value="file_list">List of SRA accession, one per line</option> 36 <option value="file_list">List of SRA accession, one per line</option>
13 <option value="file">SRA archive in current history</option> 37 <option value="file">SRA archive in current history</option>
14 </param> 38 </param>
15 <when value="accession_number"> 39 <when value="accession_number">
16 <param name="accession" type="text" label="Accession" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809"> 40 <param name="accession" type="text" label="Accession" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809">
17 <sanitizer> 41 <expand macro="sanitize_query" />
18 <valid initial="string.printable">
19 <remove value=" "/>
20 </valid>
21 <mapping initial="none">
22 <add source=" " target=""/>
23 </mapping>
24 </sanitizer>
25 <validator type="empty_field" message="An accession is required"/> 42 <validator type="empty_field" message="An accession is required"/>
26 </param> 43 </param>
27 </when> 44 </when>
28 <when value="file"> 45 <when value="file">
29 <param format="sra" name="file" type="data" label="sra archive"/> 46 <param format="sra" name="file" type="data" label="sra archive"/>