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comparison sra_pileup.xml @ 0:68527898a9ea draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
author mvdbeek
date Fri, 25 Sep 2015 09:28:56 -0400
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1 <tool id="sra_pileup" name="Generate pileup format" version="1.2.4">
2 <description>from NCBI sra.</description>
3 <macros>
4 <import>sra_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command>
8 <![CDATA[
9 ## Need to set the home directory to the current working directory,
10 ## else the tool tries to write to home/.ncbi and fails when used
11 ## with a cluster manager.
12 export HOME=\$PWD;
13 vdb-config --restore-defaults;
14 vdb-config -s "/repository/user/main/public/root=\$PWD";
15 #if ( str( $region ) == "" ):
16 ASCP_PATH=`which ascp`;
17 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh;
18 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession";
19 ##Duplicate vdb-config, in case settings changed between prefetch and
20 ##dump command.
21 #end if
22 vdb-config -s "/repository/user/main/public/root=\$PWD";
23 sra-pileup --log-level fatal
24 #if str( $region ) != "":
25
26 --aligned-region "$region"
27
28 #end if
29 #if str( $minMapq ) != "":
30 --minmapq "$minMapq"
31 #end if
32 #if $input.input_select == "file":
33 "$input.file" > "$output_file"
34 #elif $input.input_select == "accession_number":
35 "$input.accession" > "$output_accession"
36 #elif $input.input_select == "text":
37 `cat $input.text` > "$output_text"
38 #end if
39 ]]>
40 </command>
41 <version_string>sra-pileup --version</version_string>
42 <inputs>
43 <conditional name="input">
44 <param name="input_select" type="select" label="select input type">
45 <option value="accession_number">SRR accession</option>
46 <option value="file">SRA archive in current history</option>
47 <option value="text">text file containing SRR accession</option>
48 </param>
49 <when value="file">
50 <param format="sra" name="file" type="data" label="sra archive"/>
51 </when>
52 <when value="accession_number">
53 <param format="text" name="accession" type="text" label="accession"/>
54 </when>
55 <when value="text">
56 <param format="txt" name="text" type="data" label="text file"/>
57 </when>
58 </conditional>
59 <expand macro="region"/>
60 <expand macro="minMapq"/>
61 </inputs>
62 <outputs>
63 <data format="pileup" name="output_accession" label="${input.accession}.pileup">
64 <filter>input['input_select'] == "accession_number"</filter>
65 </data>
66 <data format="pileup" name="output_file" label="${input.file.name}.pileup">
67 <filter>input['input_select'] == "file"</filter>
68 </data>
69 <data format="pileup" name="output_text" label="${input.text.name}.pileup">
70 <filter>input['input_select'] == "text"</filter>
71 </data>
72 </outputs>
73 <tests>
74 <test>
75 <param name="input_select" value="accession_number"/>
76 <param name="accession" value="SRR925743"/>
77 <param name="region" value="17:41243452-41277500"/>
78 <output name="output_accession" file="sra_pileup_result.pileup" ftype="pileup"/>
79 </test>
80 </tests>
81 <help>
82 This tool produces pileup format from sra archives using sra-pileup.
83 The sra-pileup program is developed at NCBI, and is available at
84 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
85 @SRATOOLS_ATTRRIBUTION@
86 </help>
87 </tool>