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comparison sra_pileup.xml @ 0:b723c120161a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
author iuc
date Sun, 06 Dec 2015 09:04:37 -0500
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children f256cb398262
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-1:000000000000 0:b723c120161a
1 <tool id="sra_pileup" name="Generate pileup format" version="1.2.5">
2 <description>from NCBI sra.</description>
3 <macros>
4 <import>sra_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>sra-pileup --version</version_command>
8 <command>
9 <![CDATA[
10 ## Need to set the home directory to the current working directory,
11 ## else the tool tries to write to home/.ncbi and fails when used
12 ## with a cluster manager.
13 export HOME=\$PWD &&
14 vdb-config --restore-defaults &&
15 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
16 #if ( str( $adv.region ) == "" ):
17 ASCP_PATH=`command -v ascp` &&
18 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
19 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" &&
20 ## Duplicate vdb-config, in case settings changed between prefetch and
21 ## sra-pileup command.
22 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
23 #end if
24 sra-pileup --log-level fatal
25 #if str( $adv.region ) != "":
26 --aligned-region "$adv.region"
27 #end if
28 #if str( $adv.minMapq ) != "":
29 --minmapq "$adv.minMapq"
30 #end if
31 #if $input.input_select == "file":
32 "$input.file" > "$output_file"
33 #elif $input.input_select == "accession_number":
34 "$input.accession" > "$output_accession"
35 #elif $input.input_select == "text":
36 `cat "$input.text"` > "$output_text"
37 #end if
38 ]]>
39 </command>
40 <inputs>
41 <conditional name="input">
42 <param name="input_select" type="select" label="select input type">
43 <option value="accession_number">SRR accession</option>
44 <option value="file">SRA archive in current history</option>
45 <option value="text">text file containing SRR accession</option>
46 </param>
47 <when value="file">
48 <param format="sra" name="file" type="data" label="sra archive"/>
49 </when>
50 <when value="accession_number">
51 <param format="text" name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743"/>
52 </when>
53 <when value="text">
54 <param format="txt" name="text" type="data" label="text file"/>
55 </when>
56 </conditional>
57 <section name="adv" title="Advanced Options" expanded="False">
58 <expand macro="region"/>
59 <expand macro="minMapq"/>
60 </section>
61 </inputs>
62 <outputs>
63 <data format="pileup" name="output_accession" label="${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" compare="contains" 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 <expand macro="citation"/>
88 </tool>