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comparison fastq_dump.xml @ 0:20da3b075bbf 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 09:00:59 -0500
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1 <tool id="fastq_dump" name="Extract reads" version="1.2.5">
2 <description>in FASTQ/A format from NCBI SRA.</description>
3 <macros>
4 <import>sra_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <stdio>
8 <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
9 </stdio>
10 <version_command>fastq-dump --version</version_command>
11 <command>
12 <![CDATA[
13 ## Need to set the home directory to the current working directory,
14 ## else the tool tries to write to home/.ncbi and fails when used
15 ## with a cluster manager.
16 export HOME=\$PWD &&
17 vdb-config --restore-defaults &&
18 #if $input.input_select == "file":
19 fastq-dump --log-level fatal --accession '${input.file.name}'
20 #else:
21 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
22 ## Do not use prefetch if region is specified, to avoid downloading
23 ## the complete sra file.
24 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
25 ASCP_PATH=`command -v ascp` &&
26 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
27 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" $input.accession &&
28 ## Duplicate vdb-config, in case settings changed between prefetch and
29 ## dump command.
30 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
31 #end if
32 fastq-dump --accession "$input.accession"
33 #end if
34 --defline-seq '@\$sn[_\$rn]/\$ri'
35 --stdout
36 $adv.split
37 #if str( $adv.alignments ) == "aligned":
38 --aligned
39 #end if
40 #if str( $adv.alignments ) == "unaligned":
41 --unaligned
42 #end if
43 #if str( $adv.minID ) != "":
44 --minSpotId "$adv.minID"
45 #end if
46 #if str( $adv.maxID ) != "":
47 --maxSpotId "$adv.maxID"
48 #end if
49 #if str( $adv.minlen ) != "":
50 --minReadLen "$adv.minlen"
51 #end if
52 #if str( $adv.readfilter ) != "":
53 --read-filter "$adv.readfilter"
54 #end if
55 #if str( $adv.region ) != "":
56 --aligned-region "$adv.region"
57 #end if
58 #if str( $adv.spotgroups ) != "":
59 --spot-groups "$adv.spotgroups"
60 #end if
61 #if str( $adv.matepairDist ) != "":
62 --matepair-distance "$adv.matepairDist"
63 #end if
64 $adv.clip
65 $adv.skip_technical
66 #if str( $outputformat ) == "fasta":
67 --fasta
68 #end if
69 #if $input.input_select=="file":
70 "$input.file" > "$output_file"
71 #else:
72 "$input.accession" > "$output_accession"
73 #end if
74 ]]>
75 </command>
76 <inputs>
77 <expand macro="input_conditional"/>
78 <param name="outputformat" type="select" label="select output format">
79 <option value="fastqsanger">fastq</option>
80 <option value="fasta">fasta</option>
81 </param>
82 <section name="adv" title="Advanced Options" expanded="False">
83 <param name="minID" type="integer" label="minimum spot ID" optional="true"/>
84 <param name="maxID" type="integer" label="maximum spot ID" optional="true"/>
85 <param name="minlen" type="integer" label="minimum read length" optional="true"/>
86 <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="">
87 <label>split spot by read pairs</label>
88 </param>
89 <expand macro="alignments"/>
90 <expand macro="region"/>
91 <expand macro="matepairDist"/>
92 <param name="readfilter" type="select" value="">
93 <label>filter by value</label>
94 <option value="">None</option>
95 <option value="pass">pass</option>
96 <option value="reject">reject</option>
97 <option value="criteria">criteria</option>
98 <option value="redacted">redacted</option>
99 </param>
100 <param name="spotgroups" type="text" label="filter by spot-groups" optional="true"/>
101 <param name="clip" type="boolean" truevalue="--clip" falsevalue="">
102 <label>apply left and right clips</label>
103 </param>
104 <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads"/>
105 </section>
106 </inputs>
107 <outputs>
108 <data format="fastq" name="output_accession" label="${input.accession}.${outputformat}">
109 <filter>input['input_select'] == "accession_number"</filter>
110 <change_format>
111 <when input="outputformat" value="fasta" format="fasta"/>
112 </change_format>
113 </data>
114 <data format="fastq" name="output_file" label="${input.file.name}.${outputformat}">
115 <filter>input['input_select'] == "file"</filter>
116 <change_format>
117 <when input="outputformat" value="fasta" format="fasta"/>
118 </change_format>
119 </data>
120 </outputs>
121 <tests>
122 <test>
123 <param name="input_select" value="accession_number"/>
124 <param name="outputformat" value="fastqsanger"/>
125 <param name="accession" value="SRR044777"/>
126 <param name="skip_technical" value="True"/>
127 <output name="output_accession">
128 <assert_contents>
129 <not_has_text text="rRNA_primer"/>
130 <has_text text="F47USSH02GNP1D" />
131 </assert_contents>
132 </output>
133 </test>
134 <test>
135 <param name="input_select" value="accession_number"/>
136 <param name="outputformat" value="fastqsanger"/>
137 <param name="accession" value="SRR925743"/>
138 <param name="maxID" value="5"/>
139 <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastq"/>
140 </test>
141 </tests>
142 <help>
143 This tool extracts reads from SRA archives using fastq-dump.
144 The fastq-dump program is developed at NCBI, and is available at
145 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
146 @SRATOOLS_ATTRRIBUTION@
147 </help>
148 <expand macro="citation"/>
149 </tool>