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comparison sam_dump.xml @ 10:73f1fbdea468 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 48c9d7f30655d48c9b46b9ca7a17c454eb54694d
author iuc
date Fri, 17 Nov 2017 13:21:53 -0500
parents 4190f26dd5e6
children 74dd3d0a33d1
comparison
equal deleted inserted replaced
9:4190f26dd5e6 10:73f1fbdea468
1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.2"> 1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.3">
2 <description>format from NCBI SRA</description> 2 <description>format from NCBI SRA</description>
3 <macros> 3 <macros>
4 <import>sra_macros.xml</import> 4 <import>sra_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>sam-dump --version</version_command> 7 <version_command>sam-dump --version</version_command>
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 #if $input.input_select=="file_list": 10 #if $input.input_select=="file_list":
11 for acc in `cat $input.file_list` ; 11 for acc in `cat $input.file_list` ;
12 do 12 do
13 #elif $input.input_select=="accession_number": 13 #elif $input.input_select=="accession_number":
14 acc="${input.accession}" && 14 acc="${input.accession}" &&
15 #end if 15 #end if
16 16
17 #if $input.input_select=="file_list" or $input.input_select=="accession_number": 17 #if $input.input_select=="file_list" or $input.input_select=="accession_number":
18 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( 18 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
19 #end if 19 #end if
20
21
22 20
23 ## Need to set the home directory to the current working directory, 21 ## Need to set the home directory to the current working directory,
24 ## else the tool tries to write to home/.ncbi and fails when used 22 ## else the tool tries to write to home/.ncbi and fails when used
25 ## with a cluster manager. 23 ## with a cluster manager.
26 export HOME=\$PWD && 24 export HOME=\$PWD &&
36 ## dump command. 34 ## dump command.
37 vdb-config -s "/repository/user/main/public/root=\$PWD" && 35 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
38 #end if 36 #end if
39 sam-dump --log-level fatal --disable-multithreading 37 sam-dump --log-level fatal --disable-multithreading
40 #if str( $adv.region ) != "": 38 #if str( $adv.region ) != "":
41 --aligned-region "$adv.region" 39 --aligned-region '$adv.region'
42 #end if 40 #end if
43 #if str( $adv.matepairDist ) != "": 41 #if str( $adv.matepairDist ) != "":
44 --matepair-distance "$adv.matepairDist" 42 --matepair-distance '$adv.matepairDist'
45 #end if 43 #end if
46 #if str( $adv.minMapq ) != "": 44 #if str( $adv.minMapq ) != "":
47 --min-mapq "$adv.minMapq" 45 --min-mapq '$adv.minMapq'
48 #end if 46 #end if
49 #if str( $adv.header ) == "yes": 47 --header
50 --header
51 #else:
52 --no-header
53 #end if
54 #if str( $adv.alignments ) == "both": 48 #if str( $adv.alignments ) == "both":
55 --unaligned 49 --unaligned
56 #end if 50 #end if
57 #if str( $adv.alignments ) == "unaligned": 51 #if str( $adv.alignments ) == "unaligned":
58 --unaligned-spots-only 52 --unaligned-spots-only
59 #end if 53 #end if
60 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ): 54 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ):
61 --primary 55 --primary
62 #end if 56 #end if
63 #if $input.input_select == "file": 57 #if $input.input_select == "file":
64 "$input.file" 58 '$input.file'
65 #elif $input.input_select == "accession_number": 59 #elif $input.input_select == "accession_number":
66 "\$acc" 60 "\$acc"
67 #elif $input.input_select=="file_list": 61 #elif $input.input_select=="file_list":
68 "\$acc" 62 "\$acc"
69 #end if 63 #end if
70 64
71 #if str( $outputformat ) == "bam": 65 #if str( $outputformat ) == "bam":
72 | samtools view -Sb - 2> /dev/null 66 | samtools view -Sb - 2> /dev/null
73 #end if 67 #end if
74 #if $input.input_select == "file": 68 #if $input.input_select == "file":
75 > "$output_file" 69 > '$output_file'
76 #elif $input.input_select == "accession_number": 70 #elif $input.input_select == "accession_number":
77 > "$output_accession" ) 71 > '$output_accession' )
78 #end if 72 #end if
79 73
80 #if $input.input_select=="file_list": 74 #if $input.input_select=="file_list":
81 #if str( $outputformat ) == "bam": 75 #if str( $outputformat ) == "bam":
82 > "\$acc.bam" 76 > "\$acc.bam"
84 > "\$acc.sam" 78 > "\$acc.sam"
85 #end if 79 #end if
86 ) ; done 80 ) ; done
87 #end if 81 #end if
88 82
89
90 ]]> 83 ]]>
91 </command> 84 </command>
92 <inputs> 85 <inputs>
93 <expand macro="input_conditional"/> 86 <expand macro="input_conditional"/>
94 <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools."> 87 <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools.">
95 <option value="bam">bam</option> 88 <option value="bam">bam</option>
96 <option value="sam">sam</option> 89 <option value="sam">sam</option>
97 </param> 90 </param>
98 <section name="adv" title="Advanced Options" expanded="False"> 91 <section name="adv" title="Advanced Options" expanded="False">
99 <param name="header" type="select" value="yes">
100 <label>output header</label>
101 <option value="yes">Yes</option>
102 <option value="no">No</option>
103 </param>
104 <expand macro="alignments"/> 92 <expand macro="alignments"/>
105 <expand macro="region"/> 93 <expand macro="region"/>
106 <expand macro="matepairDist"/> 94 <expand macro="matepairDist"/>
107 <param name="primary" type="select" value="no"> 95 <param name="primary" type="select" value="no">
108 <label>only primary aligments</label> 96 <label>only primary aligments</label>
139 <param name="region" value="17:41243452-41277500"/> 127 <param name="region" value="17:41243452-41277500"/>
140 <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/> 128 <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/>
141 </test> 129 </test>
142 </tests> 130 </tests>
143 <help><![CDATA[ 131 <help><![CDATA[
132
144 **What it does?** 133 **What it does?**
145 134
146 This tool extracts data (in BAM_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the sam-dump_ utility of the SRA Toolkit. 135 This tool extracts data (in BAM_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the sam-dump_ utility of the SRA Toolkit.
147 136
148 **How to use it?** 137 **How to use it?**
189 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf 178 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf
190 .. _sam-dump: http://ncbi.github.io/sra-tools/sam-dump.html 179 .. _sam-dump: http://ncbi.github.io/sra-tools/sam-dump.html
191 .. _collection: https://galaxyproject.org/tutorials/collections/ 180 .. _collection: https://galaxyproject.org/tutorials/collections/
192 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies 181 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
193 182
194
195 @SRATOOLS_ATTRRIBUTION@ 183 @SRATOOLS_ATTRRIBUTION@
196 ]]></help> 184 ]]></help>
197 <expand macro="citation"/> 185 <expand macro="citation"/>
198 </tool> 186 </tool>