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comparison sam_dump.xml @ 0:878e5d4becef

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planemo upload
author jasmine_amir
date Thu, 02 Feb 2023 18:11:05 -0500
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children c9fb9ecae076
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-1:000000000000 0:878e5d4becef
1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>format from NCBI SRA</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_ontology"/>
7 <expand macro="bio_tools"/>
8 <expand macro="requirements"/>
9 <version_command>sam-dump --version | tr -d $'\n'</version_command>
10 <command detect_errors="exit_code"><![CDATA[
11 @COPY_CONFIGFILE@
12 @SET_ACCESSIONS@
13
14 ## Do not use prefetch if region is specified, to avoid downloading
15 ## the complete sra file.
16
17 #if $input.input_select == "sra_file":
18 sam-dump --log-level fatal --accession '\$acc'
19 #else:
20 #if ( str( $adv.region ) == "" ):
21 prefetch -X 200000000 "\$acc" &&
22 #end if
23 sam-dump --log-level fatal --disable-multithreading
24 #end if
25
26 #if str( $adv.region ) != "":
27 --aligned-region '$adv.region'
28 #end if
29 #if str( $adv.matepairDist ) != "":
30 --matepair-distance '$adv.matepairDist'
31 #end if
32 #if str( $adv.minMapq ) != "":
33 --min-mapq '$adv.minMapq'
34 #end if
35 --header
36 #if str( $adv.alignments ) == "both":
37 --unaligned
38 #end if
39
40 #if str( $adv.alignments ) == "unaligned":
41 --unaligned-spots-only
42 #end if
43 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ):
44 --primary
45 #end if
46 "\$acc"
47
48 #if str( $outputformat ) == "bam":
49 | samtools view -Sb - 2> /dev/null > "\$acc.bam"
50 #elif str( $outputformat ) == "sam":
51 > "\$acc.sam"
52 #end if
53
54 #if $input.input_select != "sra_file":
55 ); done;
56 #end if
57 echo "Done with all accessions."
58 ]]>
59 </command>
60 <expand macro="configfile_hack"/>
61 <inputs>
62 <expand macro="input_conditional"/>
63 <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.">
64 <option value="bam">bam</option>
65 <option value="sam">sam</option>
66 </param>
67 <section name="adv" title="Advanced Options" expanded="False">
68 <expand macro="alignments"/>
69 <expand macro="region"/>
70 <expand macro="matepairDist"/>
71 <param name="primary" type="select" value="no">
72 <label>only primary aligments</label>
73 <option value="no">No</option>
74 <option value="yes">Yes</option>
75 </param>
76 <expand macro="minMapq"></expand>
77 </section>
78 </inputs>
79 <outputs>
80 <collection name="output_collection" type="list" label="sam-dump: Downloaded SAM/BAM data">
81 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
82 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
83 </collection>
84 </outputs>
85 <tests>
86 <test>
87 <param name="input_select" value="accession_number"/>
88 <param name="accession" value="SRR925743"/>
89 <param name="outputformat" value="sam"/>
90 <param name="region" value="17:41243452-41277500"/>
91 <output_collection name="output_collection" type="list" count="1">
92 <element name="SRR925743" file="SRR925743_sam_dump_result.sam" compare="contains" ftype="sam"/>
93 </output_collection>
94 </test>
95 <test>
96 <param name="input_select" value="accession_number"/>
97 <param name="accession" value="SRR925743,SRR522874"/>
98 <param name="outputformat" value="sam"/>
99 <param name="region" value="17:41243452-41277500"/>
100 <output_collection name="output_collection" type="list" count="2">
101 <element name="SRR522874" file="SRR522874_sam_dump_result.sam" compare="contains" ftype="sam"/>
102 <element name="SRR925743" file="SRR925743_sam_dump_result.sam" compare="contains" ftype="sam"/>
103 </output_collection>
104 </test>
105 </tests>
106 <help><![CDATA[
107
108 **What it does?**
109
110 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 and returns a collection of NGS data containing one file for each accession number provided.
111
112
113 @HOW_TO_USE_IT@
114
115 @ACCESSION_LIST_HOWTO@
116
117 -----
118
119 .. _sam-dump: https://github.com/ncbi/sra-tools
120 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf
121 .. _collection: https://galaxyproject.org/tutorials/collections/
122 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&display=reads
123
124 @SRATOOLS_ATTRRIBUTION@
125 ]]></help>
126 <expand macro="citation"/>
127 </tool>