Mercurial > repos > jasmine_amir > sra_tools

annotate sam_dump.xml @ 0:878e5d4becef

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