Mercurial > repos > iuc > sra_tools

annotate sam_dump.xml @ 28:4df8de2d0e48 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 750d69467c21ff05a97b46cf23c551958dceccf2
author iuc
date Mon, 06 Feb 2023 18:17:45 +0000
parents 9a776b080193
children
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rev   line source
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1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>format from NCBI SRA</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam_ontology"/>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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9 <version_command>sam-dump --version | tr -d $'\n'</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 @COPY_CONFIGFILE@
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12 @SET_ACCESSIONS@
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14 ## Do not use prefetch if region is specified, to avoid downloading
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15 ## the complete sra file.
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16
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17 #if $input.input_select == "sra_file":
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18 sam-dump --log-level fatal --accession '\$acc'
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19 #else:
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20 #if ( str( $adv.region ) == "" ):
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21 prefetch -X 200000000 "\$acc" &&
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22 #end if
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23 sam-dump --log-level fatal --disable-multithreading
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24 #end if
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26 #if str( $adv.region ) != "":
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27 --aligned-region '$adv.region'
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28 #end if
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29 #if str( $adv.matepairDist ) != "":
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30 --matepair-distance '$adv.matepairDist'
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31 #end if
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32 #if str( $adv.minMapq ) != "":
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33 --min-mapq '$adv.minMapq'
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34 #end if
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35 --header
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36 #if str( $adv.alignments ) == "both":
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37 --unaligned
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38 #end if
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39
0
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40 #if str( $adv.alignments ) == "unaligned":
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41 --unaligned-spots-only
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42 #end if
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43 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ):
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44 --primary
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45 #end if
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46 "\$acc"
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47
0
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48 #if str( $outputformat ) == "bam":
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49 | samtools view -Sb - 2> /dev/null > "\$acc.bam"
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50 #elif str( $outputformat ) == "sam":
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51 > "\$acc.sam"
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52 #end if
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53
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54 #if $input.input_select != "sra_file":
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55 ); done;
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56 #end if
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57 echo "Done with all accessions."
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58 ]]>
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59 </command>
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60 <expand macro="configfile_hack"/>
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61 <inputs>
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62 <expand macro="input_conditional"/>
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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.">
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64 <option value="bam">bam</option>
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65 <option value="sam">sam</option>
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66 </param>
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67 <section name="adv" title="Advanced Options" expanded="False">
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68 <expand macro="alignments"/>
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69 <expand macro="region"/>
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70 <expand macro="matepairDist"/>
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71 <param name="primary" type="select" value="no">
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72 <label>only primary aligments</label>
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73 <option value="no">No</option>
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74 <option value="yes">Yes</option>
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75 </param>
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76 <expand macro="minMapq"></expand>
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77 </section>
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78 </inputs>
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79 <outputs>
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80 <collection name="output_collection" type="list" label="sam-dump: Downloaded SAM/BAM data">
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81 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
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82 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
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83 </collection>
0
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="input_select" value="accession_number"/>
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88 <param name="accession" value="SRR925743"/>
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89 <param name="outputformat" value="sam"/>
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90 <param name="region" value="17:41243452-41277500"/>
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91 <output_collection name="output_collection" type="list" count="1">
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92 <element name="SRR925743" file="SRR925743_sam_dump_result.sam" compare="contains" ftype="sam"/>
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93 </output_collection>
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94 </test>
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95 <test>
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96 <param name="input_select" value="accession_number"/>
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97 <param name="accession" value="SRR925743,SRR522874"/>
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98 <param name="outputformat" value="sam"/>
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99 <param name="region" value="17:41243452-41277500"/>
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100 <output_collection name="output_collection" type="list" count="2">
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101 <element name="SRR522874" file="SRR522874_sam_dump_result.sam" compare="contains" ftype="sam"/>
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102 <element name="SRR925743" file="SRR925743_sam_dump_result.sam" compare="contains" ftype="sam"/>
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103 </output_collection>
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104 </test>
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105 </tests>
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106 <help><![CDATA[
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107
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108 **What it does?**
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109
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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.
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111
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112
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113 @HOW_TO_USE_IT@
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114
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115 @ACCESSION_LIST_HOWTO@
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116
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117 -----
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118
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119 .. _sam-dump: https://github.com/ncbi/sra-tools
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120 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf
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121 .. _collection: https://galaxyproject.org/tutorials/collections/
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122 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&display=reads
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123
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124 @SRATOOLS_ATTRRIBUTION@
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125 ]]></help>
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126 <expand macro="citation"/>
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127 </tool>